WO2013124740A2

WO2013124740A2 - BRCA DEFICIENCY PROTEIN AND mRNA SIGNATURES USEFUL IN IDENTIFICATION OF PATIENTS WITH BRCA-DEFICIENT TUMORS AND PREDICTING BENEFIT OF ANTI-CANCER THERAPY IN CANCER PATIENTS

Info

Publication number: WO2013124740A2
Application number: PCT/IB2013/000670
Authority: WO
Inventors: Cornelia Ramona Jimenez; Marc Omer WARMOES; Thang Viet PHAM; Sven ROTTENBERG
Original assignee: Stichting Vu-Vumc; Stichting Het Nederlands Kanker Instituut
Priority date: 2012-02-23
Filing date: 2013-02-25
Publication date: 2013-08-29
Also published as: WO2013124740A3

Abstract

BRCA-deficiency signatures comprising differentially regulated proteins present in BRCA1-deficient tumors, and BRCA-deficiency signatures comprising nucleic acids isolated from BRCA1-deficient tumors, as well as methods of using the same, are disclosed.

Description

BRCA DEFICIENCY PROTEIN AND mRNA SIGNATURES USEFUL IN IDENTIFICATION OF PATIENTS WITH BRCA-DEFICIENT TUMORS AND PREDICTING BENEFIT OF ANTI-CANCER THERAPY IN CANCER PATIENTS

Cross Reference to Related Applications

[001] This Patent Cooperation Treaty patent application claims priority to United

States provisional application No 61/602,383, filed February 23, 2013, entitled "BRCA Deficiency Protein and mRNA Signatures Useful In Identification of Patients with BRCA- Deficient Tumors and Predicting Benefit of Anti-Cancer Therapy In Cancer Patients" the contents of which are incorporated herein by reference in their entirety.

Sequence Listing

[002] A sequence listing submitted in computer readable format is hereby incorporated by reference. The computer readable file is named P230557.WO.01.ST25.txt, was created on February 21, 2013, and contains 764 kilobytes (782,752 bytes).

Field

[003] The present disclosure relates to proteomes from BRCA 1 -deficient tumors and corresponding messenger RNA sequences useful in identifying patients with BRCA deficiency, identifying patients with BRCA pathway defects ("BRCAness"), identifying tumors with BRCA1 and/or BRCA2 defects, and in optimizing the therapeutic efficacy of anti-cancer therapy by detecting phenotypic genetic traits. Classifiers comprising the proteomes, and/or subsets of proteins from the proteomes, and classifiers comprising the messenger RNA sequences, and/or subsets of the messenger RNA sequences, are also disclosed.

Background

[004] Breast cancer is the most frequently occurring cancer among women in the western world. It is a heterogeneous cancer disease, consisting of several subtypes.

Molecular biology has greatly enhanced our understanding of the heterogeneity of breast cancer, but few molecular tumor features are actually used in the clinic to guide the choice of a systemic treatment strategy.

[005] (Neo)adjuvant systemic therapy has become a widely used treatment strategy for patients with early, or locally advanced, breast cancer. Despite its early and late toxicities, this treatment strategy reduces the risk of breast cancer relapse and mortality by approximately half.

[006] In spite of this advantage, a disadvantage to the use of (neo)adjuvant systemic therapy is the lack of predictive tests to individualize the choice of certain combinations of drugs for an individual breast cancer patient to ensure maximal benefit with minimal toxicity. For example, for highly toxic adjuvant treatment regimens, such as high dose alkylating chemotherapy with hematopoietic stem-cell rescue, the survival benefit when compared with standard chemotherapy is approximately 10% for patients with 10 or more positive axillary lymph nodes. It would thus be advantageous to be able to target those 10% of patients who would benefit from high dose alkylating chemotherapy. However, few predictive tests presently exist. Because of the relatively high toxicity and the low level of efficacy in unselected breast cancer patients, alkylating agents are not commonly used in the treatment of breast cancer, with the exception of cyclophosphamide.

[007] Alkylating chemotherapy and platinating agents work by causing interstrand

DNA crosslinking, which cause DNA double strand breaks. In normal cells, these double strand breaks are repaired by a process called homologous recombination. If this process is unavailable or impaired, a situation referred to as "homologous recombination deficiency" exists and alternative, error-prone DNA repair mechanisms take over, leading to genomic instability. The breast cancer genes BRCAl and BRCA2 are involved in normal homologous recombination and tumors of patients carrying germ-line inactivating mutations in one or both of these genes show homologous recombination deficiency. A major function of BRCAl is its role in homology-directed double-strand break (DSB) repair, a DNA repair mechanism that uses the sister chromatid as a template, and therefore repairs double-strand breaks in an error- free manner. Deficiencies in homology-directed DNA repair cause high levels of genomic instability that increase the risk of tumorigenesis. Breast cancer associated with BRCAl mutations accounts for only 1-2% of breast cancer cases in the Western world. BRCAl hereditary breast cancer falls into the molecular sub-type of basal-like breast cancer that has a poor prognosis. Sporadic basal-like breast tumors represent approximately 10-15% of all breast carcinomas and comprise many tumors that share key features of BRCAl - associated tumors.

[008] Emerging preclinical evidence shows that breast cancers with a defective DNA repair system, such as a mutation in the BRCAl gene, may be extremely sensitive to DNA damaging agents, such as platinum compounds and bifunctional alkylating agents. Therefore, patients with breast cancers harboring a defective DNA repair system may specifically benefit from high dose alkylating chemotherapy, a DNA double strand break (DSB)-inducing regimen. Tumors with homologous recombination deficiency have been shown to be particularly sensitive to DNA double strand break (DSB)-inducing agents, such as alkylators and platinum drugs or platinating agents. Both classes of drugs are employed in metastatic breast cancer. The novel poly(ADP-ribose) polymerase inhibitors (PARP inhibitors) are specifically effective in homologous recombination deficient tumors as well, and have shown impressive activity in clinical studies recently. A major clinical challenge remains the identification of patients that are likely to benefit from DNA (repair)-targeting therapy.

[009] Mutations of the BRCA2 gene can cause the BRCA2 protein to be abnormal and defective. Defective BRCA2 protein is unable to function normally and thus cannot repair breaks in DNA. As a result, mutations build up that can cause uncontrolled cell growth, leading to cancers. In addition to breast cancer in men and women, mutations in the BRCA2 gene can lead to an increased risk of ovarian, fallopian, prostate, and pancreatic cancers, as well as malignant melanoma. Several other types of cancer have also been seen in certain families carrying BRCA2 gene mutations. Identification of a mutation in the BRCA2 gene in a patient can assist a health care provider in determining the proper course of treatment for the patient. Additionally, mutation identification allows for pre-symptomatic mutation screening in family members.

Summary

[010] Therefore, methods of optimizing the therapeutic efficacy of anti-cancer therapies by identifying patients who would benefit from one or more anti-cancer therapies, including, without limitation, DNA double strand break-inducing regimens such as high dose alkylating chemotherapy, by reliably determining homologous recombination deficiency in tumor biopsies, and by identifying patients with cancers harboring a defective BRCAl - deficient DNA repair system or BRCA2-deficient repair system, or both (cancer deficient in homology-directed DNA repair), are useful.

[011] In various aspects, the present disclosure is based on the discovery that certain differentially expressed proteins associated with BRCAl -deficient tumors can be used to identify cancer patients with BRCAl -deficient tumors and/or BRCA2-deficient tumors and to predict whether such patients will benefit from anti-cancer therapy. The present disclosure is also based on the discovery that the analysis of tumor proteins is useful in identifying patients with BRCAl -like and/or BRCA2-like cancer and selecting patients that will benefit from tailored anti-cancer therapies.

[012] In various aspects, the present disclosure is based on the discovery that certain proteins are significantly differentially regulated between BRCAl-deficient tumors and BRCAl proficient tumors and that differential regulation can be used as a means of identifying cancer patients with BRCAl -deficient tumors and/or BRCA2-deficient tumors and predicting whether such patients will benefit from anti-cancer therapy.

[013] In various aspects, the present disclosure is based on the discovery that certain up-regulated proteins seen in BRCAl -deficient tumors can be used to identify cancer patients with BRCAl -deficient tumors and to predict whether such patients will benefit from anticancer therapy.

[014] In various aspects, the present disclosure is based on the discovery that certain up-regulated proteins seen in BRCAl -deficient tumors can be used to identify cancer patients with BRCA2-deficient tumors and to predict whether such patients will benefit from anti- cancer therapy.

[015] In various aspects, the present disclosure is based on the discovery that certain up-regulated proteins seen in BRCAl -deficient tumors that exhibit DNA-repair, chromatin remodeling and associated functions can be used to identify cancer patients with BRCA1- deficient tumors and/or BRCA2-deficient tumors (cancer deficient in homology-directed DNA repair) and to predict whether such patients will benefit from anti-cancer therapy.

[016] In certain embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 417 significantly differentially regulated proteins with DNA repair(-associated) functions set forth in Fig. 1 that can enrich for homology-directed DNA repair deficient tumors. In certain embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 417 significantly differentially regulated proteins with DNA repair(-associated) functions set forth in Fig. 1 that can identify cancer patients having a BRCAl deficiency. In some embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 417 significantly differentially regulated proteins with DNA repair- associated) functions set forth in Fig. 1 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCAl deficiency.

[017] In some embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 417 significantly differentially regulated proteins with DNA repair(-associated) functions set forth in Fig. 1 that can identify cancer patients having a BRCA2 deficiency. In some

embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 417 significantly differentially regulated proteins with DNA repair(-associated) functions set forth in Fig. 1 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCA2 deficiency.

[018] In certain embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 417 significantly differentially regulated proteins with DNA repair(- associated) functions set forth in Fig. 1 that can enrich for homology-directed DNA repair deficient tumors. In certain embodiments, the present disclosure provides a BRCA- deficiency signature comprising the 417 significantly differentially regulated proteins with DNA repair(-associated) functions set forth in Fig. 1 that can identify cancer patients having a BRCA1 deficiency. In some embodiments, the present disclosure provides a BRCA- deficiency signature comprising the 417 significantly differentially regulated proteins with DNA repair(-associated) functions set forth in Fig. 1 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCA1 deficiency.

[019] In some embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 417 significantly differentially regulated proteins with DNA repair(- associated) functions set forth in Fig. 1 that can identify cancer patients having a BRCA2 deficiency. In some embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 417 significantly differentially regulated proteins with DNA repair(- associated) functions set forth in Fig. 1 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCA2 deficiency.

[020] In the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 5 proteins selected from the 417 significantly differentially regulated proteins with DNA repair(-associated) functions set forth in Fig. 1.

[021] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 6 proteins selected from the 417 significantly differentially regulated proteins with DNA repair(-associated) functions set forth in Fig. 1.

[022] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 7 proteins selected from the 417 significantly differentially regulated proteins with DNA repair(-associated) functions set forth in Fig. 1.

[023] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 8 proteins selected from the 417 significantly differentially regulated proteins with DNA repair(-associated) functions set forth in Fig. 1.

[024] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 9 proteins selected from the 417 significantly differentially regulated proteins with DNA repair(-associated) functions set forth in Fig. 1. [025] In certain embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 45 up- regulated proteins with DNA repair(-associated) functions set forth in Fig. 2 that can enrich for homology-directed DNA repair deficient tumors. In certain embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2 that can identify cancer patients having a BRCA1 deficiency. In some embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCA1 deficiency.

[026] In some embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 45 up- regulated proteins with DNA repair(-associated) functions set forth in Fig. 2 that can identify cancer patients having a BRCA2 deficiency. In some embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCA2 deficiency.

[027] In certain embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2 that can enrich for homology-directed DNA repair deficient tumors. In certain embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2 that can identify cancer patients having a BRCA1 deficiency. In some embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2 that can enrich for homology- directed DNA repair deficient tumors and identify cancer patients having a BRCA1 deficiency.

[028] In some embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2 that can identify cancer patients having a BRCA2 deficiency. In some embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCA2 deficiency.

[029] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 5 proteins selected from the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2.

[030] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 6 proteins selected from the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2.

[031] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 7 proteins selected from the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2.

[032] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 8 proteins selected from the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2.

[033] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 9 proteins selected from the 45 up-regulated proteins with DNA repair(-associated) functions set forth in Fig. 2.

[034] In certain embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45 that can enrich for homology-directed DNA repair deficient tumors. In certain embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45 that can identify cancer patients having a BRCA1 deficiency. In some embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCA1 deficiency.

[035] In some embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45 that can identify cancer patients having a BRCA2 deficiency. In some embodiments, the present disclosure provides BRCA- deficiency signatures comprising at least one, and in some embodiments a plurality, of the amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCA2 deficiency.

[036] In certain embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45 that can enrich for homology-directed DNA repair deficient tumors. In certain embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45 that can identify cancer patients having a BRCA1 deficiency. In some embodiments, the present disclosure provides a BRCA- deficiency signature comprising the 45 amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCA1 deficiency.

[037] In some embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45 that can identify cancer patients having a BRCA2 deficiency. In some embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCA2 deficiency.

[038] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 5 amino acid sequences selected from the 45 amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45.

[039] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 6 amino acid sequences selected from the 45 amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45.

[040] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 7 amino acid sequences selected from the 45 amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45.

[041] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 8 amino acid sequences selected from the 45 amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45.

[042] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 9 amino acid sequences selected from the 45 amino acid sequences of SEQ ID NO: 1 through SEQ ID NO: 45. [043] In certain embodiments, the present disclosure provides methods of using the protein and amino acid sequence-based BRCA-deficiency signatures disclosed herein to identify cancer having a BRCA1 deficiency.

[044] In certain embodiments, the present disclosure provides methods of using the protein and amino acid sequence-based BRCA-deficiency signatures disclosed herein to identify cancer having a BRCA2 deficiency.

[045] In certain embodiments, the present disclosure provides methods of using the protein and amino acid sequence-based BRCA-deficiency signatures to predict whether a patient having cancer with a BRCA1 deficiency will benefit from anti-cancer therapy.

[046] In certain embodiments, the present disclosure provides methods of using the protein and amino acid sequence-based BRCA-deficiency signatures to predict whether a patient having cancer with a BRCA2 deficiency will benefit from anti-cancer therapy.

[047] In various aspects, the present disclosure is based on the discovery that certain nucleic acid sequences that code for differentially expressed proteins associated with BRCA1 -deficient tumors can be used to identify cancer patients with BRCA1 -deficient tumors and/or BRCA2-deficient tumors and to predict whether such patients will benefit from anti-cancer therapy. The present disclosure is also based on the discovery that the analysis of nucleic acid sequences coding for tumor proteins is useful in identifying patients with BRCAl-like cancer and/or BRCA2-like cancer and selecting patients that will benefit from tailored anti-cancer therapies.

[048] In various aspects, the present disclosure is based on the discovery that certain nucleic acid sequences code for proteins that are significantly differentially regulated between B RCA 1 -deficient tumors and BRCA1 proficient tumors and that differential regulation can be used as a means of identifying cancer patients with BRCA1 -deficient tumors and/or BRCA2-deficient tumors and predicting whether such patients will benefit from anti-cancer therapy.

[049] In various aspects, the present disclosure is based on the discovery that certain nucleic acid sequences that code for up-regulated proteins seen in BRCAl-deficient tumors can be used to identify cancer patients with BRCAl-deficient tumors and to predict whether such patients will benefit from anti-cancer therapy.

[050] In various aspects, the present disclosure is based on the discovery that certain nucleic acid sequences that code for up-regulated proteins seen in BRCAl-deficient tumors can be used to identify cancer patients with BRCA2-deficient tumors and to predict whether such patients will benefit from anti-cancer therapy. [051] In various aspects, the present disclosure is based on the discovery that certain nucleic acid sequences that code for up-regulated proteins seen in BRCAl-deficient tumors that exhibit DNA-repair, chromatin remodeling and associated functions can be used to identify cancer patients with BRCAl-deficient tumors and/or BRCA2-deficient tumors and to predict whether such patients will benefit from anti-cancer therapy.

[052] In certain embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90 that can enrich for homology- directed DNA repair deficient tumors. In certain embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90 that can identify cancer patients having a BRCAl deficiency. In some embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCAl deficiency.

[053] In some embodiments, the present disclosure provides BRCA-deficiency signatures comprising at least one, and in some embodiments a plurality, of the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90 that can identify cancer patients having a BRCA2 deficiency. In some embodiments, the present disclosure provides BRCA- deficiency signatures comprising at least one, and in some embodiments a plurality, of the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCA2 deficiency.

[054] In certain embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90 that can enrich for homology-directed DNA repair deficient tumors. In certain embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90 that can identify cancer patients having a BRCAl deficiency. In some embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCAl deficiency. [055] In some embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90 that can identify cancer patients having a BRCA2 deficiency. In some embodiments, the present disclosure provides a BRCA-deficiency signature comprising the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90 that can enrich for homology-directed DNA repair deficient tumors and identify cancer patients having a BRCA2 deficiency.

[056] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 5 nucleic acid sequences selected from the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90.

[057] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 6 nucleic acid sequences selected from the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90.

[058] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 7 nucleic acid sequences selected from the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90.

[059] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 8 nucleic acid sequences selected from the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90.

[060] In certain of the above embodiments, the BRCA-deficiency signatures may comprise a set of at least 9 nucleic acid sequences selected from the 45 nucleic acid sequences of SEQ ID NO: 46 through SEQ ID NO: 90.

[061] In certain embodiments, the present disclosure provides methods of using the nucleic acid-based BRCA-deficiency signatures disclosed herein to identify cancer having a BRCA1 deficiency.

[062] In certain embodiments, the present disclosure provides methods of using the nucleic acid-based BRCA-deficiency signatures disclosed herein to identify cancer having a BRCA2 deficiency.

[063] In certain embodiments, the present disclosure provides methods of using the nucleic acid-based BRCA-deficiency signatures to predict whether a patient having cancer with a BRCA1 deficiency will benefit from anti-cancer therapy.

[064] In certain embodiments, the present disclosure provides methods of using the nucleic acid-based BRCA-deficiency signatures to predict whether a patient having cancer with a BRCA2 deficiency will benefit from anti-cancer therapy. Brief Description of the Drawings

[065] Figure 1 provides a list of 417 proteins that are significantly differentially regulated in BRCA1 -deficient mammalian breast tumor tissue lysates, as compared to BRCA1 -proficient mammalian tumor tissue lysates.

[066] Figure 2 provides a list of 45 proteins that are up-regulated in BRCA1- deficient mammalian breast tumor tissue lysates, as compared to BRCA1 -proficient mammalian tumor tissue lysates.

Detailed Description

Definitions

[067] "Anti-cancer therapy" means any one, or a plurality, of therapies and/or drugs used to treat cancer, or any combinations thereof, including a) homologous recombination deficiency-targeted drugs and/or treatments; and b) drugs or treatments that directly or indirectly cause double strand DNA breaks. This definition includes, without limitation, high dose platinum-based alkylating chemotherapy, platinum compounds, thiotepa,

cyclophosphamide, iphosphamide, nitrosureas, nitrogen mustard derivatives, mitomycins, epipodophyllotoxins, camptothecins, anthracyclines, poly(ADP-ribose) polymerase (PARP) inhibitors, ionizing radiation, ABT-888, olaparib (AZT-2281), gemcitabine, CEP-9722, AG014699, AG014699 with Temozolomide, and BSI-201.

[068] "Array" refers to an arrangement, on a substrate surface, of multiple nucleic acid probes (as defined herein) of predetermined identity. In various embodiments, the sequences of the multiple nucleic acid probes are known. In general, an array comprises a plurality of target elements, each target element comprising one or more nucleic acid probes immobilized on one or more solid surfaces, to which sample nucleic acids can be hybridized. In various embodiments, each individual probe is immobilized to a designated, discrete location (i.e., a defined location or assigned position) on the substrate surface. In various embodiments, each nucleic acid probe is immobilized to a discrete location on an array and each has a sequence that is either specific to, or characteristic of, a particular nucleic acid sequence coding for a protein that is significantly up-regulated in BRCA1 -deficient tumors. A nucleic acid probe is specific to, or characteristic of, a particular nucleic acid sequence because it contains a nucleic acid sequence that is unique to that nucleic acid sequence. Such a probe preferentially hybridizes to a single nucleic acid molecule, relative to other nucleic acid molecules isolated from the same tissue. [069] The nucleic acid probes can contain sequence(s) corresponding to specific genes or proteins. In various embodiments, at least some of the nucleic acid probes contain sequences specific to, or characteristic of, any one or more of the proteins recited in Fig. 1. In various embodiments, at least some of the nucleic acid probes contain sequences specific to, or characteristic of, any one or more of the proteins recited in Fig. 2.

[070] The probes may be arranged on the substrate in a single density, or in varying densities. The density of each of the probes can be varied to accommodate certain factors such as, for example, the nature of the test sample, the nature of a label used during hybridization, the type of substrate used, and the like. Each probe may comprise a mixture of nucleic acids of varying lengths and, thus, varying sequences. For example, a single probe may contain more than one copy of a cloned nucleic acid, and each copy may be broken into fragments of different lengths. Each length will thus have a different sequence.

[071] The length, sequence and complexity of the nucleic acid probes may be varied. In various embodiments, the length, sequence and complexity are varied to provide optimum hybridization and signal production for a given hybridization procedure, and to provide the required resolution among different genes or genomic locations.

[072] "BRC A 1 -deficiency" means cancer, as defined herein, having cells containing a mutation of the BRCA1 locus or a deficiency in the homologous recombination-dependent double strand break DNA repair pathway that alters BRCA1 activity or function, either directly or indirectly.

[073] "BRCA2-deficiencv" means cancer, as defined herein, having cells containing a mutation of the BRCA2 locus or a deficiency in the homologous recombination-dependent double strand break DNA repair pathway that alters BRCA2 activity or function, either directly or indirectly.

[074] "Cancer" means a malignant neoplasm involving unregulated cell growth, where cells divide and grow uncontrollably forming malignant tumors. The unregulated cell growth can be caused by a deficiency in the BRCA1 gene, the BRCA2 gene, or both. In this disclosure, unless expressly stated otherwise, cancer is intended to mean unregulated cell growth arising from a BRCA1 and/or BRCA2 deficiency. The definition of cancer includes breast cancer, cancer of mammary tissue, lung cancer, ovarian cancer, colon cancer, gastric cancer and all other types of cancer that are presently known, or may hereafter be discovered, to be caused by BRCA1 and/or BRCA2 deficiency (cancer deficient in homology-directed DNA repair). [075] "Hybridization" refers to the binding of two single stranded nucleic acids via complementary base pairing. Extensive guides to the hybridization of nucleic acids can be found in: Tijssen, Laboratory Techniques in Biochemistry and Molecular Biology- Hybridization with Nucleic Acid Probes Part I, Ch. 2, "Overview of principles of hybridization and the strategy of nucleic acid probe assays" (1993), Elsevier, N.Y.; and Sambrook et ah, Molecular Cloning: A Laboratory Manual (3rd ed.) Vol. 1-3 (2001), Cold Spring Harbor Laboratory, Cold Spring Harbor Press, N.Y. The phrases "hybridizing specifically to", "specific hybridization", and "selectively hybridize to", refer to the preferential binding, duplexing, or hybridizing of a nucleic acid molecule to a particular probe under stringent conditions. The term "stringent conditions" refers to hybridization conditions under which a probe will hybridize preferentially to its target subsequence, and to a lesser extent, or not at all, to other sequences in a mixed population (e.g., a nucleic acid extraction from a tissue biopsy). "Stringent hybridization" and "stringent hybridization wash conditions" are sequence-dependent and are different under different environmental parameters.

[076] Generally, highly stringent hybridization and wash conditions are selected to be about 5° C lower than the thermal melting point (Tm) for a specific sequence at a defined ionic strength and pH. The Tm is the temperature at which 50% of the target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected to be equal to the Tm for a particular probe. Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal. An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on an array is 42° C using standard hybridization solutions, with the hybridization being carried out overnight. An example of highly stringent wash conditions is a 0.15 M NaCl wash at 72° C for 15 minutes. An example of stringent wash conditions is a wash in

0.2X Standard Saline Citrate (SSC) buffer at 65° C for 15 minutes. An example of a medium stringency wash for a duplex of, for example, more than 100 nucleotides, is IX SSC at 45° C for 15 minutes. An example of a low stringency wash for a duplex of, for example, more than 100 nucleotides, is 4X to 6X SSC at 40° C for 15 minutes.

[077] "Nucleic acid" refers to a deoxyribonucleotide or ribonucleotide in either single- or double-stranded form and includes all nucleic acids comprising naturally occurring nucleotide bases as well as nucleic acids containing any and/or all analogues of natural nucleotides. This term also includes nucleic acid analogues that are metabolized in a manner similar to naturally occurring nucleotides, but at rates that are improved for the purposes desired. This term also encompasses nucleic-acid-like structures with synthetic backbone analogues including, without limitation, phosphodiester, phosphorothioate,

phosphorodithioate, methylphosphonate, phosphoramidate, alkyl phosphotriester, sulfamate, 3'-thioacetal, methylene(methylimino), 3'-N-carbamate, morpholino carbamate, and peptide nucleic acids (PNAs) (see, e.g. : "Oligonucleotides and Analogues, a Practical Approach," edited by F. Eckstein, IRL Press at Oxford University Press (1991); "Antisense Strategies," Annals of the New York Academy of Sciences, Volume 600, Eds. Baserga and Denhardt (NYAS 1992); Milligan (1993) J. Med. Chem. 36:1923-1937; and "Antisense Research and Applications" (1993, CRC Press)). PNAs contain non-ionic backbones, such as N-(2- aminoethyl) glycine units. Phosphorothioate linkages are described in: WO 97/03211 ; WO 96/39154; and Mata (1997) Toxicol. Appl. Pharmacol. 144: 189-197. Other synthetic backbones encompassed by this term include methyl-phosphonate linkages or alternating methyl-phosphonate and phosphodiester linkages (Strauss-Soukup (1997) Biochemistry 36: 8692-8698), and benzyl-phosphonate linkages (Samstag (1996) Antisense Nucleic Acid Drug Dev 6: 153-156).

[078] "Probe" or "nucleic acid probe" refer to one or more nucleic acid fragments whose specific hybridization to a sample can be detected. In various embodiments, probes are arranged on a substrate surface in an array. The probe may be unlabelled, or it may contain one or more labels so that its binding to a nucleic acid can be detected. In various embodiments, a probe can be produced from any source of nucleic acids from one or more particular, pre-selected portions of a chromosome including, without limitation, one or more clones, an isolated whole chromosome, an isolated chromosome fragment, or a collection of polymerase chain reaction (PCR) amplification products.

[079] In some embodiments, the probe may be a member of an array of nucleic acids as described in WO 96/17958. Techniques capable of producing high density arrays can also be used for this purpose (see, e.g. , Fodor (1991) Science 767-773; Johnston (1998) Curr. Biol. 8: Rl 71 -Rl 74; Schummer (1997) Biotechniques 23: 1087-1092; Kern (1997)

Biotechniques 23: 120-124; and U.S. Patent No. 5,143,854).

[080] The sequence of the probes can be varied. In various embodiments, the probe sequence can be varied to produce probes that are substantially identical to the probes disclosed hereinbelow, but that retain the ability to hybridize specifically to the same targets or samples as the probe from which they were derived.

[081] "Reference sample" refers to BRCA-deficient protein signatures, disclosed herein, or BRCA-deficiency nucleic acid signatures, disclosed herein, whose expression levels and/or sequence identity are known. Such protein signatures or nucleic acid signatures serve as a reference to which one or more test samples are compared.

[082] "Test sample" refers to a proteome or a full complement of nucleic acid molecules isolated from a tumor obtained from a subject whose BRCAl status and/or BRCA2 status (deficient or proficient) is unknown. In various embodiments, the present disclosure is directed to the detection of the expression level of certain differentially regulated proteins and/or nucleic acid molecules of one or more test samples.

[083] Reference is now made in detail to certain embodiments of BRCA-deficiency signatures, BRCA-deficiency classifiers and related methods. The disclosed embodiments are not intended to be limiting of the claims. To the contrary, the claims are intended to cover all alternatives, modifications, and equivalents.

Protein Signatures

[084] The present inventors have confirmed that a large proportion (20%) of the proteome of mammalian mammary tumor tissue is significantly differentially regulated (either up-regulated or down-regulated) in BRCAl -deficient tumors as compared to BRCA1- proficient tumors. The differentially regulated proteins seen in BRCAl -deficient tumors are almost exclusively related to BRCAl status and only partially to cell type, making them ideally suited as predictive measures of BRCA-deficiency status in cancer. The data presented in this disclosure shows an extensive up-regulation of a broad range of DNA repair/chromatin remodeling pathways and protein complexes in BRCAl -deficient tumors.

[085] In various aspects, the present disclosure is based on the discovery that certain up-regulated proteins seen in BRCAl -deficient tumors can be used to identify cancer patients with BRCAl -deficient tumors and/or to predict whether such patients will benefit from anticancer therapy. In various aspects, the present disclosure is based on the discovery that certain up-regulated proteins seen in BRCAl -deficient tumors can be used to identify cancer patients with BRCA2-deficient tumors and/or to predict whether such patients will benefit from anti-cancer therapy.

[086] In various embodiments, BRCA-deficiency signatures comprising one or more proteins that are up-regulated in BRCAl -deficient tumors are disclosed. In various embodiments, the BRCA-deficiency signatures can be used to identify cancer patients with BRCAl -deficient tumors. In various embodiments, the BRCA-deficiency signatures can be used to identify cancer patients with BRCA2-deficient tumors. In various embodiments, the BRCA-deficiency signatures can be used to predict whether such patients will benefit from anti-cancer therapy. BRCA-deficiency Signatures Based on 417 Significantly Differentially Regulated Proteins

[087] The present inventors have identified 417 proteins that are significantly differentially regulated in BRCA1 -deficient tumors, which are useful in the methods and signatures disclosed herein. The 417 proteins are shown in Fig. 1.

[088] Therefore, in various embodiments, BRCA-deficiency signatures comprising one or more of the significantly differentially regulated proteins shown in Fig. 1 are disclosed. These BRCA-deficiency signatures can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. These BRCA-deficiency signatures can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. These BRCA-deficiency signatures can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. These BRCA-deficiency signatures can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[089] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 5 proteins selected from the following 417 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: Tacstdl, Lamal, 2610018G03Rik, Thumpdl, Mfge8, Serpine2, 1110067D22Rik, Nipsnapl, Fxyd3, Beam, Hlfx, Myhl4, Mafg, Cul5, Aldhlal, Pnptl, 1600014C10Rik, Rifl, Fl lr, Heatr2, Add3, Slc25a35, Trim33, Chd8, Gtf3cl, F12, Aqp5, Trim29, Ladl, Ppfial, Rsfl, Mrps25, Pdcd4, Otud6b, Pdzdl l, Dock9, Zfr, Kifl l, Agrn, Zfand6, Cdk9, Phlda3, Pbrml, Eif2b4, Dhxl6, Sntbl, 1500005K14Rik, B230219D22Rik, Acyl, Bysl, Gdpdl, Gemin5, Ank3, Rnf20, Dnmt3a, Vpsl3a, Epm2aipl, Coblll, Uxt, LOC100043597, Etv6, Lcmtl, Atplbl, Crym, Kctdl4, Bdhl, Lamb2, Scrib, StardlO, Gcat, Gyk, Cldn3, Dak, Azgpl, Btafl, Aldh4al, Tnn, Tcfap2c, Rab27a,

2010107G23Rik, D0HXS9928E, Ppl, Bptf, Lrrcl6, Relll, Ccdc44, Dnaja3, Ponl, Fbpl, Rtn4ipl, Hiplr, 1190003J15Rik, Ckmtl, Ccdc6, Cnnl, Ptn, Cdh3, Krt6b, Dsg2, Ephxl, Etl4, Stiml, Itgal, Txndcl4, Nudcd3, Pltp, AW549877, Trp63, Padi3, 1600027N09Rik, Mrpl44, Serpindl, Tubb3, Thumpd3, Nck2, Cstfl, Gjal, Echdc2, Mdcl, Lig3, Mtal, Cpn2, Plekha7, Fxcl, ENSMUSG00000073624, Papola, Kit, Cnp, Ppl, Aiml, Mki67, Dsp, Lama2, Nup210, Jup, Aldoc, Lama5, Dhx30, Arfgefl, Lancll, Mki67, Sin3a, Ahctfl, Fryl, Adnp, Gpc4, Tst, Itgb4, Bckdha, Gm237, Apod, NatlO, Pkp3, Acotl, Wbpl l, Agrn, Nfl, Tinagl, Mest, Aplm2, Slc7a5, Trp53bpl, Plcgl, Ubap2, 0610010K14Rik, Ep400, Ankrdl7, Addl, Tfam, Wdrl2, Gstt3, 2610528E23Rik, Poldl, Trrap, Tjp2, Bat2d, Srrm2, Akap8, Cd2ap, Ptk7, Rrpl, LOC68280, Acoxl, Peer, Cpox, Myol8a, Hebp2, Adrml, Msh6, Klkbl, Mrpl47, Fatl, Krtl4, Gtf2i, Ddx42, Cstf3, Rpal, Zfp289, Kif4, Chchd4, Mrpl4, Lgals7, Nupl07, Atm, Medl2, Nosip, Ptma, Hist3h2bb, Ppif, Ubtf, Gsttl, 1700012G19Rik, Crebbp, Pspcl, Tbl2, Slc25al3, Pds5a, Cdhl, Tmeml76b, Gsta4, Nup214, Pesl, Ctnnbl, Ncapd2, Wdr5, Pusl, Ddx27, Slc9a3rl, Rbm7, Dockl, Ndrgl, Saa4, Asfla, Dnmtl, Aqr, Usp39, Wdr43, Mllt4, Bazlb, Top2a, Nid2, Bzw2, Aridla, Ogt, Stag2, Ranbp2, Rael, Rrplb, Src, Clnsla,

492151 lH13Rik, Hint2, Dhrs7b, Ddx46, Dnajc7, Rbp4, Hcfcl, Mdnl, C330023M02Rik, Tjpl, Shmtl, Prep, Sfn, Supt5h, Lamcl, Zfp313, Raverl, Bat2, 2410003P15Rik, Numal, Fenl, Hmgb3, Tnkslbpl, H47, Cygb, Smcla, 2010100O12Rik, Ssrpl, Cdc51, Parpl, Rad21, Col4al, Nudtl611, Pcx, Smarccl, Crip2, Rps271, Msh2, Ppp5c, Ociadl, Col4a2, Grhpr, Cbr3, Nudt5, Rrpl2, Gtpbpl, Npm3, Ppmel, Tripl2, Dcps, Pus7, Smul, Ptges2, Mrpll4, Itga6, Cirbp, Apip, Drgl, 130000110 IRik, Ctnnal, Smchdl, Mgstl, Coll8al, Lin7c, Macfl, Isynal, Stat3, Huwel, Ppig, Aprin, Oat, Lama4, Sec24c, Tra2a, Csnk2al, Smc4, Ldhb, Eif4g2, Smc3, Cbxl, Acadl, Timm50, Dek, Fah, Smarca4, Ighg, Hkl, Ilf3, Ctnndl, Ddx21,

261030 lG19Rik, Nasp, Albg, Dut, Topi, Bid, Son, Sart3, Suptl6h, Cat, Ddx6, Pdcdl l,

Abcfl, Slc3a2, Luc71, Top2b, Nolcl, Eif3s4, Pycard, Vil2, Ilf2, Purb, Tpr, Esl, D10Jhu81e, Fkbp3, Hnrpul2, Mpst, Ncbpl, Lambl-1, Trim28, LOC100047252, Bat3, Eif4a3, Coll4al, Ckap5, Cnotl, Gcnlll, Fkbp4, Pcna, Gstm5, Nsun2, Chd4, Bax, Atplal, Csell, Birc6, Fabp5, Batla, Dkcl, Ddt, Ahcy, Fbl, Ascc311, Nol5a, Rab6, Nsfllc, Anp32b, Ddbl, Prpf8, Idh3a, Ssb, Hnrpd, Stipl, Sfrsl, Cbx3, Smarca5, Hmgbl, Hnrpf, Hnrpl, Uqcrcl, Sfrs3, Tufm, Dhx9, Hnrpa2bl, Ncl, and Hspdl. The BRCA-deficiency signatures comprising a set of at least 5 proteins selected from the foregoing 417 proteins can be used as diagnostic tools to detect patients who are carrying a BRCAl-mutation and/or have B RC A 1 -deficient cancer. The BRCA-deficiency signatures comprising a set of at least 5 proteins selected from the foregoing 417 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 5 proteins selected from the foregoing 417 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 5 proteins selected from the foregoing 417 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anticancer therapy.

[090] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 6 proteins selected from the following 417 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: Tacstdl, Lamal, 2610018G03Rik, Thumpdl, Mfge8, Serpine2, 1110067D22Rik, Nipsnapl, Fxyd3, Beam, Hlfx, Myhl4, Mafg, Cul5, Aldhlal, Pnptl, 1600014C10Rik, Rifl, Fl lr, Heatr2, Add3, Slc25a35, Trim33, Chd8, Gtf3cl, F12, Aqp5, Trim29, Ladl, Ppfial, Rsfl, Mrps25, Pdcd4, Otud6b, Pdzdl l, Dock9, Zfr, Kifl 1, Agrn, Zfand6, Cdk9, Phlda3, Pbrml, Eif2b4, Dhxl6, Sntbl, 1500005K14Rik, B230219D22Rik, Acyl, Bysl, Gdpdl, Gemin5, Ank3, Rnf20, Dnmt3a, Vpsl3a, Epm2aipl, Coblll, Uxt, LOC100043597, Etv6, Lcmtl, Atplbl, Crym, Kctdl4, Bdhl, Lamb2, Scrib, StardlO, Gcat, Gyk, Cldn3, Dak, Azgpl, Btafl, Aldh4al, Tnn, Tcfap2c, Rab27a,

2010107G23Rik, D0HXS9928E, Ppl, Bptf, Lrrcl6, Relll, Ccdc44, Dnaja3, Ponl, Fbpl, Rtn4ipl, Hiplr, 1190003J15Rik, Ckmtl, Ccdc6, Cnnl, Ptn, Cdh3, Krt6b, Dsg2, Ephxl, Etl4, Stiml, Itgal, Txndcl4, Nudcd3, Pltp, AW549877, Trp63, Padi3, 1600027N09Rik, Mrpl44, Serpindl, Tubb3, Thumpd3, Nck2, Cstfl, Gjal, Echdc2, Mdcl, Lig3, Mtal, Cpn2, Plekha7, Fxcl, ENSMUSG00000073624, Papola, Kit, Cnp, Ppl, Aiml, Mki67, Dsp, Lama2, Nup210, Jup, Aldoc, Lama5, Dhx30, Arfgefl, Lancll, Mki67, Sin3a, Ahctfl, Fryl, Adnp, Gpc4, Tst, Itgb4, Bckdha, Gm237, Apod, NatlO, Pkp3, Acotl, Wbpl 1, Agrn, Nfl, Tinagl, Mest,

Aplm2, Slc7a5, Trp53bpl, Plcgl, Ubap2, 0610010K14Rik, Ep400, Ankrdl7, Addl, Tfam, Wdrl2, Gstt3, 2610528E23Rik, Poldl, Trrap, Tjp2, Bat2d, Srrm2, Akap8, Cd2ap, Ptk7, Rrpl, LOC68280, Acoxl, Peer, Cpox, Myol8a, Hebp2, Adrml, Msh6, Klkbl, Mrpl47, Fatl, Krtl4, Gtf2i, Ddx42, Cstf3, Rpal, Zfp289, Kif4, Chchd4, Mrpl4, Lgals7, Nupl07, Atm, Medl2, Nosip, Ptma, Hist3h2bb, Ppif, Ubtf, Gsttl, 1700012G19Rik, Crebbp, Pspcl, Tbl2, Slc25al3, Pds5a, Cdhl, Tmeml76b, Gsta4, Nup214, Pesl, Ctnnbl, Ncapd2, Wdr5, Pusl, Ddx27, Slc9a3rl, Rbm7, Dockl, Ndrgl, Saa4, Asfla, Dnmtl, Aqr, Usp39, Wdr43, Mllt4, Bazlb, Top2a, Nid2, Bzw2, Aridla, Ogt, Stag2, Ranbp2, Rael, Rrplb, Src, Clnsla,

492151 lH13Rik, Hint2, Dhrs7b, Ddx46, Dnajc7, Rbp4, Hcfcl, Mdnl, C330023M02Rik, Tjpl, Shmtl, Prep, Sfn, Supt5h, Lamcl, Zfp313, Raverl, Bat2, 2410003P15Rik, Numal,

Fenl, Hmgb3, Tnkslbpl, H47, Cygb, Smcla, 2010100O12Rik, Ssrpl, Cdc51, Parpl, Rad21, Col4al, Nudtl611, Pcx, Smarccl, Crip2, Rps271, Msh2, Ppp5c, Ociadl, Col4a2, Grhpr, Cbr3, Nudt5, Rrpl2, Gtpbpl, Npm3, Ppmel, Tripl2, Dcps, Pus7, Smul, Ptges2, Mrpll4, Itga6, Cirbp, Apip, Drgl, 130000110 IRik, Ctnnal, Smchdl, Mgstl, Coll8al, Lin7c, Macfl, Isynal, Stat3, Huwel, Ppig, Aprin, Oat, Lama4, Sec24c, Tra2a, Csnk2al, Smc4, Ldhb, Eif4g2, Smc3, Cbxl, Acadl, Timm50, Dek, Fah, Smarca4, Ighg, Hkl, Ilf3, Ctnndl, Ddx21,

2610301G19Rik, Nasp, Albg, Dut, Topi, Bid, Son, Sart3, Suptl6h, Cat, Ddx6, Pdcdl l, Abcfl, Slc3a2, Luc71, Top2b, Nolcl, Eif3s4, Pycard, Vil2, Ilf2, Purb, Tpr, Esl, D10Jhu81e, Fkbp3, Hnrpul2, Mpst, Ncbpl, Lambl-1, Trim28, LOC100047252, Bat3, Eif4a3, Coll4al, Ckap5, Cnotl, Gcnlll, Fkbp4, Pcna, Gstm5, Nsun2, Chd4, Bax, Atplal, Csell, Birc6, Fabp5, Batla, Dkcl, Ddt, Ahcy, Fbl, Ascc311, Nol5a, Rab6, Nsfllc, Anp32b, Ddbl, Prpf8, Idh3a, Ssb, Hnrpd, Stipl, Sfrsl, Cbx3, Smarca5, Hmgbl, Hnrpf, Hnrpl, Uqcrcl, Sfrs3, Tufm, Dhx9, Hnrpa2bl, Ncl, and Hspdl. The BRCA-deficiency signatures comprising a set of at least 6 proteins selected from the foregoing 417 proteins can be used as diagnostic tools to detect patients who are carrying a BRCAl-mutation and/or have B RC A 1 -deficient cancer. The BRCA-deficiency signatures comprising a set of at least 6 proteins selected from the foregoing 417 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 6 proteins selected from the foregoing 417 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 6 proteins selected from the foregoing 417 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti- cancer therapy.

[091] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 7 proteins selected from the following 417 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: Tacstdl, Lamal, 2610018G03Rik, Thumpdl, Mfge8, Serpine2, 1110067D22Rik, Nipsnapl, Fxyd3, Beam, Hlfx, Myhl4, Mafg, Cul5, Aldhlal, Pnptl, 1600014C10Rik, Rifl, Fl lr, Heatr2, Add3, Slc25a35, Trim33, Chd8, Gtf3cl, F12, Aqp5, Trim29, Ladl, Ppfial, Rsfl, Mrps25, Pdcd4, Otud6b, Pdzdl l, Dock9, Zfr, Kifl l, Agrn, Zfand6, Cdk9, Phlda3, Pbrml, Eif2b4, Dhxl6, Sntbl, 1500005K14Rik, B230219D22Rik, Acyl, Bysl, Gdpdl, Gemin5, Ank3, Rnf20, Dnmt3a, Vpsl3a, Epm2aipl, Coblll, Uxt, LOC100043597, Etv6, Lcmtl, Atplbl, Crym, Kctdl4, Bdhl, Lamb2, Scrib, StardlO, Gcat, Gyk, Cldn3, Dak, Azgpl, Btafl, Aldh4al, Tnn, Tcfap2c, Rab27a,

Abcfl, Slc3a2, Luc71, Top2b, Nolcl, Eif3s4, Pycard, Vil2, Ilf2, Purb, Tpr, Esl, D10Jhu81e, Fkbp3, Hnrpul2, Mpst, Ncbpl, Lambl-1, Trim28, LOC100047252, Bat3, Eif4a3, Coll4al, Ckap5, Cnotl, Gcnlll, Fkbp4, Pcna, Gstm5, Nsun2, Chd4, Bax, Atplal, Csell, Birc6, Fabp5, Batla, Dkcl, Ddt, Ahcy, Fbl, Ascc311, Nol5a, Rab6, Nsfllc, Anp32b, Ddbl, Prpf8, Idh3a, Ssb, Hnrpd, Stipl, Sfrsl, Cbx3, Smarca5, Hmgbl, Hnrpf, Hnrpl, Uqcrcl, Sfrs3, Tufm, Dhx9, Hnrpa2bl, Ncl, and Hspdl. The BRCA-deficiency signatures comprising a set of at least 7 proteins selected from the foregoing 417 proteins can be used as diagnostic tools to detect patients who are carrying a BRCAl-mutation and/or have B RC A 1 -deficient cancer. The BRCA-deficiency signatures comprising a set of at least 7 proteins selected from the foregoing 417 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 7 proteins selected from the foregoing 417 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 7 proteins selected from the foregoing 417 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anticancer therapy.

[092] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 8 proteins selected from the following 417 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: Tacstdl, Lamal, 2610018G03Rik, Thumpdl, Mfge8, Serpine2, 1110067D22Rik, Nipsnapl, Fxyd3, Beam, Hlfx, Myhl4, Mafg, Cul5, Aldhlal, Pnptl, 1600014C10Rik, Rifl, Fl lr, Heatr2, Add3, Slc25a35, Trim33, Chd8, Gtf3cl, F12, Aqp5, Trim29, Ladl, Ppfial, Rsfl, Mrps25, Pdcd4, Otud6b, Pdzdl l, Dock9, Zfr, Kifl 1, Agrn, Zfand6, Cdk9, Phlda3, Pbrml, Eif2b4, Dhxl6, Sntbl, 1500005K14Rik, B230219D22Rik, Acyl, Bysl, Gdpdl, Gemin5, Ank3, Rnf20, Dnmt3a, Vpsl3a, Epm2aipl, Coblll, Uxt, LOC100043597, Etv6, Lcmtl, Atplbl, Crym, Kctdl4, Bdhl, Lamb2, Scrib, StardlO, Gcat, Gyk, Cldn3, Dak, Azgpl, Btafl, Aldh4al, Tnn, Tcfap2c, Rab27a,

261030 lG19Rik, Nasp, Albg, Dut, Topi, Bid, Son, Sart3, Suptl6h, Cat, Ddx6, Pdcdl l, Abcfl, Slc3a2, Luc71, Top2b, Nolcl, Eif3s4, Pycard, Vil2, Ilf2, Purb, Tpr, Esl, D10Jhu81e, Fkbp3, Hnrpul2, Mpst, Ncbpl, Lambl-1, Trim28, LOC100047252, Bat3, Eif4a3, Coll4al, Ckap5, Cnotl, Gcnlll, Fkbp4, Pcna, Gstm5, Nsun2, Chd4, Bax, Atplal, Csell, Birc6, Fabp5, Batla, Dkcl, Ddt, Ahcy, Fbl, Ascc311, Nol5a, Rab6, Nsfllc, Anp32b, Ddbl, Prpf8, Idh3a, Ssb, Hnrpd, Stipl, Sfrsl, Cbx3, Smarca5, Hmgbl, Hnrpf, Hnrpl, Uqcrcl, Sfrs3, Tufm, Dhx9, Hnrpa2bl, Ncl, and Hspdl. The BRCA-deficiency signatures comprising a set of at least 8 proteins selected from the foregoing 417 proteins can be used as diagnostic tools to detect patients who are carrying a BRCAl-mutation and/or have B RC A 1 -deficient cancer. The BRCA-deficiency signatures comprising a set of at least 8 proteins selected from the foregoing 417 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 8 proteins selected from the foregoing 417 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 8 proteins selected from the foregoing 417 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti- cancer therapy.

[093] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 9 proteins selected from the following 417 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: Tacstdl, Lamal, 2610018G03Rik, Thumpdl, Mfge8, Serpine2, 1110067D22Rik, Nipsnapl, Fxyd3, Beam, Hlfx, Myhl4, Mafg, Cul5, Aldhlal, Pnptl, 1600014C10Rik, Rifl, Fl lr, Heatr2, Add3, Slc25a35, Trim33, Chd8, Gtf3cl, F12, Aqp5, Trim29, Ladl, Ppfial, Rsfl, Mrps25, Pdcd4, Otud6b, Pdzdl l, Dock9, Zfr, Kifl l, Agrn, Zfand6, Cdk9, Phlda3, Pbrml, Eif2b4, Dhxl6, Sntbl, 1500005K14Rik, B230219D22Rik, Acyl, Bysl, Gdpdl, Gemin5, Ank3, Rnf20, Dnmt3a, Vpsl3a, Epm2aipl, Coblll, Uxt, LOC100043597, Etv6, Lcmtl, Atplbl, Crym, Kctdl4, Bdhl, Lamb2, Scrib, StardlO, Gcat, Gyk, Cldn3, Dak, Azgpl, Btafl, Aldh4al, Tnn, Tcfap2c, Rab27a,

Abcfl, Slc3a2, Luc71, Top2b, Nolcl, Eif3s4, Pycard, Vil2, Ilf2, Purb, Tpr, Esl, D10Jhu81e, Fkbp3, Hnrpul2, Mpst, Ncbpl, Lambl-1, Trim28, LOC100047252, Bat3, Eif4a3, Coll4al, Ckap5, Cnotl, Gcnlll, Fkbp4, Pcna, Gstm5, Nsun2, Chd4, Bax, Atplal, Csell, Birc6, Fabp5, Batla, Dkcl, Ddt, Ahcy, Fbl, Ascc311, Nol5a, Rab6, Nsfllc, Anp32b, Ddbl, Prpf8, Idh3a, Ssb, Hnrpd, Stipl, Sfrsl, Cbx3, Smarca5, Hmgbl, Hnrpf, Hnrpl, Uqcrcl, Sfrs3, Tufm, Dhx9, Hnrpa2bl, Ncl, and Hspdl. The BRCA-deficiency signatures comprising a set of at least 9 proteins selected from the foregoing 417 proteins can be used as diagnostic tools to detect patients who are carrying a BRCAl-mutation and/or have B RC A 1 -deficient cancer. The BRCA-deficiency signatures comprising a set of at least 9 proteins selected from the foregoing 417 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 9 proteins selected from the foregoing 417 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 9 proteins selected from the foregoing 417 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anticancer therapy.

[094] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 417 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: Tacstdl, Lamal, 2610018G03Rik, Thumpdl, Mfge8, Serpine2, 1110067D22Rik, Nipsnapl, Fxyd3, Beam, Hlfx, Myhl4, Mafg, Cul5, Aldhlal, Pnptl, 1600014C10Rik, Rifl, Fl lr, Heatr2, Add3, Slc25a35, Trim33, Chd8, Gtf3cl, F12, Aqp5, Trim29, Ladl, Ppfial, Rsfl, Mrps25, Pdcd4, Otud6b, Pdzdl l, Dock9, Zfr, Kifl l, Agrn, Zfand6, Cdk9, Phlda3, Pbrml, Eif2b4, Dhxl6, Sntbl, 1500005K14Rik,

B230219D22Rik, Acyl, Bysl, Gdpdl, Gemin5, Ank3, Rnf20, Dnmt3a, Vpsl3a, Epm2aipl, Coblll, Uxt, LOC100043597, Etv6, Lcmtl, Atplbl, Crym, Kctdl4, Bdhl, Lamb2, Scrib, StardlO, Gcat, Gyk, Cldn3, Dak, Azgpl, Btafl, Aldh4al, Tnn, Tcfap2c, Rab27a,

2010107G23Rik, D0HXS9928E, Ppl, Bptf, Lrrcl6, Relll, Ccdc44, Dnaja3, Ponl, Fbpl, Rtn4ipl, Hiplr, 1190003J15Rik, Ckmtl, Ccdc6, Cnnl, Ptn, Cdh3, Krt6b, Dsg2, Ephxl, Etl4, Stiml, Itgal, Txndcl4, Nudcd3, Pltp, AW549877, Trp63, Padi3, 1600027N09Rik, Mrpl44, Serpindl, Tubb3, Thumpd3, Nck2, Cstfl, Gjal, Echdc2, Mdcl, Lig3, Mtal, Cpn2, Plekha7, Fxcl, ENSMUSG00000073624, Papola, Kit, Cnp, Ppl, Aiml, Mki67, Dsp, Lama2, Nup210, Jup, Aldoc, Lama5, Dhx30, Arfgefl, Lancll, Mki67, Sin3a, Ahctfl, Fryl, Adnp, Gpc4, Tst, Itgb4, Bckdha, Gm237, Apod, NatlO, Pkp3, Acotl, Wbpl l, Agrn, Nfl, Tinagl, Mest,

2610301G19Rik, Nasp, Albg, Dut, Topi, Bid, Son, Sart3, Suptl6h, Cat, Ddx6, Pdcdl l, Abcfl, Slc3a2, Luc71, Top2b, Nolcl, Eif3s4, Pycard, Vil2, Ilf2, Purb, Tpr, Esl, D10Jhu81e, Fkbp3, Hnrpul2, Mpst, Ncbpl, Lambl-1, Trim28, LOC100047252, Bat3, Eif4a3, Coll4al, Ckap5, Cnotl, Gcnlll, Fkbp4, Pcna, Gstm5, Nsun2, Chd4, Bax, Atplal, Csell, Birc6, Fabp5, Batla, Dkcl, Ddt, Ahcy, Fbl, Ascc311, Nol5a, Rab6, Nsfllc, Anp32b, Ddbl, Prpf8, Idh3a, Ssb, Hnrpd, Stipl, Sfrsl, Cbx3, Smarca5, Hmgbl, Hnrpf, Hnrpl, Uqcrcl, Sfrs3, Tufm, Dhx9, Hnrpa2bl, Ncl, and Hspdl. The 417 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have

BRCA1 -deficient cancer. The 417 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 417 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 417 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[095] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 5 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: CDH3, OGT, KIF4A, COL14A1 and ITGB4. The foregoing 5 -protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 5 -protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 5 -protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 5 -protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[096] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 6 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: CDH3, OGT, KIF4A, COL14A1, ITGB4 and CUL5. The foregoing 6-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 6-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 6-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 6-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[097] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: CDH3, OGT, KIF4A, COL14A1, ITGB4, CUL5 and NDRG1. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[098] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 8 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: CDH3, OGT, KIF4A, COL14A1, ITGB4, CUL5, NDRG1 and BYSL. The foregoing 8-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1- deficient cancer. The foregoing 8-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The foregoing 8-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 8-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[099] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 9 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: CDH3, OGT, KIF4A, COL14A1, ITGB4, CUL5, NDRG1 , BYSL and COL4A1. The foregoing 9-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCAl-mutation and/or have B RCA 1 -deficient cancer. The foregoing 9-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 9-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 9-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0100] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCAl -deficient tumors: TBL2, UQCRC1, CUL5, ITGB4, FBL, VPS13A and TJP2. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCAl -mutation and/or have BRCAl -deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0101] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCAl -deficient tumors: PSPCl, CDK9, KIF4A, FUR, PECR, SMARCA4 and UBAP2. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCAl -mutation and/or have BRCAl -deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0102] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCAl -deficient tumors: BZW2, NUP210, SCRIB, RSFl, OTUD6B, DHRS7B and CDH3. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCAl -mutation and/or have BRCAl -deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0103] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCAl -deficient tumors: CCDC6, TRIP12, CUL5, AKAP8, NUP214, UXT and COL4A1. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCAl -mutation and/or have BRCAl -deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0104] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCAl -deficient tumors: SERPINDl, SART3, CUL5, LIN7C, ADD3, DDT and PDS5A. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCAl -mutation and/or have BRCAl -deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0105] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCAl -deficient tumors: SMARCA5, NUP210, TRIP12, CUL5, OGT, POLD1 and NF1. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0106] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: SMARCA5, DHX9, CSTF1, TRIP12, BYSL, CUL5 and JUP. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0107] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: TP53BP1, DRG1, COL14A1, FRYL, HNRNPF, ROMOl and DOCK1. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1- deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0108] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: CDK9, CUL5, CSTF3, ADD3, DHX30, DDT and EIF3G. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0109] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: NUP210, SERPIND1, BAX, CUL5, BIRC6, KRT78 and PDS5A. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0110] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 56 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: TOP2A, TOPI, SUPT16H, SSRP1, SMC3, SMC1A, SRSF3, SRSF1, PRPF8, DHX9, AGRN, AGRN, AP1M2, BZW2, CBX3, CDH1, CDH3, CKAP5, CLNS1A, COL18A1, CPOX, CRIP2, CTNNA1, CTNNB1, DAK, DEK, DNMT1, FUR, FXYD3, GPC4, ILF3, ITGB4, LAMA4, LAMA5, LAMB 2, LAMC1, LGALS7, MACF1, NCL, NOLC1, NPM3, PKP3, PLTP, PTN, PURB, SART3, SLC3A2, SLC7A5, SSB, THUMPD1 , USP39, WDR5, TINAGL1 , PTMA, LAMB 1 and HMGB1L1. The foregoing 56-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 56-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 56-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 56-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0111] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: BZW2, NUP210, GRHPR, CUL5, HMCN1, BDH1 and RAE1. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0112] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: CDH3, OGT, KIF4, ITGB4, COL14A1, BYSL and CUL5. The foregoing 7-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0113] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 15 proteins that are significantly differentially regulated in BRCA1 -deficient tumors: CDH3, OGT, KIF4, COL14A1, ITGB4, NUP210, EIF4A3, BYSL, CUL5, COL4A1, APOD, NDRG1, LAMB2, HMCN1 and PBRM1. The foregoing 15-protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 15-protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 15-protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 15-protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

BRCA-deficiency Signatures Based on 45 Up-Regulated Proteins

[0114] The present inventors have identified 45 proteins that are up-regulated in

BRCA1 -deficient tumors, which are useful in the methods and signatures disclosed herein. The 45 proteins are shown in Fig. 2.

[0115] Therefore, in various embodiments, BRCA-deficiency signatures comprising one or more of the 45 up-regulated proteins shown in Fig. 2 are disclosed. These BRCA- deficiency signatures can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. These BRCA-deficiency signatures can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. These BRCA-deficiency signatures can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. These BRCA-deficiency signatures can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0116] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 5 proteins selected from the following 45 proteins that are up-regulated in BRCAl-deficient tumors: TRRAP, BAZ1B, SMC3, NCAPD2, RPA1, SIN3A, POLD1, SNRNP200, SMC1A, TOP2A, SMARCC1, TOP2B, HCFC1, PCNA, RSF1, CSNK2A1, CDC5L, TOPI, OGT, EP400, MSH6, TRIM28, SFRS1, SRCAP, PARP1, SMARCA4, CREBBP, ATM, RAD21, PRPF8, C20ORF20, CSTF1, MTA1, DDX21, HNRNPF, NCBP1, SMARCA5, MSH2, SFRS3, DHX9, SUPT16H, CSTF3, SSRP1, SMC4, and ARID 1 A. The BRCA-deficiency signatures comprising a set of at least 5 proteins selected from the foregoing 45 proteins can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 5 proteins selected from the foregoing 45 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 5 proteins selected from the foregoing 45 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 5 proteins selected from the foregoing 45 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0117] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 6 proteins selected from the following 45 proteins that are up-regulated in BRCA1 -deficient tumors: TRRAP, BAZ1B, SMC3, NCAPD2, RPA1, SIN3A, POLD1, SNRNP200, SMC1A, TOP2A, SMARCC1, TOP2B, HCFC1, PCNA, RSF1, CSNK2A1, CDC5L, TOPI, OGT, EP400, MSH6, TRIM28, SFRS1, SRCAP, PARP1, SMARCA4, CREBBP, ATM, RAD21, PRPF8, C20ORF20, CSTFl, MTAl, DDX21, HNRNPF, NCBPl, SMARCA5, MSH2, SFRS3, DHX9, SUPT16H, CSTF3, SSRPl, SMC4, and ARIDIA. The BRCA-deficiency signatures comprising a set of at least 6 proteins selected from the foregoing 45 proteins can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 6 proteins selected from the foregoing 45 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 6 proteins selected from the foregoing 45 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 6 proteins selected from the foregoing 45 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0118] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 7 proteins selected from the following 45 proteins that are up-regulated in BRCAl-deficient tumors: TRRAP, BAZ1B, SMC3, NCAPD2, RPA1, SIN3A, POLD1, SNRNP200, SMC1A, TOP2A, SMARCC1, TOP2B, HCFC1, PCNA, RSF1, CSNK2A1, CDC5L, TOPI, OGT, EP400, MSH6, TRIM28, SFRS1, SRCAP, PARP1, SMARCA4, CREBBP, ATM, RAD21, PRPF8, C20ORF20, CSTFl, MTAl, DDX21, HNRNPF, NCBPl, SMARCA5, MSH2, SFRS3, DHX9, SUPT16H, CSTF3, SSRPl, SMC4, and ARIDIA. The BRCA-deficiency signatures comprising a set of at least 7 proteins selected from the foregoing 45 proteins can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 7 proteins selected from the foregoing 45 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 7 proteins selected from the foregoing 45 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 7 proteins selected from the foregoing 45 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0119] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 8 proteins selected from the following 45 proteins that are up-regulated in BRCA1 -deficient tumors: TRRAP, BAZ1B, SMC3, NCAPD2, RPA1, SIN3A, POLD1, SNRNP200, SMC1A, TOP2A, SMARCC1, TOP2B, HCFC1, PCNA, RSF1, CSNK2A1, CDC5L, TOPI, OGT, EP400, MSH6, TRIM28, SFRS1, SRCAP, PARP1, SMARCA4, CREBBP, ATM, RAD21, PRPF8, C20ORF20, CSTFl, MTAl, DDX21, HNRNPF, NCBPl, SMARCA5, MSH2, SFRS3, DHX9, SUPT16H, CSTF3, SSRPl, SMC4, and ARIDIA. The BRCA-deficiency signatures comprising a set of at least 8 proteins selected from the foregoing 45 proteins can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 8 proteins selected from the foregoing 45 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 8 proteins selected from the foregoing 45 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 8 proteins selected from the foregoing 45 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0120] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 9 proteins selected from the following 45 proteins that are up-regulated in BRCAl-deficient tumors: TRRAP, BAZ1B, SMC3, NCAPD2, RPA1, SIN3A, POLD1, SNRNP200, SMC1A, TOP2A, SMARCC1, TOP2B, HCFC1, PCNA, RSF1, CSNK2A1, CDC5L, TOPI, OGT, EP400, MSH6, TRIM28, SFRS1, SRCAP, PARP1, SMARCA4, CREBBP, ATM, RAD21, PRPF8, C20ORF20, CSTFl, MTAl, DDX21, HNRNPF, NCBPl, SMARCA5, MSH2, SFRS3, DHX9, SUPT16H, CSTF3, SSRPl, SMC4, and ARIDIA. The BRCA-deficiency signatures comprising a set of at least 9 proteins selected from the foregoing 45 proteins can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 9 proteins selected from the foregoing 45 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 9 proteins selected from the foregoing 45 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 9 proteins selected from the foregoing 45 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0121] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 45 proteins that are up-regulated in BRCAl- deficient tumors: TRRAP, BAZ1B, SMC3, NCAPD2, RPA1, SIN3A, POLD1, SNRNP200, SMC1A, TOP2A, SMARCC1, TOP2B, HCFC1, PCNA, RSF1, CSNK2A1, CDC5L, TOPI, OGT, EP400, MSH6, TRIM28, SFRS1, SRCAP, PARP1, SMARCA4, CREBBP, ATM, RAD21, PRPF8, C20ORF20, CSTF1, MTA1, DDX21, HNRNPF, NCBP1, SMARCA5, MSH2, SFRS3, DHX9, SUPT16H, CSTF3, SSRP1, SMC4, and ARID 1 A. The foregoing 45 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The foregoing 45 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 45 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 45 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0122] In some embodiments, BRCA-deficiency signatures are provided, the BRCA- deficiency signatures comprising the following 3 proteins that are up-regulated in BRCAl- deficient tumors: OGT, PRPF8 and POLD1. The BRCA-deficiency signatures comprising these 3 proteins can be used as diagnostic tools to detect patients who are carrying a BRCA1- mutation and/or have BRCAl-deficient cancer. The BRCA-deficiency signatures comprising these 3 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising these 3 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising these 3 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anticancer therapy.

[0123] In some embodiments, BRCA-deficiency signatures are provided, the BRCA- deficiency signatures comprising the following 4 proteins that are up-regulated in BRCA1- deficient tumors: OGT, PRPF8, POLD1 and MSH2. The BRCA-deficiency signatures comprising these 4 proteins can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have B RCA 1 -deficient cancer. The BRCA-deficiency signatures comprising these 4 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA- deficiency signatures comprising these 4 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising these 4 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0124] In some embodiments, BRCA-deficiency signatures are provided, the BRCA- deficiency signatures comprising the following 5 proteins that are up-regulated in BRCA1- deficient tumors: OGT, PRPF8, POLD1, MSH2 and HNRNPF. The BRCA-deficiency signatures comprising these 5 proteins can be used as diagnostic tools to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The BRCA- deficiency signatures comprising these 5 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising these 5 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising these 5 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0125] In some embodiments, BRCA-deficiency signatures are provided, the BRCA- deficiency signatures comprising the following 6 proteins that are up-regulated in BRCA1- deficient tumors: OGT, PRPF8, POLD1, MSH2, HNRNPF and RPA1. The BRCA- deficiency signatures comprising these 6 proteins can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The BRCA-deficiency signatures comprising these 6 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising these 6 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising these 6 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0126] In some embodiments, BRCA-deficiency signatures are provided, the BRCA- deficiency signatures comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: OGT, PRPF8, POLD1, MSH2, HNRNPF, RPA1 and TOP2B. The BRCA- deficiency signatures comprising these 7 proteins can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The

BRCA-deficiency signatures comprising these 7 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising these 7 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising these 7 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0127] In some embodiments, BRCA-deficiency signatures are provided, the BRCA- deficiency signatures comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: OGT, PRPF8, POLD1, MSH2, RPA1, TOP2B and NCBP1. The BRCA- deficiency signatures comprising these 7 proteins can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The BRCA-deficiency signatures comprising these 7 proteins can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising these 7 proteins can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising these 7 proteins can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0128] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 5 proteins that are up-regulated in BRCA1- deficient tumors: OGT, PRPF8, POLD1, MSH2 and NCBP1. The foregoing 5 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have B RCA 1 -deficient cancer. The foregoing 5 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 5 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 5 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0129] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 6 proteins that are up-regulated in BRCA1- deficient tumors: OGT, PRPF8, POLDl, MSH2, NCBPl and RPAl. The foregoing 6 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have B RCA 1 -deficient cancer. The foregoing 6 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 6 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 6 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0130] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: OGT, PRPF8, POLDl, MSH2, NCBPl, RPAl and SSRP1. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0131] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 8 proteins that are up-regulated in BRCA1- deficient tumors: OGT, PRPF8, POLDl, MSH2, NCBPl, RPAl, SSRP1 and TOP2B. The foregoing 8 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 8 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 8 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 8 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0132] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 9 proteins that are up-regulated in BRCA1- deficient tumors: OGT, PRPF8, POLD1, MSH2, NCBP1, RPA1, SSRP1, TOP2B and MTA1. The foregoing 9 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 9 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 9 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 9 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0133] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: MTA1, MSH6, TOP2B, RPA1, PRPF8, POLD1 and NCBP1. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0134] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: MSH2, SRCAP, RPA1, SMC4, PRPF8, POLD1 and NCBP1. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0135] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: MSH2, RPA1, PRPF8, DDX21, POLD1, SIN3A and NCBP1. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0136] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: ARID 1 A, TRIM28, RPA1, CSTF3, PRPF8, POLD1 and SIN3A. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy. [0137] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: SMARCA5, MTA1, TOP2B, RPAl, DDX21, POLDl and TOP2A. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0138] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: MSH2, TOP2B, RPAl, ATM, PRPF8, POLDl and TRRAP. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0139] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: MSH2, DHX9, TOP2B, RPAl, PRPF8, TRRAP and NCBP1. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0140] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: MSH2, TRIM28, MTAl, TOP2B, RPAl, ATM and PRPF8. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0141] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: MSH2, CREBBP, RPAl, SMC4, PRPF8, POLD1 and NCBP1. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0142] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: TRIM28, TOP2B, RPAl, PRPF8, POLD1, TRRAP and HNRNPF. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0143] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 36 proteins that are up-regulated in BRCA1- deficient tumors: TOP2A, TRIM28,MSH2, DHX9, SMC4, RPA1, MSH6, POLD1, TRRAP, CREBBP, PCNA, ATM, MTA1, PARP1, TOPI, DDX21, SMC1A, SFRS1, C20ORF20, RAD21, CSTF1, OGT, TOP2B, ARID 1 A, RSF1, CSNK2A1, SMARCA4, SMARCC1, SUPT16H, SMC3, SFRS3, SSRP1, PRPF8, HCFC1, NCAPD2 and CDC5L. The foregoing 36 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 36 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 36 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 36 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0144] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 21 proteins that are up-regulated in BRCA1- deficient tumors: TOP2A, TRIM28, MSH2, DHX9, SMC4, RPA1, MSH6, POLD1, TRRAP, CREBBP, PCNA, ATM, MTA1, PARP1, TOPI, DDX21, SMC1A, SFRS1, C20ORF20, RAD21 and CSTF1. The foregoing 21 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1- deficient cancer. The foregoing 21 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The foregoing 21 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 21 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0145] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 9 proteins that are up-regulated in BRCA1- deficient tumors: TOP2A, TRIM28, MSH2, DHX9, SMC4, RPA1, MSH6, POLD1 and TRRAP. The foregoing 9 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 9 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 9 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 9 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0146] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: DHX9, SMC4, TRRAP, RAD21, CSTF1, NCAPD2 and CDC5L. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0147] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 20 proteins that are up-regulated in BRCA1- deficient tumors: DHX9, SMC4, RAD21, TOP2A, TRIM28, MSH2, RPA1, MSH6, POLD1, CREBBP, PCNA, ATM, MTA1, PARP1, TOPI, DDX21, OGT, TOP2B, ARID 1 A and RSF1. The foregoing 20 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 20 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 20 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 20 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0148] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 10 proteins that are up-regulated in BRCA1- deficient tumors: DHX9, TOP2A, TOPI, SMC1A, SFRS1, SUPT16H, SMC3, SFRS3,

SSRP1 and PRPF8. The foregoing 10 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1- deficient cancer. The foregoing 10 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The foregoing 10 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 10 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0149] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 10 proteins that are up-regulated in BRCA1- deficient tumors: TOP2A, TOPI, SUPT16H, SSRP1, SMC3, SMC1A, SFRS3, SFRS1, PRPF8 and DHX9. The foregoing 10 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1- deficient cancer. The foregoing 10 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The foregoing 10 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 10 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0150] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 9 proteins that are up-regulated in BRCA1- deficient tumors: TRRAP, BAZ1B, SMC1A, TOP2A, MSH6, PARP1, ATM, MSH2 and SMC4. The foregoing 9 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 9 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 9 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 9 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0151] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: TRRAP, NCAPD2, CDC5L, RAD21, DHX9, CSTF3 and SMC4. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0152] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 8 proteins that are up-regulated in BRCA1- deficient tumors: TRRAP, NCAPD2, TOP2A, CDC5L, RAD21, DHX9, CSTF3 and SMC4. The foregoing 8 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 8 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 8 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 8 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0153] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 33 proteins that are up-regulated in BRCA1- deficient tumors: TRRAP, BAZ1B, SMC3, NCAPD2, SIN3A, POLD1, SNRNP200, SMCIA, TOP2A, SMARCCl, TOP2B, PCNA, RSFl, CSNK2A1, CDC5L, MSH6, TRIM28, SRCAP, PARP1, SMARCA4, CREBBP, ATM, RAD21, DDX21, HNRNPF, SMARCA5, MSH2, DHX9, SUPT16H, CSTF3, SSRP1, SMC4 and ARID 1 A. The foregoing 33 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCAl -mutation and/or have BRCAl -deficient cancer. The foregoing 33 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 33 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 33 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0154] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 37 proteins that are up-regulated in BRCA1- deficient tumors: TRRAP, BAZ1B, SMC3, NCAPD2, SIN3A, POLD1, SNRNP200, SMC1A, TOP2A, SMARCC1, TOP2B, PCNA, RSFl, CSNK2A1, CDC5L, EP400, MSH6, TRIM28, SRCAP, PARP1, SMARCA4, CREBBP, ATM, RAD21, C20ORF20, CSTF1, DDX21, HNRNPF, NCBP1, SMARCA5, MSH2, DHX9, SUPT16H, CSTF3, SSRP1, SMC4 and ARID1A. The foregoing 37 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCAl -mutation and/or have BRCAl - deficient cancer. The foregoing 37 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The foregoing 37 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 37 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0155] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 36 proteins that are up-regulated in BRCAl - deficient tumors: TRRAP, SMC3, NCAPD2, RPA1, POLD1, SMC1A, TOP2A, SMARCC1, TOP2B, HCFCl, PCNA, RSFl, CSNK2A1, CDC5L, TOPI, OGT, MSH6, TRIM28, SFRSl, PARP1, SMARCA4, CREBBP, ATM, RAD21, PRPF8, C20ORF20, CSTF1, MTA1, DDX21, MSH2, SFRS3, DHX9, SUPT16H, SSRP1, SMC4 and ARID 1 A. The foregoing 36 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCAl -mutation and/or have BRCAl -deficient cancer. The foregoing 36 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 36 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 36 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0156] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 21 proteins that are up-regulated in BRCA1- deficient tumors: TRRAP, RPA1, POLD1, SMC1A, TOP2A, PCNA, TOPI, MSH6, TRIM28, SFRS1, PARP1, CREBBP, ATM, RAD21, C20ORF20, CSTF1, MTA1, DDX21, MSH2, DHX9 and SMC4. The foregoing 21 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 21 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 21 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 21 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0157] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 9 proteins that are up-regulated in BRCA1- deficient tumors: TRRAP, RPA1, POLD1, TOP2A, MSH6, TRIM28, MSH2, DHX9 and SMC4. The foregoing 9 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 9 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 9 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 9 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0158] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: TRRAP, NCAPD2, CDC5L, RAD21, CSTF1, DHX9 and SMC4. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0159] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 20 proteins that are up-regulated in BRCA1- deficient tumors: RPA1, POLD1, TOP2A, TOP2B, PCNA, RSF1, TOPI, OGT, MSH6, TRIM28, PARP1, CREBBP, ATM, RAD21, MTA1, DDX21, MSH2, DHX9, SMC4 and ARID 1 A. The foregoing 20 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 20 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The foregoing 20 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 20 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0160] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 10 proteins that are up-regulated in BRCA1- deficient tumors: SMC3, SMC1A, TOP2A, TOPI, SFRS1, PRPF8, SFRS3, DHX9,

SUPT16H and SSRP1. The foregoing 10 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCAl-mutation and/or have BRCA1- deficient cancer. The foregoing 10 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The foregoing 10 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 10 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0161] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 16 proteins that are up-regulated in BRCA1- deficient tumors: SIN3A, POLD1, TOP2A, TOP2B, OGT, TRIM28, SFRS1, CREBBP, ATM, C20ORF20, HNRNPF, NCBP1, MSH2, SSRP1, SMC4 and ARID 1 A. The foregoing 16 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 16 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 16 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 16 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0162] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: TRRAP, RPAl, POLDl, TOP2B, ATM, PRPF8 and MSH2. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0163] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 proteins that are up-regulated in BRCA1- deficient tumors: RPAl, POLDl, TOP2B, OGT, PRPF8, NCBP1 and MSH2. The foregoing 7 protein BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The foregoing 7 protein BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The foregoing 7 protein BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The foregoing 7 protein BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy. [0164] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 5 amino acid sequences selected from the following 45 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID NO: 45. The BRCA-deficiency signatures comprising a set of at least 5 amino acid sequences selected from the foregoing 45 amino acid sequences can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The BRCA-deficiency signatures comprising a set of at least 5 amino acid sequences selected from the foregoing 45 amino acid sequences can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 5 amino acid sequences selected from the foregoing 45 amino acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 5 amino acid sequences selected from the foregoing 45 amino acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0165] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 6 amino acid sequences selected from the following 45 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID NO: 45. The BRCA-deficiency signatures comprising a set of at least 6 amino acid sequences selected from the foregoing 45 amino acid sequences can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The BRCA-deficiency signatures comprising a set of at least 6 amino acid sequences selected from the foregoing 45 amino acid sequences can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 6 amino acid sequences selected from the foregoing 45 amino acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 6 amino acid sequences selected from the foregoing 45 amino acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0166] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 7 amino acid sequences selected from the following 45 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID NO: 45. The BRCA-deficiency signatures comprising a set of at least 7 amino acid sequences selected from the foregoing 45 amino acid sequences can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The BRCA-deficiency signatures comprising a set of at least 7 amino acid sequences selected from the foregoing 45 amino acid sequences can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 7 amino acid sequences selected from the foregoing 45 amino acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 7 amino acid sequences selected from the foregoing 45 amino acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0167] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 8 amino acid sequences selected from the following 45 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID NO: 45. The BRCA-deficiency signatures comprising a set of at least 8 amino acid sequences selected from the foregoing 45 amino acid sequences can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The BRCA-deficiency signatures comprising a set of at least 8 amino acid sequences selected from the foregoing 45 amino acid sequences can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 8 amino acid sequences selected from the foregoing 45 amino acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 8 amino acid sequences selected from the foregoing 45 amino acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0168] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 9 amino acid sequences selected from the following 45 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID NO: 45. The BRCA-deficiency signatures comprising a set of at least 9 amino acid sequences selected from the foregoing 45 amino acid sequences can be used as diagnostic tools to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The BRCA-deficiency signatures comprising a set of at least 9 amino acid sequences selected from the foregoing 45 amino acid sequences can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signatures comprising a set of at least 9 amino acid sequences selected from the foregoing 45 amino acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 9 amino acid sequences selected from the foregoing 45 amino acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0169] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 45 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID NO: 45. The 45 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1- deficient cancer. The 45 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 45 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 45 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy. [0170] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 5 amino acid sequences: SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 7, SEQ ID NO: 38 and SEQ ID NO: 36. The 5 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have B RCA 1 -deficient cancer. The 5 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 5 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 5 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0171] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 6 amino acid sequences: SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 7, SEQ ID NO: 38, SEQ ID NO: 36 and SEQ ID NO: 5. The 6 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The 6 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 6 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 6 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0172] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 7, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 5 and SEQ ID NO: 43. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0173] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 8 amino acid sequences: SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 7, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 5, SEQ ID NO: 43 and SEQ ID NO: 12. The 8 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The 8 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 8 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 8 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0174] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 9 amino acid sequences: SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 7, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 5, SEQ ID NO: 43, SEQ ID NO: 12 and SEQ ID NO: 33. The 9 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1- mutation and/or have BRCAl-deficient cancer. The 9 amino acid sequence BRCA- deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 9 amino acid sequence BRCA- deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 9 amino acid sequence BRCA- deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0175] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 33, SEQ ID NO: 21, SEQ ID NO: 12, SEQ ID NO: 5, SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 36. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0176] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 38, SEQ ID NO: 24, SEQ ID NO: 5, SEQ ID NO: 44, SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 36. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0177] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 38, SEQ ID NO: 5, SEQ ID NO: 30, SEQ ID NO: 34, SEQ ID NO: 7, SEQ ID NO: 6 and SEQ ID NO: 36. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0178] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 45, SEQ ID NO: 22, SEQ ID NO: 5, SEQ ID NO: 42, SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 6. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0179] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 37, SEQ ID NO: 33, SEQ ID NO: 12, SEQ ID NO: 5, SEQ ID NO: 34, SEQ ID NO: 7 and SEQ ID NO: 10. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0180] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 38, SEQ ID NO: 12, SEQ ID NO: 5, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 1. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0181] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 12, SEQ ID NO: 5, SEQ ID NO: 30, SEQ ID NO: 1 and SEQ ID NO: 36. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0182] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 38, SEQ ID NO: 22, SEQ ID NO: 33, SEQ ID NO: 12, SEQ ID NO: 5, SEQ ID NO: 28 and SEQ ID NO: 30. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0183] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 38, SEQ ID NO: 27, SEQ ID NO: 5, SEQ ID NO: 44, SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 36. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0184] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 22, SEQ ID NO: 12, SEQ ID NO: 5, SEQ ID NO: 30, SEQ ID NO: 7, SEQ ID NO: 1 and SEQ ID NO: 35. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0185] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 36 amino acid sequences: SEQ ID NO: 10, SEQ ID NO: 22, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 5, SEQ ID NO: 21, SEQ ID NO: 7, SEQ ID NO: 1, SEQ ID NO: 27, SEQ ID NO: 14, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 25, SEQ ID NO: 18, SEQ ID NO: 34, SEQ ID NO: 9, SEQ ID NO: 23, SEQ ID NO: 31, SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 19, SEQ ID NO: 12, SEQ ID NO: 45, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 26, SEQ ID NO: 11, SEQ ID NO: 41, SEQ ID NO: 3, SEQ ID NO: 39, SEQ ID NO: 43, SEQ ID NO: 30, SEQ ID NO: 13, SEQ ID NO: 4 and SEQ ID NO: 17. The 36 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1- mutation and/or have BRCAl-deficient cancer. The 36 amino acid sequence BRCA- deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 36 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 36 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anticancer therapy.

[0186] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 21 amino acid sequences: SEQ ID NO: 10,

SEQ ID NO: 22, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 5, SEQ ID NO: 21, SEQ ID NO: 7, SEQ ID NO: 1, SEQ ID NO: 27, SEQ ID NO: 14, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 25, SEQ ID NO: 18, SEQ ID NO: 34, SEQ ID NO: 9, SEQ ID NO: 23, SEQ ID NO: 31, SEQ ID NO: 29 and SEQ ID NO: 32. The 21 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have B RCA 1 -deficient cancer. The 21 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 21 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 21 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0187] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 9 amino acid sequences: SEQ ID NO: 10, SEQ ID NO: 22, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 5, SEQ ID NO: 21, SEQ ID NO: 7 and SEQ ID NO: 1. The 9 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1- mutation and/or have BRCAl-deficient cancer. The 9 amino acid sequence BRCA- deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 9 amino acid sequence BRCA- deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 9 amino acid sequence BRCA- deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0188] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 1, SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 4 and SEQ ID NO: 17. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy. [0189] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 20 amino acid sequences: SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 29, SEQ ID NO: 10, SEQ ID NO: 22, SEQ ID NO: 38, SEQ ID NO: 5, SEQ ID NO: 21, SEQ ID NO: 7, SEQ ID NO: 27, SEQ ID NO: 14, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 25, SEQ ID NO: 18, SEQ ID NO: 34, SEQ ID NO: 19, SEQ ID NO: 12, SEQ ID NO: 45 and SEQ ID NO: 15. The 20 amino acid sequence BRCA- deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The 20 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 20 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 20 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti- cancer therapy.

[0190] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 10 amino acid sequences: SEQ ID NO: 40, SEQ ID NO: 10, SEQ ID NO: 18, SEQ ID NO: 9, SEQ ID NO: 23, SEQ ID NO: 41, SEQ ID NO: 3, SEQ ID NO: 39, SEQ ID NO: 43 and SEQ ID NO: 30. The 10 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The 10 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 10 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 10 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0191] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 10 amino acid sequences: SEQ ID NO: 10, SEQ ID NO: 18, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 3, SEQ ID NO: 9, SEQ ID NO: 39, SEQ ID NO: 23, SEQ ID NO: 30 and SEQ ID NO: 40. The 10 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The 10 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 10 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 10 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0192] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 9 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 21, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 38, and SEQ ID NO: 44. The 9 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1- mutation and/or have BRCAl-deficient cancer. The 9 amino acid sequence BRCA- deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 9 amino acid sequence BRCA- deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 9 amino acid sequence BRCA- deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0193] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 17, SEQ ID NO: 29, SEQ ID NO: 40, SEQ ID NO: 42, and SEQ ID NO: 44. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0194] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 8 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 10, SEQ ID NO: 17, SEQ ID NO: 29, SEQ ID NO: 40, SEQ ID NO: 42, and SEQ ID NO: 44. The 8 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The 8 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 8 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 8 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0195] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 33 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, and SEQ ID NO: 45. The 33 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The 33 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 33 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 33 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0196] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 37 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, and SEQ ID NO: 45. The 37 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have B RCA 1 -deficient cancer. The 37 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 37 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 37 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0197] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 36 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO:

43, SEQ ID NO: 44, and SEQ ID NO: 45. The 36 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1- mutation and/or have BRCAl-deficient cancer. The 36 amino acid sequence BRCA- deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 36 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 36 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anticancer therapy.

[0198] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 21 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 14, SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 38, SEQ ID NO: 40, and SEQ ID NO: 44. The 21 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have B RCA 1 -deficient cancer. The 21 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 21 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 21 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0199] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 9 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 10, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 38, SEQ ID NO: 40, and SEQ ID NO: 44. The 9 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1- mutation and/or have BRCAl-deficient cancer. The 9 amino acid sequence BRCA- deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 9 amino acid sequence BRCA- deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 9 amino acid sequence BRCA- deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0200] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 17, SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 40, and SEQ ID NO: 44. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy. [0201] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 20 amino acid sequences: SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 44, and SEQ ID NO: 45. The 20 amino acid sequence BRCA- deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The 20 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 20 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 20 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti- cancer therapy.

[0202] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 10 amino acid sequences: SEQ ID NO: 3, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 18, SEQ ID NO: 23, SEQ ID NO: 30, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, and SEQ ID NO: 43. The 10 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The 10 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 10 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 10 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0203] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 16 amino acid sequences: SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 19, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 31, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 43, SEQ ID NO: 44, and SEQ ID NO: 45. The 16 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The 16 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The 16 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 16 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0204] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 1, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 12, SEQ ID NO: 28, SEQ ID NO: 30, and SEQ ID NO: 38. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0205] In some embodiments, a BRCA-deficiency signature is provided, the BRCA- deficiency signature comprising the following 7 amino acid sequences: SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 12, SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 36, and SEQ ID NO: 38. The 7 amino acid sequence BRCA-deficiency signature can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The 7 amino acid sequence BRCA-deficiency signature can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The 7 amino acid sequence BRCA-deficiency signature can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

Uses of Protein Signatures [0206] The BRCA-deficiency protein signatures disclosed herein can be used as diagnostic tools, to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1- deficient cancer and to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. Therefore, in various aspects, the BRCA-deficiency protein signatures provided in this disclosure are capable of determining whether an individual cancer patient has BRCA1 -deficient cancer and/or BRCA2-deficient cancer.

[0207] Identification of BRCA1 pathway dysfunction and/or BRCA2 pathway dysfunction provides an opportunity for therapeutic intervention. Emerging preclinical evidence shows that cancers with a defective DNA repair system, such as a mutation in the BRCAlgene and/or the BRCA2 gene, may be extremely sensitive to DNA damaging agents, such as platinum compounds and bifunctional alkylating agents. Therefore, patients with cancers harboring a defective BRCA1 -deficient and/or BRCA2-deficient DNA repair system may specifically benefit from high dose alkylating chemotherapy, a DNA double strand break (DSB)-inducing regimen. Tumors with homologous recombination deficiency (such as deficiency in the BRCA1 gene and/or BRCA2 gene pathway) have been shown to be particularly sensitive to DNA double strand break (DSB)-inducing agents, such as alkylators and platinum drugs or platinating agents. Both classes of drugs are employed in metastatic breast cancer. The novel poly(ADP-ribose) polymerase inhibitors (PARP inhibitors) are specifically effective in homologous recombination deficient tumors as well, and have shown impressive activity in clinical studies recently. Therefore, BRCA1 -deficient and BRCA2- deficient cancers are susceptible to treatment with anti-cancer therapy (as defined herein) and patients having BRCAl-deficient and/or BRCA2-deficient cancers will benefit from receipt of anti-cancer therapy.

[0208] The BRCA-deficiency protein signatures provided in this disclosure are therefore capable of predicting benefit of anti-cancer therapy in an individual patient and can also be used as predictive tests to identify cancer patients likely to benefit from anti-cancer therapy.

[0209] In various aspects, the present disclosure provides methods of using the BRCA-deficiency protein signatures disclosed herein to determine whether a patient has cancer caused by a BRCA1 deficiency. In various aspects, the present disclosure provides methods of using the BRCA-deficiency protein signatures disclosed herein to determine whether a patient has cancer caused by a BRCA2 deficiency. In some embodiments, the methods comprise generating a test sample comprising the proteome of a cancer isolated from a patient; measuring the expression level of the proteins of the test sample; comparing the expression level of the proteins of the test sample to at least one of the BRCA-deficiency protein signatures provided by the present disclosure; and identifying the cancer as BRCA1- deficient or B RC A 1 -proficient and/or BRCA2-deficient or BRCA2-proficient; wherein when the expression level of the proteins of the test sample is similar to the expression level of the corresponding proteins in the at least one of the BRCA-deficiency protein signatures, the tumor is classified as BRCA1- and/or BRCA2-deficient.

[0210] In some embodiments, the methods comprise generating a test sample comprising the proteome of a cancer isolated from a patient; measuring the expression level of the proteins of the test sample; comparing the expression level of the proteins of the test sample to at least one of the BRCA-deficiency protein signatures provided by the present disclosure; and identifying the tumor as B RC A 1 -deficient or BRCA1 -proficient and/or BRCA2-deficient or BRCA2-proficient; wherein when the expression level of the proteins of the test sample is the same (within acceptable levels of experimental error) as the expression level of the corresponding proteins in the at least one of the BRCA-deficiency protein signatures, the cancer is classified as BRCA1- and/or BRCA2-deficient.

[0211] In some embodiments, the methods comprise generating a test sample comprising the proteome of a cancer isolated from a blood sample obtained from a patient; measuring the expression level of the proteins of the test sample; comparing the expression level of the proteins of the test sample to at least one of the BRCA-deficiency protein signatures provided by the present disclosure; and identifying the tumor as BRCA1 -deficient or BRCA1 -proficient and/or BRCA2-deficient or BRCA2-proficient; wherein when the expression level of the proteins of the test sample is the same (within acceptable levels of experimental error) as the expression level of the corresponding proteins in the at least one of the BRCA-deficiency protein signatures, the cancer is classified as BRCA1- and/or BRCA2- deficient.

[0212] Additionally, in various aspects the present disclosure provides methods of using the BRCA-deficiency protein signatures disclosed herein to optimize anti-cancer therapy. In some embodiments, the methods comprise generating a test sample comprising the proteome of a cancer isolated from a patient; measuring the expression level of the proteins of the test sample; comparing the expression level of the proteins of the test sample to at least one of the BRCA-deficiency protein signatures provided by the present disclosure; and administering anti-cancer therapy to the patient when the expression level of the proteins of the test sample is similar to the expression level of the corresponding proteins in the at least one of the BRCA-deficiency protein signatures. [0213] In some embodiments, the methods comprise generating a test sample comprising the proteome of a cancer isolated from a patient; measuring the expression level of the proteins of the test sample; comparing the expression level of the proteins of the test sample to at least one of the BRCA-deficiency protein signatures provided by the present disclosure; and administering anti-cancer therapy to the patient when the expression level of the proteins of the test sample is the same (within acceptable levels of experimental error) as the expression level of the corresponding proteins in the at least one of the BRCA-deficiency protein signatures.

[0214] In some embodiments, the methods comprise generating a test sample comprising the proteome of a cancer isolated from a blood sample obtained from a patient; measuring the expression level of the proteins of the test sample; comparing the expression level of the proteins of the test sample to at least one of the BRCA-deficiency signatures provided by the present disclosure; and administering anti-cancer therapy to the patient when the expression level of the proteins of the test sample is the same (within acceptable levels of experimental error) as the expression level of the corresponding proteins in the at least one of the BRCA-deficiency signatures.

[0215] Any one or more of the BRCA-deficiency protein signatures disclosed herein may be used in the foregoing methods.

[0216] Using the methods described above, in various aspects, the BRCA-deficiency protein signatures provided by the present disclosure are capable of determining whether or not a tumor is BRCAl-deficient. Using the methods described above, in various aspects, the BRCA-deficiency protein signatures provided by the present disclosure are capable of determining whether or not a tumor is BRCA2-deficient.

[0217] Using the methods described above, in various aspects, the BRCA-deficiency protein signatures provided by the present disclosure can be used to predict an individual subject's benefit of anti-cancer therapy.

[0218] Determination of Protein Expression Levels

[0219] The expression levels of the up-regulated proteins comprising the protein signatures of the present disclosure are known and/or may be readily determined {see, e.g. , Example 1). In that regard, the protein signatures of the present disclosure can serve as reference samples (as defined herein). The expression levels of the up-regulated

proteins/reference samples may be compared to the expression levels of a test sample of cancer proteins obtained from a patient. Therefore, the expression levels of the proteins comprising any of the protein signatures disclosed herein (reference samples) can be compared to the expression level of the same proteins obtained from a cancer in a patient (test sample).

[0220] In some embodiments, similarity between the expression level of a test sample of cancer proteins obtained from a patient and the expression levels of any one or more of the reference sample protein signatures disclosed herein identifies the cancer as BRCA1 - deficient. In some embodiments, similarity between the expression level of a test sample of cancer proteins obtained from a patient and the expression levels of any one or more of the reference sample protein signatures disclosed herein identifies the cancer as BRCA2- deficient.

[0221 ] In some embodiments, substantial similarity between the expression level of a test sample of cancer proteins obtained from a patient and the expression levels of any one or more of the reference sample protein signatures disclosed herein identifies the cancer as B RCA 1 -deficient. In some embodiments, substantial similarity between the expression level of a test sample of cancer proteins obtained from a patient and the expression levels of any one or more of the reference sample protein signatures disclosed herein identifies the cancer as BRCA2-deficient. In each case, identity (or "identical") can be established when the protein expression levels between the test and reference samples provide output readings that are the same within acceptable levels of experimental error.

[0222] In some embodiments, the degree of similarity between the level of expression of the proteins comprising a test sample and the level of expression of the proteins comprising a reference sample is determined based on signal intensity, such as that derived from an assay (e.g. , ELISA, see below). In certain embodiments, the ratio of the signal intensity of the proteins comprising a test sample, as compared to the signal intensity of the proteins comprising a reference sample is calculated. This calculation quantifies the differential level of expression of the proteins of the test sample, as compared to the reference sample, if any. In some embodiments, this calculation is carried out quantitatively or semi- quantitatively. In certain embodiments, it is not necessary to determine an exact number associated with the level of expression of the proteins comprising the test sample and the reference sample. The reference sample comprises proteins taken from a tumor, or collection of tumors, known to be BRCA-deficient. As such, the signal intensity produced by any given reference sample is representative of BRCA-deficiency and detection of a statistically significant deviation (increase or decrease) in the signal intensity produced by the proteins of the test sample, as compared to the signal produced by the proteins of the reference sample, is sufficient. Therefore, in several embodiments the quantification of the expression levels of proteins of a test sample comprises an estimation of the level of expression, as a semiquantitative or relative measure, that is sufficient to predict the presence or absence of BRCA-deficiency (as compared to a reference sample) and thus prospectively direct the determination of therapy for a subject.

[0223] In various aspects, determination of a level of protein expression in a test sample that is the same, or greater, than that produced by the reference sample is indicative of BRCA deficiency in the tumor from which the test sample was derived. Therefore, in certain embodiments detection of signal intensity from a test sample that is the same, within experimentally acceptable margins of error, as the signal intensity produced by the reference sample is sufficient to classify the tumor from which the test sample was produced as BRCA- deficient. In certain embodiments, detection of signal intensity from a test sample that is greater, within experimentally acceptable margins of error, than the signal intensity produced by the reference sample is sufficient to classify the tumor from which the test sample was produced as BRCA-deficient.

[0224] In certain embodiments, detection of signal intensity from a test sample that is less, within experimentally acceptable margins of error, than the signal intensity produced by the reference sample is sufficient to classify the tumor from which the test sample was produced as BRCA-proficient. In certain embodiments, the deviation of signal intensity of the test sample from the reference sample is measured as a percent difference. In certain embodiments, a reference sample is deemed to have produced a signal that is less than the reference sample if the signal intensity of the test sample measures at the level selected from: the signal intensity of the reference sample less 5%; the signal intensity of the reference sample less 10%; the signal intensity of the reference sample less 15%; the signal intensity of the reference sample less 20%; the signal intensity of the reference sample less 25%; the signal intensity of the reference sample less 30%; the signal intensity of the reference sample less 35%; the signal intensity of the reference sample less 40%; the signal intensity of the reference sample less 45%; the signal intensity of the reference sample less 50%; the signal intensity of the reference sample less 55%; the signal intensity of the reference sample less 60%; the signal intensity of the reference sample less 65%; the signal intensity of the reference sample less 70%; the signal intensity of the reference sample less 75%; the signal intensity of the reference sample less 80%; the signal intensity of the reference sample less 85%; the signal intensity of the reference sample less 90%; the signal intensity of the reference sample less 95%; and the signal intensity of the reference sample less 100% (or no signal produced by the test sample). [0225] In certain embodiments, the deviation of signal intensity of the test sample from the reference sample is measured as a -fold difference, or a difference based upon unit signal production. In certain embodiments, a reference sample is deemed to have produced a signal that is less than the reference sample if the signal intensity of the test sample is selected from: two-fold less than the signal intensity of the reference sample; three-fold less than the signal intensity of the reference sample; four-fold less than the signal intensity of the reference sample; five-fold less than the signal intensity of the reference sample; six-fold less than the signal intensity of the reference sample; seven-fold less than the signal intensity of the reference sample; eight-fold less than the signal intensity of the reference sample; nine- fold less than the signal intensity of the reference sample; ten-fold less than the signal intensity of the reference sample; and greater than ten-fold less than the signal intensity of the reference sample.

[0226] In some embodiments, complete identity between the expression level of a test sample of cancer proteins obtained from a patient and the expression levels of any one or more of the reference sample protein signatures disclosed herein identifies the tumor as

BRCAl -deficient. In some embodiments, complete identity between the expression level of a test sample of cancer proteins obtained from a patient and the expression levels of any one or more of the reference sample protein signatures disclosed herein identifies the tumor as BRCA2-deficient.

[0227] Tumors with homologous recombination deficiency have been shown to be particularly sensitive to anti-cancer therapy which can include, without limitation, DNA double strand break (DSB)-inducing agents, such as alkylators and platinum drugs or platinating agents. BRCAl- and BRCA2-deficient tumors are therefore sensitive to anticancer therapy (as defined herein). In some embodiments, identification of a tumor as BRCAl -deficient, using any one or more of the protein signatures disclosed herein, identifies the patient as one who will benefit from anti-cancer therapy. In some embodiments, identification of a tumor as BRCA2-deficient, using any one or more of the protein signatures disclosed herein, identifies the patient as one who will benefit from anti-cancer therapy.

[0228] The expression level of any one or more of the up-regulated proteins comprising the BRCA-deficiency protein signatures disclosed herein, and/or the expression levels of any one or more proteins isolated from a test sample (i.e., from a cancer obtained from a patient), can be determined using any one or more of a number of techniques. In some embodiments, the expression levels can be determined using routine assays such as, for example, antibody-based methods such as immunohistochemistry and enzyme-linked immunosorbent assay (ELISA), of which the latter allows for non-invasive testing. In some embodiments, the expression levels can be determined using targeted multiplex mass spectrometry as a means of quantifying protein signatures in tumor tissues or blood taken from a subject. In some embodiments, the expression levels can be determined using mass- spectrometry based proteomics technologies (see, e.g. , Example 1), which have matured to the extent that they can now identify and quantify thousands of proteins.

[0229] In some embodiments, protein expression levels can be determined via immunohistochemistry, which is a process capable of detecting proteins directly in the cells of a section of isolated and fixed tissue via the use of antibodies that bind specifically to the proteins of interest. Immunohistochemistry is a widely used technique to visualize the distribution and localization of differentially expressed proteins between two tissues. When using this technique, a tissue sample is taken from a subject and properly fixed (e.g. , by heat fixation, perfusion, immersion or chemical fixation) to make the epitopes of the proteins of interest available for binding by the antibodies. In some embodiments, the tissue sample may be taken from cancer in a subject known to have a BRCAl -deficient tumor to create a reference sample. In some embodiments, the tissue sample may be taken from cancer in a subject known to have a BRCA2-deficient tumor to create a reference sample. In some embodiments, the tissue sample may be taken from a tumor in subject whose BRCAl and/or BRCA2 status (deficient or proficient) is unknown, to create a test sample. In some embodiments, the tissue samples are taken from corresponding tissues and corresponding regions within the tissues in order to create similar testing parameters between the reference and test samples. The proteins in the reference sample and the test sample can be analyzed in parallel or individually.

[0230] Detecting the protein(s) of interest in a reference sample or a test sample can be accomplished by contact with an antibody that is specifically directed to the protein(s) of interest. One or more antibodies may be used, depending on the number of proteins to be tested in a single reference or test sample. Detection via contact with an antibody may be done directly, whereby the antibody itself is coupled with a label that will allow for visualization of binding to the protein, or indirectly, where a second antibody that specifically binds to the first antibody is used, the second antibody having the label to allow for visualization. Visualizing an antibody-protein interaction can be accomplished in a number of ways. In the direct detection method, the antibody itself is conjugated to an agent that allows for visualization such as an enzyme (e.g. , a peroxidase) that can catalyze a color- producing reaction, or a fluorophore (e.g. , fluorescein or rhodamine) that fluoresces under certain conditions to visually display binding. In the indirect detection method, a second antibody is used that is conjugated to an agent that allows for visualization, such as an enzyme or a fluorophore. The level of differential expression of a protein between a reference sample and a test sample may be determined by measuring the difference in intensity of the visualization means employed. In that regard, in some embodiments the same means of visualization is utilized in both samples. If the signal produced by the reference sample is different from the signal produced in the test sample, then the protein of interest is present in different quantities in the samples, indicating differential expression. The means of visualizing the signal in each sample is linked to an antibody and each antibody will bind to a limited number of proteins in the sample. Therefore, the number of antibodies binding to proteins of a sample is directly proportional to the total number of proteins present in the sample and the strength of the signal produced by the antibody-protein interaction in a sample is directly proportional to the amount of protein present in the sample. The ratio of the signal intensity of the test sample to that of the reference sample is then calculated, to measure the protein expression levels between the test sample and the reference sample. The difference in the signal ratio determines whether the total level of protein expression of each protein in the test sample is increased or decreased, as compared to the reference sample. If the signal produced by the reference sample is the same (within acceptable levels of experimental error) as the signal produced in the test sample, then the protein of interest is present in

approximately the same quantity in each sample.

[0231] In some embodiments, protein expression levels can be determined via enzyme-linked immunosorbent assay (ELISA), which is an analytic assay that utilizes a solid-phase enzyme immunoassay to detect the presence of a protein in an isolated sample. Typically the sample is in liquid form. In ELISA, an unknown amount of a sample is affixed to a substrate surface and an antibody is placed into contact with the substrate surface such that the antibody is also placed into contact with the sample. The antibody will bind to the sample provided that an antigen capable of being bound by the antibody is present in the sample. The antibody is typically linked to some means of visualizing binding, which in some embodiments is an enzyme, so that binding of the antibody to the sample can be detected. A substance that contains the enzyme's substrate is placed into contact with the surface, and thus the antibody, such that the subsequent enzymatic reaction produces a detectable signal. The signal may be a color change in the substrate or a fluorescent emission. In some embodiments, a protein sample isolated from a cancer known to be BRCA1 -deficient is affixed to a substrate surface to create a reference sample. In some embodiments, a protein sample isolated from a cancer known to be BRCA2-deficient is affixed to a substrate surface to create a reference sample. In some embodiments, a protein sample isolated from a tumor in a subject whose BRCA1 and/or BRCA2 status (deficient or proficient) is unknown, is affixed to a substrate surface to create a test sample. In some embodiments, the proteins in each sample are the same (the reference sample protein is the same as the test sample protein); by way of example, the reference sample can contain TOP2A isolated from a BRCAl-deficient breast tumor and the test sample can contain TOP2A isolated from a breast tumor whose BRCA status is not known. The substrate surface may contain more than one isolated area (e.g. , wells) such that the reference sample protein and the test sample protein are each affixed in their own isolated area and also so that the same substrate surface may accommodate multiple proteins from the reference sample and the test sample. In some embodiments, the substrate surface is a microtiter plate.

[0232] At least one antibody having specificity for the protein in the reference and test samples is placed in contact with the protein in the reference and test samples so that it may bind to the protein. The proteins in the reference sample and the test sample can be analyzed in parallel or individually. The antibody can be covalently linked to an enzyme, or can itself be detected by a secondary antibody that is linked to an enzyme. The substrate of the enzyme is then placed in contact with each of the reference sample and the test sample to produce a visible signal, which indicates the quantity of protein in each sample. If the signal produced in the reference sample is different from the signal produced in the test sample, then the protein is present in different quantities in the samples, indicating differential expression. The means of visualizing the signal in each sample is linked to an antibody and each antibody will bind to a limited number of proteins in the sample. Therefore, the number of antibodies binding to proteins of a sample is directly proportional to the total number of proteins present in the sample and the strength of the signal produced by the antibody-protein interaction in a sample is directly proportional to the amount of protein present in the sample. The ratio of the signal intensity of the test sample to that of the reference sample is then calculated, to measure the protein expression levels between the test sample and the reference sample. The difference in the signal ratio determines whether the total level of protein expression of each protein in the test sample is increased or decreased, as compared to the reference sample. If the signal in the reference sample is the same (within acceptable levels of experimental error) as the signal produced in the test sample, then the protein of interest is present in

approximately the same quantity in each sample. [0233] In some embodiments, protein expression levels can be determined via targeted multiplex mass spectrometry. For example, in some embodiments LC-MS/MS can be used to determine the expression level of proteins isolated from a BRCA1- and/or BRCA2-deficient cancer, and thus create a reference sample. Similarly, LC-MS/MS can be used to determine the expression level of proteins isolated from a cancer whose BRCAl/2 status is not known to create a test sample. The levels of protein expression can then be compared between the two samples. In some embodiments, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-MS) can be used to image histological sections taken from BRCA1- and/or BRCA2-deficient tumors (reference samples) and histological sections taken from tumor samples whose BRCAl/2 status are not known (test samples). MALDI-MS can be used to image naturally occurring molecules, such as proteins, within a reference sample and within a test sample such that the presence and the levels of expression of the proteins can be compared between the two samples.

[0234] The protein based BRCA-deficiency signatures disclosed herein are advantageous in comparison to transcript-based and genomic markers, as the expression level of the disclosed proteins comprising the deficiency signatures can be measured using routine assays such as, for example, antibody-based methods such as immunohistochemistry and ELISA, of which the latter allows for non-invasive testing.

Creation of Protein Signatures

[0235] The protein signatures disclosed herein can be generated in a number of ways.

In some embodiments, protein profiles of BRCA1- and/or BRCA2-deficient mouse cancers can be generated using high-resolution tandem mass spectrometry-based proteomics. For example, proteomics can be employed based on ID gel electrophoresis in combination with nano-LC-MS/MS and spectral counting to compare the protein profile of a BRCA1- and/or BRCA2-deficient cancer and the protein profile of a BRCA1- and/or BRCA2 -proficient cancer. The two protein profiles can then be compared in order to determine which proteins are differentially regulated between the two cancer types. Pathway and protein complex analysis can then be used to identify the functions of the proteins that are differentially regulated between the two cancer types. In some embodiments, one or more proteins that are significantly up-regulated in B RCA 1 -deficient tumors and that have DNA repair and related functions can be utilized in one or more of the protein signatures disclosed herein.

[0236] In some embodiments, mass spectrometry based proteomics can be used to identify proteins associated with BRCA1- and/or BRCA2-deficient cancers. In certain embodiments, inbred mouse models of human BRCAl-deficient breast cancer that display a minimal amount of genetic variability can be used. Such models can harbor conditional tissue-specific mutations in the BRCA1 and p53 genes. The majority of the tumors manifested by the mouse models are highly similar to their human counterparts with respect to histological and molecular characteristics and show a high level of genomic instability. Therefore, in certain embodiments, proteomics can be employed based on ID gel electrophoresis in combination with nano-LC-MS/MS and spectral counting to compare the protein profile of tumors isolated from inbred mouse models of human BRCA1 -deficient breast cancer and the protein profile of tumors isolated from inbred mouse models of human BRCA1 -proficient breast cancer. Differentially expressed proteins, including but not limited to up-regulated proteins, can be determined using such techniques.

[0237] Isolation of proteins from tissue samples can be accomplished via any number of techniques. For example, in certain embodiments, a tissue sample from a BRCA1- deficient cancer may be taken and homogenized. Similarly, a tissue sample from a BRCA1- proficient cancer may be taken and separately homogenized. As will be evident to a person of ordinary skill in the art, each sample is processed separately to avoid cross-contamination and to ensure that the comparison between the two samples is scientifically sound. For purposes of brevity, the following description relates to the sample taken from a BRCA1- deficient cancer, however the same processing can be performed on the BRCA1 -proficient cancer.

[ 0238] After homogenization, the proteins in the cancer tissue sample are solubilized in an appropriate buffer (e.g. , a buffer containing an anionic surfactant such as sodium dodecyl sulfate), and then heat denatured. The proteins can then be fractionated according to their electrophoretic mobility using any number of gel electrophoresis techniques such as, for example, one-dimensional sodium dodecyl sulfate -polyacrylamide gel electrophoresis. Upon completion of electrophoresis, the gel can be fixed and stained to reveal the bands of fractionated proteins isolated from the BRCA1 -deficient cancer. Data relating to electrophoretic mobility and band color intensity can be obtained.

[0239] In order to liberate the proteins from the gel, each of the individual gel lanes can be cut into a plurality of bands and each band can be processed separately to remove the proteins therefrom, thereby creating a library of individual pools of proteins isolated from the B RCA 1 -deficient cancer. In certain embodiments, each gel band can be processes for in-gel digestion by reducing any cysteine bonds that may be present in the proteins in each band (e.g. , by treatment with dithiotreitol) and then incubating each band with an appropriate protease (e.g. , trypsin). The resulting peptides can then be extracted from each gel band and stored prior to LC-MS analysis.

[0240] The peptides in each pool (produced by extraction of each individual gel band) can then be separated by LC-MS/MS. The MS/MS spectra obtained from each pool can then be analyzed (e.g. , by use of one or more algorithms and comparison to known databases) to determine the intact protein and peptide fragment composition. In some embodiments, the MS/MS spectra of the proteins contained in each gel band pool can be searched against the human IPI database, and the results imported into one or more software programs that can organize the gel-band data, validate peptide identifications and generate a list of identified proteins for the gel band pool (see, e.g., Example 1). MS/MS analysis can also serve to quantify the amount of each protein and peptide present in each gel band pool.

[0241] This data can then be compared against the corresponding data obtained from the BRCAl -proficient cancer to determine which of the proteins are differentially expressed between the two samples. In some embodiments, proteins that are significantly differentially expressed in a BRCAl -deficient cancer are suitable for use in the protein signatures disclosed herein. In some embodiments, proteins that are significantly differentially expressed in a BRCAl -deficient cancer, as compared to a BRCAl -proficient cancer, are suitable for use in the protein signatures disclosed herein. In some embodiments, proteins that are significantly up-regulated in a BRCAl -deficient cancer, as compared to a BRCAl -proficient cancer, are suitable for use in the protein signatures disclosed herein. In some embodiments, proteins that are significantly up-regulated in a BRCAl -deficient cancer and exhibit DNA-repair, chromatin remodeling and associated functions, as compared to a BRCAl -proficient cancer, are suitable for use in the protein signatures disclosed herein.

[0242] Kits

[0243] In further aspects, the present disclosure provides kits for use in the methods described above. The kits can comprise one or more of the BRCA-deficiency protein signatures as well as any one or more of the reagents required to perform the methods described herein. In some embodiments, the kits comprise instructions for using the BRCA- deficiency protein classifiers to perform the methods provided by the present disclosure. Such kits may include any or all of the following: assay reagents, buffers, one or more of the BRCA-deficiency protein signatures, one or more substrates for immobilization of the proteins of the BRCA-deficiency protein signatures and the proteins of a test sample, and optionally enzyme conjugated antibodies and substrate solutions. In addition, the kits may include instructional materials containing directions (i.e. , protocols) for the practice of the methods of this invention. While the instructional materials typically comprise written or printed materials they are not limited to such. Any medium capable of storing such instructions and communicating them to an end user is contemplated by this invention. Such media include, but are not limited to electronic storage media (e.g., magnetic discs, tapes, cartridges, chips), optical media (e.g., CD ROM), and the like. Such media may include addresses to internet sites that provide such instructional materials.

Messenger RNA Signatures

[0244] The present inventors have confirmed that a large proportion (20%) of the proteome of mammalian mammary tumor tissue is significantly differentially regulated (either up-regulated or down-regulated) in BRCA1 -deficient tumors as compared to BRCA1- proficient tumors. The differentially regulated proteins seen in B RCA 1 -deficient tumors are almost exclusively related to BRCA1 status and only partially to cell type, making them and their corresponding nucleic acid sequences, ideally suited as predictive measures of BRCA- deficiency status in cancer. The data presented in this disclosure shows an extensive up- regulation of a broad range of DNA repair/chromatin remodeling pathways and protein complexes in BRCA1 -deficient tumors.

[0245] In various aspects, the present disclosure is based on the discovery that certain up-regulated proteins seen in BRCA1 -deficient cancer, and the nucleic acid sequences that code for those up-regulated proteins, can be used to identify cancer patients with BRCA1- deficient cancer and/or to predict whether such patients will benefit from anti-cancer therapy. In various aspects, the present disclosure is based on the discovery that certain up-regulated proteins seen in BRCA1 -deficient cancer, and the nucleic acid sequences that code for those up-regulated proteins, can be used to identify cancer patients with BRCA2-deficient cancer and/or to predict whether such patients will benefit from anti-cancer therapy.

[0246] In various embodiments, BRCA-deficiency signatures comprising one or more nucleic acid sequences of proteins that are up-regulated in BRCA1 -deficient tumors are disclosed. In various embodiments, the BRCA-deficiency signatures can be used to identify cancer patients with BRCA1 -deficient tumors. In various embodiments, the BRCA- deficiency signatures can be used to identify cancer patients with BRCA2-deficient tumors. In various embodiments, the BRCA-deficiency signatures can be used to predict whether such patients will benefit from anti-cancer therapy.

BRCA-deficiency Signatures Based on Nucleic Acid Sequences of 45 Up-Regulated Proteins [0247] The present inventors have identified 45 proteins that are up-regulated in BRCA1 -deficient tumors and have elucidated the corresponding nucleic acid sequences of each of the 45 up-regulated proteins, which are useful in the methods and signatures disclosed herein. The 45 proteins are shown in Fig. 2 and their corresponding nucleic acid sequences are disclosed as SEQ ID NOS: 46 - 90. Therefore, in various embodiments,

BRCA-deficiency signatures comprising one or more of SEQ ID NOS: 46 - 90 are disclosed.

[0248] In some embodiments, the BRCA-deficiency signatures comprise at least one of SEQ ID NOS: 46-90. These BRCA-deficiency signatures can be used as diagnostic tools to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. These BRCA-deficiency signatures can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. These BRCA- deficiency signatures can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. These BRCA-deficiency signatures can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0249] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 5 nucleic acid sequences selected from the following 45 nucleic acid sequences that code for proteins that are up-regulated in BRCA1 -deficient tumors: SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90. The BRCA-deficiency signatures comprising a set of at least 5 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can be used as diagnostic tools to detect patients who are carrying a BRCAl-mutation and/or have BRCA1- deficient cancer. The BRCA-deficiency signatures comprising a set of at least 5 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The BRCA-deficiency signatures comprising a set of at least 5 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 5 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0250] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 6 nucleic acid sequences selected from the following 45 nucleic acid sequences that code for proteins that are up-regulated in BRCA1 -deficient tumors: SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90. The BRCA-deficiency signatures comprising a set of at least 6 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can be used as diagnostic tools to detect patients who are carrying a BRCAl-mutation and/or have BRCA1- deficient cancer. The BRCA-deficiency signatures comprising a set of at least 6 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The BRCA-deficiency signatures comprising a set of at least 6 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 6 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0251] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 7 nucleic acid sequences selected from the following 45 nucleic acid sequences that code for proteins that are up-regulated in BRCA1 -deficient tumors: SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90. The BRCA-deficiency signatures comprising a set of at least 7 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can be used as diagnostic tools to detect patients who are carrying a BRCAl-mutation and/or have BRCA1- deficient cancer. The BRCA-deficiency signatures comprising a set of at least 7 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The BRCA-deficiency signatures comprising a set of at least 7 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 7 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0252] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 8 nucleic acid sequences selected from the following 45 nucleic acid sequences that code for proteins that are up-regulated in BRCA1 -deficient tumors: SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90. The BRCA-deficiency signatures comprising a set of at least 8 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can be used as diagnostic tools to detect patients who are carrying a BRCAl-mutation and/or have BRCA1- deficient cancer. The BRCA-deficiency signatures comprising a set of at least 8 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The BRCA-deficiency signatures comprising a set of at least 8 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 8 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0253] In some embodiments, BRCA-deficiency signatures are provided comprising a set of at least 9 nucleic acid sequences selected from the following 45 nucleic acid sequences that code for proteins that are up-regulated in BRCA1 -deficient tumors: SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90. The BRCA-deficiency signatures comprising a set of at least 9 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can be used as diagnostic tools to detect patients who are carrying a BRCAl-mutation and/or have BRCA1- deficient cancer. The BRCA-deficiency signatures comprising a set of at least 9 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can also be used as diagnostic tools to detect patients who are carrying a BRCA2-mutation and/or have BRCA2- deficient cancer. The BRCA-deficiency signatures comprising a set of at least 9 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signatures comprising a set of at least 9 nucleic acid sequences selected from the foregoing 45 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy. [0254] In some embodiments, a BRCA-deficiency signature is provided comprising the following 45 nucleic acid sequences that code for proteins that are up-regulated in BRCA1 -deficient tumors: SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90. The BRCA- deficiency signature comprising the foregoing 45 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1- deficient cancer. The BRCA-deficiency signature comprising the foregoing 45 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2- mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 45 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA- deficiency signature comprising the foregoing 45 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0255] In some embodiments, a BRCA-deficiency signature is provided comprising the following 16 nucleic acid sequences that code for proteins that are up-regulated in BRCA1 -deficient tumors: SEQ ID NO: 55, SEQ ID NO: 68, SEQ ID NO: 89, SEQ ID NO: 67, SEQ ID NO: 83, SEQ ID NO: 52, SEQ ID NO: 76, SEQ ID NO: 88, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 64, SEQ ID NO: 57, SEQ ID NO: 90, SEQ ID NO: 80, SEQ ID NO: 51 and SEQ ID NO: 81. The BRCA-deficiency signature comprising the foregoing 16 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have B RCA 1 -deficient cancer. The BRCA-deficiency signature comprising the foregoing 16 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 16 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 16 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0256] In some embodiments, a BRCA-deficiency signature is provided comprising the following 9 nucleic acid sequences that code for proteins that are up-regulated in BRCAl - deficient tumors: SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 66, SEQ ID NO: 70, SEQ ID NO: 73, SEQ ID NO: 83 and SEQ ID NO: 89. The BRCA-deficiency signature comprising the foregoing 9 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCAl-mutation and/or have BRCA1- deficient cancer. The BRCA-deficiency signature comprising the foregoing 9 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2- mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 9 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA- deficiency signature comprising the foregoing 9 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0257] In some embodiments, a BRCA-deficiency signature is provided comprising the following 7 nucleic acid sequences that code for proteins that are up-regulated in BRCAl - deficient tumors: SEQ ID NO: 46, SEQ ID NO: 49, SEQ ID NO: 62, SEQ ID NO: 74, SEQ ID NO: 85, SEQ ID NO: 87 and SEQ ID NO: 89. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCAl-mutation and/or have BRCAl -deficient cancer. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0258] In some embodiments, a BRCA-deficiency signature is provided comprising the following 8 nucleic acid sequences that code for proteins that are up-regulated in BRCAl - deficient tumors: SEQ ID NO: 46, SEQ ID NO: 49, SEQ ID NO: 55, SEQ ID NO: 62, SEQ ID NO: 74, SEQ ID NO: 85, SEQ ID NO: 87 and SEQ ID NO: 89. The BRCA-deficiency signature comprising the foregoing 8 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The BRCA-deficiency signature comprising the foregoing 8 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 8 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 8 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0259] In some embodiments, a BRCA-deficiency signature is provided comprising the following 33 nucleic acid sequences that code for proteins that are up-regulated in BRCA1 -deficient tumors: SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90. The BRCA-deficiency signature comprising the foregoing 33 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCA1 -deficient cancer. The BRCA-deficiency signature comprising the foregoing 33 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 33 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 33 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0260] In some embodiments, a BRCA-deficiency signature is provided comprising the following 37 nucleic acid sequences that code for proteins that are up-regulated in BRCA1 -deficient tumors: SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90. The BRCA-deficiency signature comprising the foregoing 37 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The BRCA-deficiency signature comprising the foregoing 37 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 37 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 37 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0261] In some embodiments, a BRCA-deficiency signature is provided comprising the following 36 nucleic acid sequences that code for proteins that are up-regulated in BRCAl-deficient tumors: SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90. The BRCA-deficiency signature comprising the foregoing 36 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCA1- mutation and/or have BRCAl-deficient cancer. The BRCA-deficiency signature comprising the foregoing 36 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 36 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 36 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy. [0262] In some embodiments, a BRCA-deficiency signature is provided comprising the following 21 nucleic acid sequences that code for proteins that are up-regulated in BRCA1 -deficient tumors: SEQ ID NO: 46, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 59, SEQ ID NO: 63, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 83, SEQ ID NO: 85 and SEQ ID NO: 89. The BRCA-deficiency signature comprising the foregoing 21 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCA1 -mutation and/or have BRCAl-deficient cancer. The BRCA-deficiency signature comprising the foregoing 21 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 21 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 21 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0263] In some embodiments, a BRCA-deficiency signature is provided comprising the following 9 nucleic acid sequences that code for proteins that are up-regulated in BRCAl- deficient tumors: SEQ ID NO: 46, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 55, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 83, SEQ ID NO: 85 and SEQ ID NO: 89. The

BRCA-deficiency signature comprising the foregoing 9 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCAl-mutation and/or have BRCAl- deficient cancer. The BRCA-deficiency signature comprising the foregoing 9 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2- mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 9 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA- deficiency signature comprising the foregoing 9 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0264] In some embodiments, a BRCA-deficiency signature is provided comprising the following 7 nucleic acid sequences that code for proteins that are up-regulated in BRCAl- deficient tumors: SEQ ID NO: 46, SEQ ID NO: 49, SEQ ID NO: 62, SEQ ID NO: 74, SEQ ID NO: 77, SEQ ID NO: 85 and SEQ ID NO: 89. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a B RC A 1 -mutation and/or have BRCA1 -deficient cancer. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0265] In some embodiments, a BRCA-deficiency signature is provided comprising the following 20 nucleic acid sequences that code for proteins that are up-regulated in BRCA1 -deficient tumors: SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 89 and SEQ ID NO: 90. The BRCA-deficiency signature comprising the foregoing 20 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCA1- mutation and/or have BRCAl-deficient cancer. The BRCA-deficiency signature comprising the foregoing 20 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 20 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 20 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0266] In some embodiments, a BRCA-deficiency signature is provided comprising the following 10 nucleic acid sequences that code for proteins that are up-regulated in BRCAl-deficient tumors: SEQ ID NO: 48, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 63, SEQ ID NO: 68, SEQ ID NO: 75, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86 and SEQ ID NO: 88. The BRCA-deficiency signature comprising the foregoing 10 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCA1- mutation and/or have BRCAl-deficient cancer. The BRCA-deficiency signature comprising the foregoing 10 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 10 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 10 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0267] In some embodiments, a BRCA-deficiency signature is provided comprising the following 16 nucleic acid sequences that code for proteins that are up-regulated in BRCAl -deficient tumors: SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 64, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 76, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 83, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90. The BRCA-deficiency signature comprising the foregoing 16 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCAl -mutation and/or have BRCAl -deficient cancer. The BRCA-deficiency signature comprising the foregoing 16 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 16 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 16 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0268] In some embodiments, a BRCA-deficiency signature is provided comprising the following 7 nucleic acid sequences that code for proteins that are up-regulated in BRCAl - deficient tumors: SEQ ID NO: 46, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 57, SEQ ID NO: 73, SEQ ID NO: 75 and SEQ ID NO: 83. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCAl -mutation and/or have BRCAl -deficient cancer. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

[0269] In some embodiments, a BRCA-deficiency signature is provided comprising the following 7 nucleic acid sequences that code for proteins that are up-regulated in BRCAl - deficient tumors: SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 57, SEQ ID NO: 64, SEQ ID NO: 75, SEQ ID NO: 81 and SEQ ID NO: 83. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can be used as a diagnostic tool to detect patients who are carrying a BRCAl -mutation and/or have BRCAl -deficient cancer. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can also be used as a diagnostic tool to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can be used in one or more of the methods disclosed herein to predict the benefit of anti-cancer therapy in an individual patient. The BRCA-deficiency signature comprising the foregoing 7 nucleic acid sequences can also be used in one or more of the methods disclosed herein as a predictive test to identify cancer patients likely to benefit from anti-cancer therapy.

Uses of Nucleic Acid Signatures

[0270] The BRCA-deficiency signatures comprising nucleic acid sequences coding for proteins that are up-regulated in BRCAl -deficient tumors disclosed herein can be used as diagnostic tools, to detect patients who are carrying a BRCAl -mutation and/or have a

BRCAl -deficient cancer and to detect patients who are carrying a BRCA2-mutation and/or have BRCA2-deficient cancer. Therefore, in various aspects, the BRCA-deficiency nucleic acid signatures provided in this disclosure are capable of determining whether an individual cancer patient has a BRCAl -deficient tumor. Additionally, in various aspects, the BRCA- deficiency nucleic acid signatures provided in this disclosure are capable of determining whether an individual cancer patient has a BRCA2-deficient tumor.

[0271] Identification of BRCAl and/or BRCA2 pathway dysfunction provides an opportunity for therapeutic intervention. Emerging preclinical evidence shows that cancers with a defective DNA repair system, such as a mutation in the BRCAl gene and/or the BRCA2 gene, may be extremely sensitive to DNA damaging agents, such as platinum compounds and bifunctional alkylating agents. Therefore, patients with cancers harboring a defective BRCAl - and/or BRCA2-deficient DNA repair system may specifically benefit from high dose alkylating chemotherapy, a DNA double strand break (DSB)-inducing regimen. Tumors with homologous recombination deficiency (such as deficiency in the BRCAl and/or BRCA2 gene pathways) have been shown to be particularly sensitive to DNA double strand break (DSB)-inducing agents, such as alkylators and platinum drugs or platinating agents. Both classes of drugs are employed in metastatic breast cancer. The novel poly(ADP-ribose) polymerase inhibitors (PARP inhibitors) are specifically effective in homologous recombination deficient tumors as well, and have shown impressive activity in clinical studies recently. Therefore, BRCAl- and BRCA2-deficient cancers are susceptible to treatment with anti-cancer therapy (as defined herein) and patients having BRCAl - and BRCA2-deficient cancers will benefit from receipt of anti-cancer therapy.

[0272] The BRCA-deficiency nucleic acid signatures provided in this disclosure are therefore capable of predicting benefit of anti-cancer therapy in an individual patient and can also be used as predictive tests to identify cancer patients likely to benefit from anti-cancer therapy.

[0273] In various aspects, the present disclosure provides methods of using the BRCA-deficiency nucleic acid signatures disclosed herein to determine whether a tumor has a BRCAl and/or BRCA2 deficiency. In some embodiments, the methods comprise generating a test sample comprising nucleic acid sequences isolated from a cancer from a patient; measuring the expression level of the nucleic acid sequences of the test sample; comparing the expression level of the nucleic acid sequences of the test sample to at least one of the BRCA-deficiency nucleic acid signatures provided by the present disclosure; and identifying the cancer as BRCAl -deficient or BRCAl -proficient and/or BRCA2-deficient or BRCA2 -proficient; wherein when the expression level of the nucleic acid sequences of the test sample is similar to the expression level of the corresponding nucleic acid sequences in the at least one of the BRCA-deficiency nucleic acid signatures, the cancer is classified as BRCAl - and/or BRCA2-deficient.

[0274] In some embodiments, the methods comprise generating a test sample comprising nucleic acid sequences isolated from a cancer form a patient; measuring the expression level of the nucleic acid sequences of the test sample; comparing the expression level of the nucleic acid sequences of the test sample to at least one of the BRCA-deficiency nucleic acid signatures provided by the present disclosure; and identifying the cancer as BRCAl -deficient or BRCAl -proficient and/or BRCA2-deficient or BRCA2-proficient; wherein when the expression level of the nucleic acid sequences of the test sample is the same as the expression level of the corresponding nucleic acid sequences in the at least one of the BRCA-deficiency nucleic acid signatures, the cancer is classified as BRCAl -deficient. [0275] Additionally, in various aspects the present disclosure provides methods of using the BRCA-deficiency nucleic acid signatures disclosed herein to optimize anti-cancer therapy. In some embodiments, the methods comprise generating a test sample comprising nucleic acid sequences isolated from a cancer from a patient; measuring the expression level of the nucleic acid sequences of the test sample; comparing the expression level of the nucleic acid sequences of the test sample to at least one of the BRCA-deficiency nucleic acid signatures provided by the present disclosure; and administering anti-cancer therapy to the patient when the expression level of the nucleic acid sequences of the test sample is similar to the expression level of the corresponding nucleic acid sequences in the at least one of the BRCA-deficiency nucleic acid signatures.

[0276] In some embodiments, the methods comprise generating a test sample comprising nucleic acid sequences isolated from a cancer from a patient; measuring the expression level of the nucleic acid sequences of the test sample; comparing the expression level of the nucleic acid sequences of the test sample to at least one of the BRCA-deficiency nucleic acid signatures provided by the present disclosure; and administering anti-cancer therapy to the patient when the expression level of the nucleic acid sequences of the test sample is the same (within acceptable levels of experimental error) as the expression level of the corresponding nucleic acid sequences in the at least one of the BRCA-deficiency nucleic acid signatures.

[0277] Any one or more of the BRCA-deficiency nucleic acid signatures disclosed herein may be used in the foregoing methods.

[0278] Using the methods described above, in various aspects, the BRCA-deficiency nucleic acid signatures provided by the present disclosure are capable of determining whether or not a cancer is BRCA1 -deficient. Using the methods described above, in various aspects, the BRCA-deficiency nucleic acid signatures provided by the present disclosure are capable of determining whether or not a cancer is BRCA2-deficient.

[0279] Using the methods described above, in various aspects, the BRCA-deficiency nucleic acid signatures provided by the present disclosure can be used to predict an individual subject's benefit of anti-cancer therapy.

[0280] Determination of Nucleic Acid Expression Levels

[0281] The expression levels of the up-regulated nucleic acid sequences comprising the nucleic acid signatures of the present disclosure are known and/or may be readily determined. In that regard, the nucleic acid signatures of the present disclosure can serve as reference samples (as defined herein). The expression levels of the up-regulated nucleic acid sequences/reference samples may be compared to the expression levels of a test sample of nucleic acid sequences isolated from a cancer tissue sample obtained from a patient.

Therefore, the expression levels of the nucleic acid sequences comprising any of the nucleic acid signatures disclosed herein (reference samples) can be compared to the expression level of the corresponding nucleic acid sequences obtained from a cancer in a patient (test sample).

[0282] In some embodiments, similarity between the expression level of a test sample of nucleic acid isolated from a cancer obtained from a patient and the expression levels of any one or more of the reference sample nucleic acid signatures disclosed herein identifies the tumor as BRCAl-deficient. In some embodiments, similarity between the expression level of a test sample of nucleic acid isolated from a cancer obtained from a patient and the expression levels of any one or more of the reference sample nucleic acid signatures disclosed herein identifies the tumor as BRCA2-deficient.

[0283] In some embodiments, substantial similarity between the expression level of a test sample of nucleic acid sequences isolated from a cancer obtained from a patient and the expression levels of any one or more of the reference sample nucleic acid signatures disclosed herein identifies the tumor as BRCAl -deficient. In some embodiments, substantial similarity between the expression level of a test sample of nucleic acid sequences isolated from a cancer obtained from a patient and the expression levels of any one or more of the reference sample nucleic acid signatures disclosed herein identifies the tumor as BRCA2- deficient. In some embodiments, substantial similarity means that the expression level of at least one nucleic acid sequence of the test sample is 50-90% identical to the expression level of the corresponding nucleic acid sequence(s) in the reference sample. In some

embodiments, substantial similarity means that the expression level of a plurality of nucleic acid sequences of the test sample is 50-90% identical to the expression level of the corresponding nucleic acid sequences in the reference sample. In some embodiments, substantial similarity means that the expression level of all of the nucleic acid sequences of the test sample is 50-90% identical to the expression level of the corresponding nucleic acid sequences in the reference sample. In each case, identity (or "identical") can be established when the protein expression levels between the test and reference samples provide output readings that are the same within acceptable levels of experimental error.

[0284] In some embodiments, the degree of similarity between the level of expression of the nucleic acid sequences comprising a test sample and the level of expression of the nucleic acid sequences comprising a reference sample is determined based on signal intensity, such as that derived from an assay (e.g. , aCGH, see below). In certain embodiments, the ratio of the signal intensity of the nucleic acid sequences comprising a test sample, as compared to the signal intensity of the nucleic acid sequences comprising a reference sample, is calculated. This calculation quantifies the differential level of expression of the nucleic acid sequences of the test sample, as compared to the reference sample, if any. In some embodiments, this calculation is carried out quantitatively or semi-quantitatively. In certain embodiments, it is not necessary to determine an exact number associated with the level of expression of the nucleic acid sequences comprising the test sample and the reference sample. The reference sample comprises nucleic acid sequences taken from a tumor, or collection of tumors, known to be BRCA-deficient. As such, the signal intensity produced by any given reference sample is representative of BRCA-deficiency and detection of a statistically significant deviation (increase or decrease) in the signal intensity produced by the nucleic acid sequences of the test sample, as compared to the signal produced by the nucleic acid sequences of the reference sample, is sufficient. Therefore, in several embodiments the quantification of the expression levels of nucleic acid sequences of a test sample comprises an estimation of the level of expression, as a semi-quantitative or relative measure, that is sufficient to predict the presence or absence of BRCA-deficiency (as compared to a reference sample) and thus prospectively direct the determination of therapy for a subject.

[0285] In various aspects, determination of a level of expression of the nucleic acid sequences in a test sample that is the same, or greater, than that produced by the reference sample is indicative of BRCA deficiency in the tumor from which the test sample was derived. Therefore, in certain embodiments detection of signal intensity from a test sample that is the same, within experimentally acceptable margins of error, as the signal intensity produced by the reference sample is sufficient to classify the tumor from which the test sample was produced as BRCA-deficient. In certain embodiments, detection of signal intensity from a test sample that is greater, within experimentally acceptable margins of error, than the signal intensity produced by the reference sample is sufficient to classify the tumor from which the test sample was produced as BRCA-deficient.

[0286] In certain embodiments, detection of signal intensity from a test sample that is less, within experimentally acceptable margins of error, than the signal intensity produced by the reference sample is sufficient to classify the tumor from which the test sample was produced as BRCA-proficient. In certain embodiments, the deviation of signal intensity of the test sample from the reference sample is measured as a percent difference. In certain embodiments, a reference sample is deemed to have produced a signal that is less than the reference sample if the signal intensity of the test sample measures at a level selected from: the signal intensity of the reference sample less 5%; the signal intensity of the reference sample less 10%; the signal intensity of the reference sample less 15%; the signal intensity of the reference sample less 20%; the signal intensity of the reference sample less 25%; the signal intensity of the reference sample less 30%; the signal intensity of the reference sample less 35%; the signal intensity of the reference sample less 40%; the signal intensity of the reference sample less 45%; the signal intensity of the reference sample less 50%; the signal intensity of the reference sample less 55%; the signal intensity of the reference sample less 60%; the signal intensity of the reference sample less 65%; the signal intensity of the reference sample less 70%; the signal intensity of the reference sample less 75%; the signal intensity of the reference sample less 80%; the signal intensity of the reference sample less 85%; the signal intensity of the reference sample less 90%; the signal intensity of the reference sample less 95%; and the signal intensity of the reference sample less 100% (or no signal produced by the test sample).

[0287] In certain embodiments, the deviation of signal intensity of the test sample from the reference sample is measured as a -fold difference, or a difference based upon unit signal production. In certain embodiments, a reference sample is deemed to have produced a signal that is less than the reference sample if the signal intensity of the test sample is selected from: two-fold less than the signal intensity of the reference sample; three-fold less than the signal intensity of the reference sample; four-fold less than the signal intensity of the reference sample; five-fold less than the signal intensity of the reference sample; six-fold less than the signal intensity of the reference sample; seven-fold less than the signal intensity of the reference sample; eight-fold less than the signal intensity of the reference sample; ninefold less than the signal intensity of the reference sample; ten-fold less than the signal intensity of the reference sample; and greater than ten-fold less than the signal intensity of the reference sample.

[0288] In some embodiments, complete identity between the expression level of a test sample of nucleic acid sequences isolated from a cancer obtained from a patient and the expression levels of any one or more of the reference sample nucleic acid signatures disclosed herein identifies the tumor as BRCA1 -deficient. In some embodiments, complete identity between the expression level of a test sample of nucleic acid sequences isolated from a cancer obtained from a patient and the expression levels of any one or more of the reference sample nucleic acid signatures disclosed herein identifies the tumor as BRCA2-deficient.

[0289] Tumors with homologous recombination deficiency have been shown to be particularly sensitive to anti-cancer therapy which can include, without limitation, DNA double strand break (DSB)-inducing agents, such as alkylators and platinum drugs or platinating agents. BRCA1- and BRCA2-deficient tumors are therefore sensitive to anticancer therapy (as defined herein). In some embodiments, identification of a tumor as BRCA1- and/or BRCA2-deficient, using any one or more of the nucleic acid signatures disclosed herein, identifies the patient as one who will benefit from anti-cancer therapy.

[0290] The expression level of any one or more of the up-regulated nucleic acid sequences comprising the BRCA-deficiency nucleic acid signatures disclosed herein, and/or the expression levels of any one or more nucleic acid sequences isolated from a test sample (i.e. , from a cancer obtained from a patient), can be determined using any one or more of a number of techniques.

[0291] In some embodiments, the expression level of the nucleic acid sequences of a test sample and/or the expression level of the nucleic acid sequences of a reference sample may be measured via array-based comparative genomic hybridization. Array comparative genomic hybridization (aCGH) is a technique that is used to detect copy number variations of nucleic acids at a higher level of resolution than chromosome-based comparative genomic hybridization. In aCGH, nucleic acids from a test sample and nucleic acids from a reference sample are labelled differentially. The test sample and the reference sample are then hybridized to an array comprising a plurality of probes, which are derived from sequences of interest. The differential labelling is then used to visualize the hybridized nucleic acids from the test and reference samples. The ratio of the signal intensity of the test sample to that of the reference sample is then calculated, to measure the copy number changes between the test sample and the reference sample. The difference in the signal ratio determines whether the total copy numbers of the nucleic acids in the test sample are increased or decreased, as compared to the reference sample. The test sample and the reference sample may be hybridized to the array separately or they may be mixed together and hybridized

simultaneously. Exemplary methods of performing aCGH can be found, for example, in U.S. Patent Nos. 5,635,351 ; 5,665,549; 5,721,098; 5,830,645; 5,856,097; 5,965,362; 5,976,790; 6,159,685; 6,197,501 ; and 6,335,167; European Patent Nos. EP 1 134 293 and EP 1 026 260; van Beers et al., Brit. J. Cancer (2006), 20; Joosse et al., BMC Cancer (2007), 7:43; Pinkel et al., Nat. Genet. (1998), 20: 207-211 ; Pollack et al., Nat. Genet. (1999), 23: 41-46; and Cooper, Breast Cancer Res. (2001), 3: 158-175.

[0292] Samples that are labelled differentially are labelled such that one of the two samples is labelled with a first detectable agent and the other of the two samples is labelled with a second detectable agent, wherein the first detectable agent and the second detectable agent produce distinguishable signals. Detectable agents that produce distinguishable signals can include, for example, matched pairs of fluorescent dyes.

[0293] In some embodiments, the methods of the present disclosure comprise analyzing at least one test sample of nucleic acid molecules isolated from a cancer obtained from a patient by array-based comparative genomic hybridization to obtain information relating to the level of expression of the nucleic acid molecules(s), if any, and comparing the level of expression to corresponding nucleic acid molecules comprising one or more of the BRCA-deficiency nucleic acid signatures disclosed herein. Based on the information obtained, the tumor may be classified as BRCAl -deficient or BRCAl -proficient and/or BRCA2-deficient or BRCA2-proficient.

[0294] Information relating to the expression level of the nucleic acid sequences present in a sample can include, for example, an increase in expression level in one or more nucleic acid molecules, a decrease in expression level in one or more nucleic acid molecules, and/or no change in the expression level of one or more nucleic acid molecules. This information is obtained by analyzing the difference in signal intensity between the test sample and a reference sample at one or more corresponding locations on the array representing one or more nucleic acid sequences of interest. The analysis can be performed using any of a variety of methods, means and variations thereof for carrying out array-based comparative genomic hybridization.

[0295] In various embodiments, the reference samples are any one or more of the

BRCA-deficiency nucleic acid signatures provided by the present disclosure, which represent nucleic acid isolated from a known BRCAl -deficient cancer that code for proteins that are significantly differentially up-regulated as compared to BRCAl -proficient cancers. The reference samples are derived from cancers that are known to be BRCAl -deficient. In some embodiments, the reference samples are derived from a pool of subjects. In some embodiments, the reference samples comprise pooled nucleic acid isolated from BRCAl - deficient cancers from a plurality (e.g. at least 4-10) of female subjects. In some

embodiments, the reference samples comprise pooled nucleic acid isolated from BRCA2- deficient cancers from a plurality (e.g. at least 4-10) of female subjects. In some

embodiments, the reference samples are derived from inbred genetic mouse models of

BRCAl -deficiency. In some embodiments, the reference samples comprise an average of the expression levels of nucleic acid coding for proteins that are significantly differentially up- regulated in BRCA-deficient cancers. In certain embodiments, the nucleic acid expression levels are known and are obtainable from one or more publicly available data sets. In some embodiments, the reference samples comprise an average of the expression levels of nucleic acid coding for proteins that are significantly differentially up-regulated in BRCA1 -deficient cancers set forth in the Johnsen data set (see, e.g. , Example 1). In some embodiments, the reference samples comprise an average of the expression levels of nucleic acid coding for proteins that are significantly differentially up-regulated in BRCA2-deficient cancers set forth in the Johnsen data set (see, e.g. , Example 1). In some embodiments, the reference samples comprise an average of the expression levels of nucleic acid coding for proteins that are significantly differentially up-regulated in sporadically arising cancers set forth in the Johnson data set (see, e.g. , Example 1).

[0296] The nucleic acid molecules comprising the test samples and the reference samples may be obtained by any suitable method of nucleic acid isolation and/or extraction. In various aspects, the test sample and the reference sample are mRNA. Methods of mRNA extraction are well known in the art and several kits for the extraction and purification of mRNA from tissue samples are commercially available from, e.g. , Clontech (Mountain View, CA), Qiagen (Valencia, CA) and Life Technologies/Invitrogen (Carlsbad, CA), among others.

[0297] The test samples and the reference samples may be differentially labelled with any detectable agents or moieties. In various embodiments, the detectable agents or moieties are selected such that they generate signals that can be readily measured and such that the intensity of the signals is proportional to the amount of labelled nucleic acids present in the sample. In various embodiments, the detectable agents or moieties are selected such that they generate localized signals, thereby allowing resolution of the signals from each spot on an array.

[0298] Methods for labeling nucleic acids are well-known in the art. For exemplary reviews of labelling protocols, label detection techniques and recent developments in the field, see: Kricka, Ann. Clin. Biochem. (2002), 39: 114-129; van Gijlswijk et al., Expert Rev. Mol. Diagn. (2001), 1 : 81-91 ; and Joos et al., J. Biotechnol. (1994), 35: 135-153. Standard nucleic acid labeling methods include: incorporation of radioactive agents, direct attachment of fluorescent dyes or of enzymes, chemical modification of nucleic acids to make them detectable immunochemically or by other affinity reactions, and enzyme-mediated labeling methods including, without limitation, random priming, nick translation, PCR and tailing with terminal transferase. Other suitable labeling methods include psoralen-biotin, photoreactive azido derivatives, and DNA alkylating agents. In various embodiments, test sample and reference sample nucleic acids are labelled by Universal Linkage System, which is based on the reaction of monoreactive cisplatin derivatives with the N7 position of guanine moieties in DNA (see, e.g. , Heetebrij et al., Cytogenet. Cell. Genet. (1999), 87: 47-52).

[0299] Any of a wide variety of detectable agents or moieties can be used to label test and/or reference samples. Suitable detectable agents or moieties include, but are not limited

32 35 3 14 125 131

to: various ligands; radionuclides such as, for example, P, S, H, C, I, I, and others; fluorescent dyes; chemiluminescent agents such as, for example, acridinium esters, stabilized dioxetanes, and others; microparticles such as, for example, quantum dots, nanocrystals, phosphors and others; enzymes such as, for example, those used in an ELISA, horseradish peroxidase, beta-galactosidase, lucif erase, alkaline phosphatase and others; colorimetric labels such as, for example, dyes, colloidal gold and others; magnetic labels such as, for example, Dynabeads™; and biotin, dioxigenin or other haptens and proteins for which antisera or monoclonal antibodies are available.

[0300] In some embodiments, the test samples and the reference samples are labelled with fluorescent dyes. Suitable fluorescent dyes include, without limitation, Cy-3, Cy-5, Texas red, FITC, Spectrum Red, Spectrum Green, phycoerythrin, rhodamine, and fluorescein, as well as equivalents, analogues and/or derivatives thereof. In some embodiments, the fluorescent dyes selected display a high molar absorption coefficient, high fluorescence quantum yield, and photostability. In some embodiments, the fluorescent dyes exhibit absorption and emission wavelengths in the visible spectrum (i.e., between 400nm and 750nm) rather than in the ultraviolet range of the spectrum (i.e., lower than 400nm). In some embodiments, the fluorescent dyes are Cy-3 (3-N,N'-diethyltetramethylindo-dicarbocyanine) and Cy-5 (5-N,N'-diethyltetramethylindo-dicarbocyanine). Cy-3 and Cy-5 form a matched pair of fluorescent labels that are compatible with most fluorescence detection systems for array-based instruments. In some embodiments, the fluorescent dyes are Spectrum Red and Spectrum Green.

[0301] A key component of aCGH is the hybridization of a test sample and a reference sample to an array. Exemplary hybridization and wash protocols are described, for example, in Sambrook et al. (2001), supra; Tijssen (1993), supra; and Anderson (Ed.), "Nucleic Acid Hybridization" (1999), Springer Verlag: New York, N.Y. In some

embodiments, the hybridization protocols used for aCGH are those of Pinkel et al., Nature Genetics (1998), 20:207-211. In some embodiments, the hybridization protocols used for aCGH are those of Kallioniemi, Proc. Natl. Acad. Sci. USA (1992), 89:5321-5325.

[0302] Methods of optimizing hybridization conditions are well known in the art (see, e.g. , Tijssen, (1993), supra). To create competitive hybridization conditions, the array may be contacted simultaneously with differentially labelled nucleic acid sequences of the test sample and the reference sample. This may be done by, for example, mixing the labelled test sample and the labelled reference sample together to form a hybridization mixture, and contacting the array with the mixture.

[0303] The specificity of hybridization may be enhanced by inhibiting repetitive sequences. In some embodiments, repetitive sequences (e.g. , Alu sequences, LI sequences, satellite sequences, MRE sequences, simple homo-nucleotide tracts, and/or simple oligonucleotide tracts) present in the nucleic acids of the test sample, reference sample and/or probes immobilized on the array are either removed, or their hybridization capacity is disabled. Removing repetitive sequences or disabling their hybridization capacity can be accomplished using any of a variety of well-known methods. These methods include, but are not limited to, removing repetitive sequences by hybridization to specific nucleic acid sequences immobilized to a solid support (see, e.g., Brison et ah, Mol. Cell. Biol. (1982), 2: 578- 587); suppressing the production of repetitive sequences by PCR amplification using adequately designed PCR primers; inhibiting the hybridization capacity of highly repeated sequences by self-reassociation (see, e.g. , Britten et al , Methods of Enzymology (1974), 29: 363-418); or removing repetitive sequences using hydroxyapatite which is commercially available from a number of sources including, for example, Bio-Rad Laboratories, Richmond, VA. In some embodiments, the hybridization capacity of highly repeated sequences in a test sample and/or in a reference sample is competitively inhibited by including, in the hybridization mixture, unlabelled blocking nucleic acids. The unlabelled blocking nucleic acids are therefore mixed with the hybridization mixture, and thus with a test sample and a reference sample, before the mixture is contacted with an array. The unlabelled blocking nucleic acids act as a competitor for the highly repeated sequences and bind to them before the hybridization mixture is contacted with an array. Therefore, the unlabelled blocking nucleic acids prevent labelled repetitive sequences from binding to any highly repetitive sequences of the nucleic acid probes, thus decreasing the amount of background signal present in a given hybridization. In some embodiments, the unlabelled blocking nucleic acids are Human Cot- 1 DNA. Human Cot- 1 DNA is commercially available from a number of sources including, for example, Gibco/BRL Life Technologies (Gaithersburg, MD).

[0304] Once hybridization is complete, the ratio of the signal intensity of the test sample as compared to the signal intensity of the reference sample is calculated. This calculation quantifies the differential level of expression of the nucleic acid molecules of the test sample, as compared to the reference sample, if any. In some embodiments, this calculation is carried out quantitatively or semi-quantitatively. In certain embodiments, it is not necessary to determine the exact number associated with differential expression of the nucleic acid molecules comprising the test sample and the reference sample, as detection of a significant increase or decrease in expression level from the expression level in the reference sample is sufficient. Therefore, in several embodiments the quantification of the expression levels of the nucleic acid molecules of a test sample comprises an estimation of the level of expression, as a semi-quantitative or relative measure usually suffices to predict the presence or absence of BRCA-deficiency and thus prospectively direct the determination of therapy for a subject.

[0305] Quantitative techniques may be used to determine the expression level of the nucleic acid molecules present in a test sample and/or in a reference sample. Several quantitative and semi-quantitative techniques to determine expression levels exist including, for example, semi-quantitative PCR analysis or quantitative real-time PCR. The Polymerase Chain Reaction (PCR) per se is not a quantitative technique, however PCR-based methods have been developed that are quantitative or semi-quantitative in that they give a reasonable estimate of original copy numbers of nucleic acids present in a tissue sample {i.e., expression level of nucleic acid), within certain limits. Examples of such PCR techniques include, for example, quantitative PCR and quantitative real-time PCR (also known as RT-PCR, RQ- PCR, QRT-PCR or RTQ-PCR). In addition, many techniques exist that give estimates of relative copy numbers, as calculated relative to a reference. Such techniques include many array-based techniques. Absolute copy number estimates may be obtained by in situ hybridization techniques such as, for example, fluorescence in situ hybridization or chromogenic in situ hybridization.

[0306] Fluorescence in situ hybridization permits the analysis of the expression level of individual nucleic acid molecules and can be used to study the expression level of individual nucleic acid molecules across tissue samples obtained from different donor sources (see, e.g. , Pinkel et al., Proc. Natl. Acad. Sci. U.S.A. (1988), 85, 9138-42). Comparative genomic hybridization can also be used to probe for nucleic acid expression levels (see, e.g. , Kallioniemi et al, Science (1992), 258: 818-21 ; and Houldsworth et al, Am. J. Pathol.

(1994), 145: 1253-60).

[0307] The expression level of nucleic acid molecules of interest may also be determined using quantitative PCR techniques such as real-time PCR (see, e.g. , Suzuki et al, Cancer Res. (2000), 60:5405-9). For example, quantitative microsatellite analysis can be performed for rapid measurement of relative nucleic acid sequence copy numbers. In quantitative micros atellite analysis, the copy numbers of a test sample relative to a reference sample is assessed using quantitative, real-time PCR amplification of loci carrying simple sequence repeats. Simple sequence repeats are used because of the large numbers that have been precisely mapped in numerous organisms. Exemplary protocols for quantitative PCR are provided in Innis et al., PCR Protocols, A Guide to Methods and Applications (1990), Academic Press, Inc. N.Y. Semi -quantitative techniques that may be used to determine specific copy numbers include, for example, multiplex ligation-dependent probe

amplification {see, e.g. , Schouten et al. Nucleic Acids Res. (2002), 30(12):e57; and Sellner et al., Human Mutation (2004), 23(5):413-419) and multiplex amplification and probe hybridization {see, e.g. , Sellner et al. (2004), supra).

[0308] Kits

[0309] In further aspects, the present disclosure provides kits for use in the methods described above. The kits can comprise one or more of the BRCA-deficiency nucleic acid signatures as well as any one or more of the reagents required to perform the methods described herein. In some embodiments, the kits comprise instructions for using the BRCA- deficiency nucleic acid signatures to perform the methods provided by the present disclosure. Such kits may include any or all of the following: assay reagents, buffers, one or more of the BRCA-deficiency nucleic acid signatures, and pre-made arrays comprising probes corresponding to sequences of interest. In addition, the kits may include instructional materials containing directions {i.e. , protocols) for the practice of the methods of this invention. While the instructional materials typically comprise written or printed materials they are not limited to such. Any medium capable of storing such instructions and communicating them to an end user is contemplated by this invention. Such media include, but are not limited to electronic storage media (e.g., magnetic discs, tapes, cartridges, chips), optical media (e.g., CD ROM), and the like. Such media may include addresses to internet sites that provide such instructional materials.

Examples

[0310] The following examples describe in detail certain embodiments of the BRCA- deficiency protein and BRCA-deficiency nucleic acid signatures disclosed herein. It will be apparent to those skilled in the art that many modifications, both to materials and methods, may be practiced without departing from the scope of the disclosure.

Example 1

Proteomics of mouse BRCAl-deficient mammary tumors identifies DNA repair proteins with diagnostic and prognostic value in human breast cancer [0311] BRCAl hereditary breast cancer, a type of cancer with defects in the homology-directed DNA repair pathway, would benefit from the identification of proteins for diagnosis which might also be of potential use as screening, prognostic or predictive markers. Sporadic breast cancers with defects in the BRCAl pathway might also be diagnosed. In this study, proteomics were employed based on ID gel electrophoresis in combination with nano- LC-MS/MS and spectral counting to compare the protein profiles of mammary tumor tissues of genetic mouse models. Specifically, the protein profiles of BRCAl -deficient mouse models were compared to the protein profiles of BRCAl -proficient mouse models. A total of 3,545 proteins were identified, of which 801 were significantly differentially regulated between the BRCAl -deficient and proficient breast tumors. Pathway and protein complex analysis identified DNA repair and related functions as the major processes associated with the up-regulated proteins in the BRCAl -deficient tumors. In addition, by selecting highly connected nodes, a BRCAl -deficiency signature of 45 proteins was identified that enriches for homology-directed DNA repair deficiency in human gene expression breast cancer datasets. This signature also exhibits prognostic power across multiple datasets, with optimal performance in a dataset enriched in tumors deficient in homology-directed DNA repair. By comparing mouse proteomes from BRCAl -proficient and deficient mammary tumors, several markers associated with BRCAl -deficiency and a prognostic signature for human breast cancer deficient in homology-directed DNA repair were identified.

[0312] The analysis of BRCAl -proficient and deficient tumor proteins is useful in selecting patients that might benefit from tailored anti-cancer therapy. Mass-spectrometry based proteomics technologies have matured to the extent that they can now identify and quantify thousands of proteins. Applying these approaches to cancer tissues provides a complementary insight in breast cancer biology and can identify novel diagnostic and prognostic protein profiles and candidate biomarkers. Protein based biomarkers are of particular advantage in comparison to transcript based and genomic markers, as they can be measured in routine assays, e.g. , by antibody-based methods such as immunohistochemistry and ELISA, of which the latter allows for non-invasive testing. In addition, targeted multiplex mass spectrometry is emerging as a novel quantitative strategy for measuring protein signatures in tumor tissues or blood. Proteomic studies of breast cancer cells and tissues have

17-22

already shown the potential for candidate biomarkers discovery ^" . In a promising pilot study using SELDI-TOF-MS, serum peptide profiles could distinguish women with BRCAl mutations who developed breast cancer from those who did not (Carrier), normal volunteers, and women with sporadic breast cancer with good sensitivity and specificity.²³ To date, no studies employing in-depth nano-LC-MS/MS -based proteomics have focused on BRCA1- deficient tumor tissues.

[0313] In this study, state-of-the-art mass spectrometry based proteomics was employed to identify proteins associated with BRCA1 -deficient breast tumors. To this end, inbred mouse models that display a minimal amount of genetic variability were used. As a model for human breast cancer deficient in BRCA1, mouse mammary tumors harboring

24

conditional tissue-specific mutations in BRCA1 and p53 were analyzed . The majority of these tumors are highly similar to their human counterpart with respect to histological and molecular characteristics and show a high level of genomic instability. For comparison, two BRCA1 -proficient reference tumor models that are genomically stable were analyzed²⁵. A BRCA1 -deficiency signature was elucidated based on 45 proteins with DNA repair- associated) functions that can enrich for homology-directed DNA repair deficient tumors and identify breast cancer patients with a poor prognosis in various publicly available breast cancer gene expression datasets.

[0314] Materials

[0315] All chemicals, unless otherwise specified, were obtained from Sigma (Sigma Aldrich, Zwijndrecht, The Netherlands). HPLC solvents, LC-MS grade water, acetonitrile and formic acid, were obtained from Biosolve (Biosolve B.V., Valkenswaard, The

Netherlands). Porcine sequence-grade modified trypsin was obtained from Promega (Promega Benelux B.V., Leiden, The Netherlands).

[0316] Mouse strains and tumors

[0317] Generation of conditional mutants and K14cre transgenic mice has been described previously²⁴'²⁵. All animal experiments were approved by the Animal Ethics Committee of the Netherlands Cancer Institute (NKI). When grown to a size of

approximately 500 mm³, tumors were dissected, snap frozen and stored at -80 °C until use.

[0318] Tissue homogenization and fractionation using gel electrophoresis

[0319] For homogenization, a piece of mammary tumor tissue, approximately 20 mg in size, was cut in a bath of liquid nitrogen into smaller parts. The proteins in the mammary tumor tissue samples were solubilised in 800 lx reducing Sodium Dodecyl Sulfate (SDS) Sample Buffer (containing 62.5 mM Tris-HCl, 2% w/v SDS, 10% v/v glycerol, and 0.0025% bromophenol blue, 100 mM DTT, pH 6.8) using a Pellet Pestles micro grinder system (Kontes glassware, Vineland, NJ). Subsequently the proteins were denatured by heating at 100°C for 10 min. Any insoluble debris was removed by centrifuging for 15 min at maximum speed (16.1 rcf) in a benchtop centrifuge. [0320] Proteins were fractionated using one-dimensional sodium dodecyl sulfate- polyacrylamide gel electrophoresis (SDS-PAGE). 25 μL· of each homogenized sample (containing about 50 μg protein) was loaded on a well of a pre-cast NuPAGE 4-12% w/v Bis-Tris 1.5-mm minigel (Invitrogen, Carlsbad, CA). The stacking gel contained 4% w/v acrylamide/Bis-Tris. Electrophoresis was carried out at 200 V in NuPAGE MES SDS running buffer (50 mM Tris base, 50 mM MES, 0.1% w/v SDS, 1 mM EDTA, pH 7.3) until the dye front reached the end of the gel. Following electrophoresis, gels were fixed with a solution of 50% ethanol and 3% phosphoric acid. Staining was carried out in a solution of 34% methanol, 3% phosphoric acid, 15% ammonium sulfate and 0.1 % Coomassie Blue G- 250 (Bio-Rad, Hercules, CA) with subsequent destaining in milli-Q water.

[0321] In-gel digestion and nanoLC-FTMS

[0322] In-gel digestion: each of the Gel lanes were cut into 10 individual bands and each band was processed for in-gel digestion according to the method of Shevchenko et al.²⁶. Briefly, bands were washed/dehydrated 3 times in 50 mM ammonium bicarbonate (ABC, pH 7.9) / 50 mM ABC + 50% acetonitrile (ACN). Subsequently, cysteine bonds were reduced with 10 mM DTT (dithiotreitol) for one hour at 56°C and alkylated with 50 mM

iodoacetamide for 45 minutes at room temperature in the dark. After two subsequent wash/dehydration cycles the bands were dried for 10 minutes in a vacuum centrifuge and incubated overnight with 0.06 μg/μl trypsin at 25 °C. Peptides were extracted once in 1% formic acid and subsequently twice in 50% ACN in 5% formic acid. The volume was reduced to 50 μΐ in a vacuum centrifuge prior to LC-MS analysis.

[0323] NanoLC-MS/MS: Peptides were separated by an Ultimate 3000 nanoLC system (Dionex LC-Packings, Amsterdam, The Netherlands) equipped with a 20 cm x 75 μιη ID fused silica column custom packed with 3 μιη 100 A ReproSil Pur CI 8 aqua (Dr. Maisch GMBH, Ammerbuch-Entringen, Germany) as described before²⁷. After injection, peptides were trapped at 30 μΐ/min on a 0.5 cm x 300 μιη ID Pepmap CI 8 cartridge (Dionex LC- Packings, Amsterdam, The Netherlands) at 2% buffer B ( buffer A: 0.05% formic acid in MQ; buffer B: 80 % ACN + 0.05% formic acid in MQ) and separated at 300 nl/min in a 10- 40% buffer B gradient in 60 minutes. Eluting peptides were ionized at 1.7 kV in a Nanomate Tri versa Chip-based nanospray source using a Tri versa LC coupler (Advion, Ithaca, NJ). Intact peptide mass spectra and fragmentation spectra were acquired on a LTQ-FT hybrid mass spectrometer (Thermo Fisher, Bremen, Germany). Intact masses were measured at resolution 50.000 in the ICR cell using a target value of 1 x 10⁶ charges. In parallel, following an FT pre-scan, the top 5 peptide signals (charge-states 2+ and higher) were submitted to MS/MS in the linear ion trap (3 amu isolation width, 30 ms activation, 35% normalized activation energy, Q value of 0.25 and a threshold of 5000 counts). Dynamic exclusion was applied with a repeat count of 1 and an exclusion time of 30 seconds.

[0324] LC-SRM-analyses

Independent B RC A 1 -deficient and -proficient mouse breast tumors (N=5 in each group) were analysed in triplicate on an Ultimate 3000 RSCL Nanosystem (Dionex) that was hyphenated to an QTRAP® 5500 instrument (AB SCIEX, Foster City,CA) operated in positive SRM mode and equipped with a nano-electrospray source with applied voltage of 2.404 kV and a capillary heater temperature of 225 °C. The Nanoflow LC system and QTRAP® 5500 system were both controlled using Analyst 1.5.1 Software. The combined information from each SRM-IDA experiment was used to perform Mascot searches against the IPI-mouse database v3.65 and MultiQuant™ software version 2.1 (AB SCIEX, Foster City, CA).

[0326] The scheduled SRM mode comprised the following parameters: SRM detection window of 420 sec, target scan time of 3.0 s, curtain gas of 15, ion source gas 1 of 15, declustering potential of 80, entrance potential of 10. Ql resolution was set to unit and Q3 resolution to unit. Pause between mass ranges was set to 1 ms. Collision cell exit potentials (CXP)was set to 36 for all transitions. Peak integration was performed using MultiQuant™ software version 2.1 (AB SCIEX, Foster City, CA) software and manually reviewed.

[0327] Chromatographic separation of peptides was performed by a 68 min gradient at 300 nL/min. Solvent A (0.05% formic acid water) and solvent B (0.05% formic acid, 80% acetonitrile) were mixed at 2%B from 0-3 min, 15%B at 4 min, 36%B at 49 min, 99%B from 50-54 min, 2%B at 55-68 min. The nano-LC columns were made in house and consisted of 20 cm x 75 μιη ID fused silica custom packed with 3 μιη 100 A ReproSil Pur C18 aqua (Dr Maisch GMBH, Ammerbuch-Entringen, Germany) as described before²⁷. After injection, peptides were trapped at 6 μΐ/min at 2% buffer B.

[0328] SRM assay development An SRM assay for the target proteins (NCAPD2, SIN3A, BAZ1B, TOP2A, TOP2B, PARP1) was developed using the MRMPilot™ software version 2.1 from AB SCIEX (Concord, ON, Canada). The software requires an amino acid sequence of the protein of interest, a starter method containing the LC conditions and an empty SRM-IDA experiment. The software performs an in-silico digest of the protein and creates a set of peptides that would result after full tryptic digestion. For each of these peptides, it will generate an SRM transition for the calculated m/z of the precursor ion and an appropriate fragment ion. Assay development subsequently entails Verification of the peptides and CE-optimisation of the transitions, both in multiplexed LC-SRM analyses. During verification, the highest responding peptides/transitions at a theoretically calculated optimum CE-energy are determined, as well as the identity of the peptide via SRM triggered MS/MS. During CE-optimisation, the transitions selected after verification are optimised during the chromatographic elution of the peptide.

[0329] Verification A mixture of samples previously analysed using FTMS and indicating abundance of the target candidates was analysed in 10 unscheduled SRM analyses to find the highest responding tryptic peptides from the target proteins, as well as their elution time during the chromatographic run. For each peptide, 10 theoretically predicted transitions were assessed for detection response and identity. Identity was confirmed using MIDAS (MRM Initiated Detection And Sequencing) with a threshold of 500 counts for an SRM transition response to trigger 2 MS/MS spectra of the peptide to be acquired at rolling collision energy. Each of the 10 verification analyses was set up to detect 289 of all theoretically predicted transitions and their theoretically predicted optimum collision energy for all theoretically predicted peptides that can result after tryptic digestion of the candidate proteins. The total scan time for each cycle of the instrument during verification was 3.757 seconds, resulting in a dwell time of 10 ms for each transition in the unscheduled verification analyses.

[0330] CE-optimisation All data of unscheduled analyses were uploaded to the MRMPilot, which was set to select the five best detected transitions for each peptide and assign a chromatographic retention time to each peptide. Subsequently collision energy for each transition was optimised in 13 LC-SRM-analyses, each analysis set-up to detect 104 scheduled transitions that resulted from verification, at 9 different collision energies, centered at 3 Volt intervals around the theoretically predicted optimum with a dwell time of 25ms. All data of CE-optimisation cycles were uploaded to the MRMPilot and for each peptide three transitions at the experimentally found optimum and the experimentally found retention time were included in the final assay.

[0331 ] The final assay contained 129 scheduled transitions, 3 for each peptide, 1-5 peptides for each of the 7 candidate proteins.

[0332] Data analysis

[0333] Protein identification: MS/MS spectra were searched against the human IPI database 3.31(67,511 entries) using Sequest (version 27, rev 12), which is part of the Bio Works 3.3 data analysis package (Thermo Fisher, San Jose, CA). MS/MS spectra were searched with a maximum allowed deviation of 10 ppm for the precursor mass and 1 amu for fragment masses. Methionine oxidation and cysteine caboxamidomethylation were allowed modifications, 2 missed cleavages were allowed and the minimum number of tryptic termini was 1. After database searching the DTA and OUT files were imported into Scaffold 1.07 (Proteome software, Portland, OR). Scaffold was used to organize the gel-band data and to

28 '29

validate peptide identifications using the Peptide Prophet algorithm ' . Only identifications with a probability >95% were retained. Subsequently, the Protein Prophet algorithm was applied and protein identifications with a probability of >99% with two peptides or more were retained in at least one sample. False discovery rate for the detected proteins using this workflow is on average around 0.5%, and was not calculated again. Proteins that contained similar peptides and could not be differentiated based on MS/MS analysis alone were grouped to satisfy the principles of parsimony. For each protein identified, the total number of MS/MS spectra detected for each protein identified (spectral counts) was exported to Excel 2003 (Microsoft, Redmond, USA).

[ 0334 ] Spectral count normalization and statistics: Normalization was performed as

30'31

described previously ' . The spectral counts of each protein were divided by the total spectral counts of all proteins within a sample. This number was multiplied with a constant equal to the average of total spectral counts of all samples to obtain a normalized spectral

30 count value in the same range as the non-normalized spectral counts. The beta-binomial test was applied to find proteins that show significant differences in spectral count numbers between the tumor group and the reference group. Proteins with a p-value less than 0.05 were designated as being significant. Hierarchical clustering was carried out using R. For analysis of reproducibility, we calculated the average coefficient of variation (CV) of the normalized spectral counts from overlapping proteins for three technical replicates.

[0335] SRM data analysis Technical replicates were removed until % CV of all triplicate analysis was < 20%. Subsequently in each remaining analysis, the ratio of the AUC of Transitionl/Transition2, Transition 2/Transition3 and Transitionl/Transition3 was calculated. The two transitions resulting in the lowest % CV over all analyses were selected for further calculations; the sum of the AUC of these two transitions was determined in each sample and a fold change for each peptide between the groups was determined by the ratio of the summed AUC in each group. The average of the fold changes of peptides belonging to one protein were determined for each protein. When the % CV of the average of the fold changes of the peptides of one protein was >10%, the transitions of these peptides were visually inspected and excluded when co-eluting false positive responses were observed that had not been detected by Multiquant smoothing and peak splitting algorithms or in-house developed R-script processing. The calculated levels for each approved peptide were normalised on the level of Tubalb in each sample.

[0336] Pathway analysis: The list of identified proteins was uploaded into the Ingenuity Pathways Analysis (IP A) software (Ingenuity Systems, Redwood City, CA) as a tab-delimited text file containing IPI accession numbers, /^-values and fold changes calculated with a correction factor (adding 0.5 to the spectral counts of all proteins before

normalization). Proteins were uploaded and mapped to corresponding "gene objects" in the Ingenuity Pathways Knowledge Base. Functional analysis was performed to identify the high level biological functions that were most significantly associated to the differentially regulated proteins in the dataset. Significantly regulated proteins within the high level functions are displayed graphically as nodes (proteins/gene objects) and edges (the biological relationships between the nodes). All edges are supported by at least one reference from the literature, textbook or canonical information stored in the Ingenuity knowledgebase.

Ingenuity Pathways Analysis computes one or more p- values for each specific function within a high level function according to the fit of the user's set of significant proteins. The significance of functional enrichment is computed by a Fisher' s exact test. Finally, the Path Designer feature was used to create graphically rich network images. In addition, the COFECO tool was used for the mapping of significantly differentially regulated proteins to protein complexes³². The obtained complexes were further visualized using STRING ³³ and Cytoscape, respectively.

[0337] Human gene expression datasets

[0338] Identifier mapping of mouse protein symbols to human gene symbols of public gene expression datasets: To explore the diagnostic and prognostic value of the protein expression data from the mouse models, publicly available human gene expression datasets were used. To map the up-regulated mouse BRCA1 -deficiency proteins to public datasets of human arrays, first mouse gene symbols were matched to human gene symbols using the BioMart website (http://www.biomart.org). Layout documentation files for the various microarray platforms were used from Gene Expression Omnibus

(http://www.ncbi.nlm.nih.gov/geo), MIAMExpress (http://www.ebi.ac.uk/miamexpress/) or Rosetta Inpharmatics (http://www.rii.com/publications/default.html/) to retrieve the matching gene symbols on each platform. The following human breast cancer datasets were used:

[0339] 1. Van de Vijver dataset¹². A validation study of a prognostic gene expression signature (MammaPrint®), which included 295 young patients with early stage breast cancer, of which 151 were lymph node negative, 226 were estrogen receptor-positive, and 110 had received adjuvant chemotherapy. p53 mutational status for 204 tumors was also retrieved from this dataset.

[0340] 2. Van't Veer dataset¹. In this discovery study for a prognostic signature (MammaPrint®), the authors analyzed 18 BRCAl and 2 BRCA2 samples on the same platform used for the Van de Vijver dataset¹².

[0341] 3. E-UCON-1 dataset ¹⁰ (subsequently referred to as the Naderi dataset). This dataset was used for discovery of a prognosis profile in a set of women with early stage breast cancer representative of breast cancer demographics. Out of the 132 breast cancer tissues, a subset of 120 patients was used for survival analysis that had the same orientation in dye labeling concerning the reference and tumor samples and which also had associated survival data.

[0342] 4. GSE2034 dataset³⁴ (subsequently referred to as Wang dataset). This was a discovery and validation analysis of a gene signature for the prediction of breast cancer patient outcomes. It consists of 286 lymph node-negative breast cancer patients who never received adjuvant chemotherapy and of which 209 were estrogen receptor-positive. The normalized intensity values were logged; zero mean and unit variance normalization were also performed.

[0343] 5. GSE22133 dataset⁸ (subsequently referred to as the Jonsson dataset). This discovery dataset consists of 359 breast tumors including 186 familial of which 22 were BRCAl -mutated, and 32 were BRCA2 mutated.

[0344] 6. GSE19177 dataset¹⁴ (subsequently referred to as the Waddell dataset). This dataset contains familial tumors only. 19 had a BRCAl mutation, 30 had a BRCA2 mutation while 25 did not have an identifiable mutation. One tumor was excluded from analysis because it had unknown mutational status.

[ 0345] For all datasets, normalized log ratios were used in the analyses, unless specified otherwise above.

[0346] Centroid classification and survival analysis

[0347] A nearest centroid classifier was used to test the diagnostic and prognostic power of the mapped protein/gene signature on the public human gene expression datasets in combination with leave-one-out-cross-validation (LOOCV). First, the signature protein/genes in the validation sets were identified. A centroid classification scheme was used to assess BRCAl and homology-directed DNA repair deficiency, whereby centroids were built by taking the average expression value for each signature gene in the diagnostic groups, excluding the leave-out sample. The leave-out samples were then classified into different diagnostic groups using the nearest correlation criterion. For classification with a centroid on external datasets, genes were collapsed by taking the median across all probes. This centroid classification scheme was also used for classifications in the Kaplan-Meier survival analysis. In all datasets, patients who survived 5 years or more constituted the good prognosis group (centroid), while patients who survived less than 5 years were used for the poor prognosis group (centroid)¹⁰'¹²'³⁴. The average expression value for each signature gene in the good and poor prognosis centroid was computed without the leave-out sample. The leave-out samples were then classified into good or poor prognostic groups using the nearest correlation criterion. To see if a gene list performed better than random, both in the diagnostic and in the survival analysis, an analysis with 1000 random gene lists of the same size using the same scheme was run. Probes were only included on the arrays which were annotated with a gene symbol. The same scheme was applied for the prognostics mRNA based signatures used as a comparison.

[0348] Results

[ 0349] Protein regulations in BRCA1 -deficient versus proficient mouse mammary tumors

[0350] For comparative protein profiling, a label-free workflow was employed based on protein fractionation by gel electrophoresis coupled to nanoLC-MS/MS of in-gel digested proteins and spectral counting. Before embarking on a differential analysis, the

reproducibility of the discovery workflow was assessed by analyzing three aliquots of a pooled mammary tumor lysate by Gel-LC-MS/MS. In this analysis, 2,220 of 2,473 proteins (90%) were identified in all 3 replicates with an average CV of 24% of the normalized spectral counts, indicating a very good reproducibility of the entire discovery workflow.

[0351] To identify proteins associated with BRCAl-deficient mammary tumors, the protein expression profiles in 5 BRCAl-deficient mammary tumors (p53^' ;BRCAV ^', carcinoma histology) was compared with 5 BRCA1 -proficient tumors (two p53^' and three p53^~/~;CDH ^/~ tumors, all carcinosarcomas). Whereas the carcinomas have an epithelial phenotype, the carcinosarcomas have a mesenchymal phenotype characterized by spindle cell morphology. The protein band patterns obtained after gel electrophoresis of the 10 tumor lysates and coomassie staining were similar in terms of overall pattern and intensity. A total of 3,545 proteins were identified across all 10 samples. The number of proteins identified in the BRCAl-deficient tumor samples was 3,409, with 1,894 proteins identified in all 5 mammary tumors indicating acceptable reproducibility of protein identification and quantification across different biological samples. Similar values were obtained for the five BRCA1 -proficient tumors.

[0352] To obtain a global overview of the dataset, unsupervised hierarchical clustering was performed using the normalized spectral count data from all 3,545 identified proteins. The BRCA1 -deficient and proficient tumors clustered in separate groups. The two different BRCA1 -proficient tumor types (p53^' and p53^~/~;CDH ^/~) did not form two separate groups, but were intermingled, indicating that BRCA1 status and/or histology type were the predominant factors separating the samples. Overlap analysis showed that 338 proteins were uniquely identified in the BRCA1 -deficient samples and 136 uniquely identified in the

30

B RCA 1 -proficient tumors. Statistical testing revealed 801 proteins with significantly altered abundance in the BRCA1 -deficient and proficient groups (p<0.05), of which 417 were up- regulated in the BRCA1 -deficient tumors, while 384 were down-regulated. Supervised hierarchical clustering using the 801 differential proteins clearly showed two different groups that clustered according to BRCAl/cell type status. For integration with transcriptomics, the dataset of Liu et al. was employed containing gene expression data for the same BRCA1- proficient and deficient mouse models as used in this study, with the exception that most of the tumors in the discovery set were mammary carcinomas. Of the 801 differential proteins, mRNA expression data was retrieved for 565 proteins, of which 429 (76%) had the same direction of differential expression with 201 of these mRNAs (36%) being significantly differentially expressed.

[0353] In summary, a large proportion (23%) of the mammary tumor tissue proteome is regulated in BRCA1 -deficient tumors as compared to proficient tumors. Because a large fraction of proteins showed co-regulation with a transcriptomics dataset that only used BRCA1 deficient carcinomas versus BRCA1 proficient carcinomas, the differential proteins are related mainly to BRCA1 status and only partially to cell type.

[0354] Identification of known markers of human BRCA1 -deficient breast cancer

[0355] Since B RC A 1 -deficient breast tumors often belong to the highly proliferative basal-like subtype, the abundance of protein markers known in basal-like breast cancer were examined in the dataset. In addition, known markers of human BRCA1 -deficiency were sought out. Two basal cytokeratin markers (Krtl4 and Krt6b) were significantly up-regulated in the BRCA1 -deficient mouse tumors. The third cytokeratin (Krt5) was up-regulated (p- value = 0.066) with a fold-change of 3.2. ALDH1 , a cancer stem cell marker, was exclusively detected in BRCA1 -deficient mouse tumors, in accordance with previous findings³⁵. PCNA and KI67, two well-known proliferation markers , were also significantly up-regulated in the BRCA1 -deficient mouse tumors.

[0356] These confirmatory findings underscore the value of these genetic mouse tumor models and the validity of the proteomics approach disclosed herein to identify proteins associated with BRCA1 -related or basal-like breast cancers in patients.

[0357] DNA repair pathways and protein complexes are associated with proteins up-regulated in BRCA1 -deficient mammary tumors

[0358] To associate biological functions with the differentially expressed BRCA1- deficiency proteins of the mouse mammary tumors, the software tool "Ingenuity Pathway Analysis" was used. The "Molecular and Cellular-functions" associated with the up-regulated proteins in BRCA1 -deficient mammary tumors were determined, with the number one function identified as "DNA Replication, Recombination, and Repair" (61 proteins). The network created using Ingenuity contained a number of highly connected nodes (i.e.

proteins), among which several are well-established drug targets (i.e. , TOPI, TOP2A, PARPl and SRC). The top "Molecular and Cellular function" associated with the down-regulated proteins was "Cellular Movement." The 61 DNA repair proteins up-regulated in BRCA1- deficient mammary tumors were involved in sub-functions like excision repair, chromatin remodeling and modification, double-strand DNA repair and DNA damage response, amongst others. Moreover, canonical pathways associated with the up-regulated proteins in BRCA1 -deficient tumors were involved in DNA repair, including "ATM signalling","P53 signaling" and "Role of BRCA1 in DNA damage response."

[0359] To identify protein complexes underlying the differential proteins and to further dissect the DNA repair pathways, the COFECO tool³² was employed. The up- regulated proteins were linked to 53 significant protein complexes (corrected p- value <0.05), of which 44 have a DNA repair(-associated) function. After removing the redundant protein complexes, where all members were present in one of the other significant complexes, 29 DNA repair(-associated) complexes were obtained. The DNA repair complexes were involved in chromosome condensation, chromosome cohesion, chromosome remodeling, RNA processing, histone methylation, histone acetylation and the topoisomerase complex, amongst others. Five complexes were also identified that could not be readily linked to a physiological process involved in DNA repair. These non-nuclear complexes were involved in integrin cell-surface interactions with laminins and collagens. Although these complexes have been implicated in evading apoptosis after DNA damage³⁷, these non-nuclear complexes were not included for further analysis. The down-regulated proteins in BRCA1 -deficient tumors were not associated with any DNA repair protein complex in a COFECO analysis, but instead revealed complexes involved in integrin signaling, cytoskeleton regulation and extracellular matrix (ECM) signalling, amongst others.

[0360] Subsequent analyses focused on the proteins up-regulated in BRCAl - deficienct tumors with a link to DNA repair, as it was hypothesized that the up-regulation of DNA repair proteins and pathways is linked to BRCAl status and reflects a compensatory response to the loss of BRCAl DNA repair function. The 29 non-redundant DNA repair protein complexes associated with the up-regulated proteins in the BRCAl -deficient tumors were visualized using Cytoscape. Based on this analysis, it was apparent that many protein complexes had multiple up-regulated members. Examples of DNA repair(-associated) complexes included the BRCAl Associated Complex (BASC), involved in double- stranded DNA repair³⁸ and the Condensin I-PARP1-XRCC1 complex with established functions in single-strand DNA repair³⁹. In addition, 5 out of 7 members of the toposome complex including the drug targets TOPI and TOP2A were significantly up-regulated⁴⁰. Moreover, many chromatin remodeling complexes, with a wide involvement in different types of DNA repair processes⁴¹, were highly prevalent in the dataset. Examples included the WINAC complex, the PBAF complex, the SWI/SNF complex, the GCN5-TRRAP histone acetyl- transferase complex and the DNMT3B histone methylation complex.

[ 0361 ] Together, the analyses point to a major up-regulation of a broad range of DNA repair/chromatin remodeling pathways and protein complexes in BRCAl -deficient mammary tumors.

[0362] Identification of a BRCAl -deficiency DNA repair signature

[0363] To identify a protein signature with biological relevance for BRCAl -deficient breast tumors, it was determined that the signature should represent the range of up-regulated DNA repair processes in these tumors and therefore contain selected up-regulated members of each of the 29 non-redundant protein complexes described above. To this end, the most connected up-regulated node in each of the 29 DNA repair protein complexes were selected. This strategy had the advantage of yielding multiple proteins per protein complex, since some nodes show the same level of connectivity. Using this strategy, a BRCAl-deficiency signature of 45 proteins was obtained (Fig. 2). The signature includes PARP1, involved in single-strand base repair; TRRAP, a large adaptor protein involved in histone acetylation; TOP2A, a topoisomerase; SMC1 A and SMC4, involved in chromatid cohesion and condensation; BAZ1B and ATM, involved in phosphorylation of H2AX upon DNA damage; MSH2 and MSH6, involved in mismatch repair. [0364] Up-regulated proteins mapped to human transcripts identify human BRCAl/2 deficient tumors

[0365] To investigate the power of the 45 protein BRCAl -deficiency signature in separating BRCAl -deficient breast cancers from BRCAl -proficient breast cancers in humans in comparison with all up-regulated proteins, an in silico analysis was performed using publicly available gene expression datasets, as disclosed herein. Additionally, the specificity of the 45 protein BRCAl -deficiency signature for BRCA2, a gene involved in the same pathway as BRCAl, was investigated to examine the ability of the signature to identify deficiency in homology-directed DNA repair in general⁴². This is important because of the recent availability of drugs targeting this particular deficiency⁴³.

[0366] The Jonsson dataset containing 22 BRCAl and 32 BRCA2-mutated tumors and other familial and sporadic tumors was utilized first, since this whole genome gene expression dataset contained the largest number of BRCAl/2 mutated tumors. Hierarchical clustering using all up-regulated proteins showed that the majority of BRCAl-mutated tumors were clustered within one branch of the resulting dendrogram, which coincides with the basal-like tumors. The BRCA2 samples were also clustered largely together within the middle branch of the dendrogram. A clustering using the BRCAl -deficiency signature was also determined. In the resulting dendogram, a large proportion of the BRCAl and BRCA2 fall within one branch of the dendrogram, making up approximately one third of the tumors. Thus, the cluster analysis indicates that the 45 protein BRCAl-deficiency signature shows specificity, not only for BRCAl-mutated tumors, but also for BRCA2 mutated tumors.

[0367] The nearest centroid classification method was employed to characterize more precisely the sensitivity and specificity of the mouse BRCAl-deficiency signature for BRCAl and BRCA2-mutated tumors, as well as for the list of all up-regulated proteins. The classification results on the Jonsson dataset with leave-one-out cross validation (LOOCV) indicate that the sensitivities for BRCAl-mutated tumors were 77% and 82% for the 417 up- regulated proteins and the BRCAl-deficiency signature, respectively. Classification for the combination of BRCAl and BRCA2-mutated tumors yielded a similar performance, 83% sensitivity for all up-regulated proteins and 81 % for the BRCAl-deficiency signature. The performance of 1,000 sets of genes randomly sampled from the whole genome was also assessed and, in a more stringent approach, from the list of "DNA replication, recombination and repair" genes as defined by IPA. The BRCAl-deficiency signature compared favorably to both random gene lists sampled from all genes and from random DNA repair lists, showing confidence in the classification accuracies. [0368] In addition to LOOCV, completely independent validation was performed using the two other datasets containing samples with BRCAl/2 mutation status (the combined Van de Vijver and Van 't Veer cohorts and the Waddell cohort). The centroids constructed from the Jonsson et al. dataset can classify BRCAl/2 samples in the Van de Vijver/Van't Veer cohorts with a very high sensitivity of 95% for both the up-regulated proteins and the BRCAl -deficiency signature. For the Waddell cohort, we obtained sensitivity of 79% and 68% for BRCAl patients by the up-regulated proteins and BRCA1- deficiency signature respectively, which is comparable with the result of 74% sensitivity reported by the authors of the dataset. Our result is significant given that the test data is completely independent from the training data, whereas internal validation was used in Waddell et al.¹⁴.

[0369] These data show that the 417 up-regulated proteins in BRCAl -deficient mouse tumors, as well as the BRCAl -deficiency signature of 45 proteins, can classify human BRCAl -deficient breast tumors when mapped to human transcriptomics datasets.

Importantly, the classification results for the mapped mouse BRCAl deficiency protein signature were better than the results that we obtained with the published mouse

24

transcriptome data from which we also constructed a signature using the same network- based, in silico approach. For example, sensitivities of the protein signature for selecting BRCAl deficient tumors were 81.8%, 94.4 %, and 68.4% in the Jonsson, combined Vijver and Van 't Veer and Waddell datasets, whereas these values were 63.6%, 50.0% and 57.9% for the transcriptome signature. The set of all up-regulated proteins achieved the best performance for diagnosing BRCAl mutations in comparison to random (DNA repair) genes. BRCA2-deficient tumors were also classified, implying enrichment for homology-directed repair-deficient tumors in general. Moreover, the 45 protein signature and all up-regulated proteins also classify a number of familial tumors without BRCAl/2 mutation and sporadic patients as BRCAl/2-like, suggesting that these tumors might be deficient in homology- directed DNA repair.

[0370] BRCAl-deficiency signature proteins show prognostic power when mapped to human breast cancer gene expression datasets

[0371] In order to investigate if the BRCAl-deficiency proteins and signature have prognostic power, the mapped mRNAs of the up-regulated proteins in the four public breast cancer gene expression datasets which have associated clinical end-point data were utilized (Van de Vijver, Wang, Naderi and Jonsson⁸'¹⁰'¹²'³⁴) to perform a Kaplan-Meier survival analysis. The Jonsson dataset was the only cohort that has an enrichment of familial (BRCAl/2 -related) patients. For comparison, a Kaplan-Meier analysis was also performed using two commercially available prognostic gene signatures (MammaPrint^® and Oncotype DX^®). In a third comparison, the Naderi signature (discovered in the Naderi cohort) that has been shown to also have prognostic power in both the Van de Vijver and Wang cohorts¹⁰ was used.

[0372] The mapped list of all 417 up-regulated proteins in BRCA1 -deficient tumors yielded highly significant p- values for survival analysis across all datasets, but these were only significantly better than random gene lists in the Van de Vijver dataset. When sampling from a DNA repair gene background, no significant p- values for the permutation analysis were obtained. It is of note here that the external (commercial) gene expression-based signatures in some instances showed a similar level of underperformance when compared to random DNA-repair gene lists in the sporadic datasets and were performing non-significantly in all permutation settings in the Jonsson cohort. Not surprisingly, the two mRNA signatures identified within their discovery cohort, (MammaPrint® in the Van de Vijver cohort¹'¹², and Naderi signature in the Naderi Cohort¹⁰), outperformed all other signatures within their cohort.

[0373] The mapped BRCA1 -deficiency signature has highly significant prognostic value. Performance was comparable to the gene expression-based signatures in the three sporadic cohorts (the Van de Vijver, Wang and Caldas datasets). Importantly, in the dataset with an overrepresentation of familial (BRCAl/2) tumors (the Jonsson cohort), the mapped mouse BRCA1 -deficiency signature outperformed all human gene expression-based signatures, and performance was still significant when compared to random (DNA-repair) gene lists.

[0374] In summary, these data demonstrate that the mouse BRCAl-deficiency protein signature, when mapped to human gene expression data, has prognostic value and outperforms (commercial) gene expression-based signatures in a cohort enriched for breast cancer with defects in the homology-directed DNA repair pathway.

[0375] Poor outcome human breast tumors identified by BRCAl-deficiency signature show enrichment in p53 mutations

[0376] p53 mutations have the capacity to disrupt the signaling between accumulated

DNA damage and the induction of apoptosis. Moreover, loss of functional p53 is often associated with BRCA1 -related hereditary breast cancer in humans⁴⁵'⁴⁶. For this reason, the poor prognosis patients identified in the survival analysis were investigated to determine if they showed a significant enrichment for p53 mutations. For the Van de Vijver cohort, p53 mutational status was retrieved for 204 of the 295 tumors. Enrichment of p53 mutation in the poor prognosis patients was assessed using the Fisher's exact test. Both the total list of 417 up-regulated proteins and the B RC A 1 -deficiency signature showed a highly significant enrichment for p53 mutations in poor prognosis patients (both p-value < 10^"10).

[0377] These data highlight the finding that the BRCA1 -deficiency proteins and signature associate with p53 mutation as well as with survival.

[0378] Protein quantitation by targeted mass spectrometry

[0379] Several proteins were selected for follow-up at the protein level: 4 genes/ proteins that showed discordant regulations: significantly up-regulated protein levels and down-regulated mRNA expression levels (NCAPD2, SIN3A, BAZ1B, TOP2B) in the

BRCA1 deficient breast tumors of the mouse model. One gene was also included for which no probe was available on the microarray (TOP2A) and one protein for which protein and mRNA regulation was concordant (PARP1) in the mouse model. Of these gene products, SIN3A and TOP2B had also down-regulated mRNAs in the human dataset of Jonsson, whereas PARP1 was not regulated, TOP2A was upregulated and for NCAPD2 and BAZ1B no probes were available. First, the protein regulations as revealed by the spectral count data in the discovery samples were confirmed using an independent measure of label-free protein quantitation i.e., the area under the curve of the extracted ion chromatograms. Second, targeted mass spectrometry was performed by SRM-MS in 10 independent mouse breast tumors, all carcinomas. The regulation of SIN3A, NCAPD2, TOP2A, TOP2B and PARP1 was confirmed by SRM-MS in independent tumors, with all peptides being significantly up- regulated in BRCA1 deficient breast tumors whereas only BAZ1B was not significantly up- regulated. Hierarchical clustering using all peptides from the discordant proteins clearly separated this pilot validation set according BRCA1 status.

[0380] In conclusion, the SRM validation of protein expression levels for which the

RNA levels were discordant underscores the fact that RNA expression levels cannot always be simply translated to protein expression levels as well as the importance of analysis of the end products of genes by proteomics.

[0381] Discussion

[ 0382 ] The present study aimed to identify proteins that are associated with the loss of expression of BRCA1, which is involved in homology-directed DNA repair. These proteins could potentially find use as screening, prognostic or predictive biomarkers. To this end, protein profiles in BRCA1 -proficient and deficient mouse breast tumors were analyzed using a high-resolution tandem mass spectrometry-based proteomics approach. Using this approach, 3,545 proteins were identified, of which 801 were significantly differentially regulated. A BRCAl -deficiency 45 protein signature was defined through the use of pathway and protein complex analysis, with good performance in human gene expression datasets enriched for BRCAl deficiency. This is the first comprehensive in-depth proteomics analysis in genetic breast cancer.

[0383] Up-regulated proteins in BRCAl -deficient mouse breast tumors contain basal like markers, multiple drug targets and DNA repair(-associated) proteins

[0384] Significant up-regulation of basal-like markers that are known to occur in breast cancer of the basal-like subtype was found. This is in line with the fact that human BRCAl -mutated tumors belong predominantly to the basal-like breast cancer subtype. These confirmatory findings underscore the human relevance of the BRCAl -deficient mouse tumor models. BRCAl has recently, through its function as a transcription factor, been linked to the basal transcription machinery, whereby functional BRCAl represses transcription of basal keratins⁴⁷. In addition, a number of up-regulated proliferative markers were identified, a feature that is more prevalent in human basal-like breast cancer.

[0385] Pathway and protein complex analysis identified DNA repair and associated processes as the most important biological function associated with the up-regulated proteins of the BRCAl -deficient tumors. This is in line with previous reports that loss of functional homology-directed DNA repair through knock-out of BRCAl might be partially

42 '48

compensated for by other DNA repair mechanisms ' Importantly, a number of therapeutic targets were found to be up-regulated in the BRCAl -deficient tumors, including PARP1, TOPI , TOP2A and TOP2B. PARP1 has been shown to be a bona fide drug target for human BRCAl -mutated tumors⁴³. Up-regulation of the PARP1 protein may be a marker for the loss of functional homology-directed DNA repair in general, and might therefore be a predictive marker for the efficacy of PARP1 inhibition. In line with this, the tumors of the BRCAl - deficient mice used in this study responded well to the PARP inhibitor olaparib, whereas the BRCAl -proficient mouse tumor models did not⁴⁹. Moreover, up-regulation of the topoisomerases TOPI , TOP2A and TOP2B was also found, which are drug targets for topotecan (TOPI inhibitor) and doxorubicin (TOP2A and TOP2B inhibitor). These drugs inhibit the re-ligation step of topoisomerases and therefore also induce indirectly DNA breaks. Higher levels of these proteins might have predictive value, since the BRCAl - deficient mouse tumors used in the present study have been shown to be sensitive to topotecan⁵⁰ and doxorubicin⁵¹. A number of other potential drug targets were also detected. HDAC 1 and HDAC2, two proteins involved in chromatin remodeling by histone acetylation, were also up-regulated, although this was not significant (p=0.07 and p=0.14, respectively). At least 11 kinases were significantly up-regulated, of which established drug targets included KIT and SRC (IPA drug targets). Novel kinase candidate drug targets included MAPK14, CDK9 and CSFR1. Multiple proteins up-regulated in the BRCAl-deficient mice tumors act upstream of BRCAl function in the homology-directed DNA repair pathway (ATM, BAZ1B, and TP53BP1), which may indicate an accumulation of these proteins in

24

response to BRCAl loss. In a previous study, Liu et al. have used gene expression analysis in the same mouse models as used in this study. Using gene set enrichment analysis, they reported a number of processes that were induced after BRCAl loss, including

recombinatorial repair, mitotic recombination, telomere maintenance and transcriptional regulation (e.g. chromatin remodelling).

[0386] Mouse BRCAl-deficiency protein signature with diagnostic and prognostic value in human gene expression datasets

[0387] An in silico validation approach was used to show that mouse proteins up- regulated in BRCAl-deficient tumors, including a BRCAl-deficiency signature, could classify human BRCAl and BRCA2 tumors in cohorts that contained both sporadic and hereditary breast cancers. Using the BRCAl-deficiency signature, high sensitivities were achieved for classifying homology-directed DNA repair deficient tumors in datasets known to be enriched for these patients¹⁴. The BRCAl-deficiency signature also classified a considerable number of sporadic and familial tumors as BRCAl/2-like. This result may be explained by the possibility that a number of sporadic and familial tumors lacking mutations in BRCA genes might still harbor undetected deficiencies in homology-directed DNA repair, and might therefore benefit from treatment with DNA-damaging agents. There is growing evidence that the majority of sporadic basal-like breast cancer have BRCAl dysfunctionality other than a mutation in BRCAl itself^9;13.

[0388] The BRCAl-deficiency DNA repair signature showed prognostic power across a wide variety of breast cancer datasets. Moreover, the mouse protein signature outperformed two commercially available prognostic RNA-based signatures (MammaPrint^® and Oncotype DX^®) in a dataset enriched for homology repair-deficient tumors. Finally, in breast cancer, proteins with prognostic power may have predictive value as well. Examples are the hormone receptor ESR1 and the receptor tyrosine kinase ERBB2, the expression of which predicts response to targeted therapy as well as prognosis⁵⁴.

[0389] Furthermore, patients with sporadic breast cancer identified as poor outcome by the BRCAl-deficiency signature were highly enriched for p53 mutations. Although both mouse models used to develop the BRCAl -deficiency signature were p53 deficient, this result is explained by the clinical observation that BRCAl -deficient breast cancers frequently comprise p53 mutations, and both BRCAl and p53 alterations are enriched in triple-negative breast cancer⁴⁵'⁴⁶. The up-regulation of drug targets involved in DNA repair (PARP1, TOPI, TOP2A and HDAC1), may indicate the predictive potential of the BRCAl -deficiency DNA repair candidates.

[0390] Several breast cancer proteomic studies have been reported to date. Biological materials used ranged from mouse tissue²¹'⁵⁵, human breast cancer cell lines and

tissues¹⁸'²⁰'²¹'^56"58. A few studies yielded a number of markers with potential for treatment prediction. Umar et a/.¹⁹ have recently identified a protein profile in microdissected breast tumor cells putatively predictive for the efficacy of tamoxifen. Moreover, the differential up- regulation and activity of a number of kinases across a panel of breast cancer cell lines correlated with differential responsiveness to small molecule inhibitors in these cancer cell lines⁵⁹.

[0391] This study demonstrates that in-depth high-resolution proteomics of tumor tissues from different mouse models is a successful strategy to discover candidate protein biomarkers with screening, prognostic and possibly also predictive potential for human BRCAl and homology-directed DSB repair deficient breast tumors. The proteins up- regulated in mammary tumors from mouse models with a deficiency in BRCAl are enriched in DNA repair(-associated) proteins, which points towards a potential rescue mechanism for the loss of homology-directed DNA repair. In addition, pathway in conjunction with protein complex analysis has proven to be a promising strategy to construct a signature that has diagnostic and prognostic potential across multiple human breast cancer gene expression datasets. This signature shows specificity for BRCAl and homology-directed DNA repair deficiency and has high prognostic potential in breast cancer datasets enriched with homology repair deficient tumors. Several up-regulated DNA repair proteins within this signature have been shown to be drug targets in "homology-directed DNA repair"-deficient tumors, suggesting that they may have predictive power for tailored therapies. Since multiple drug targets are up-regulated, these tumors might also benefit from combination therapy.

[0392] The BRCAl deficiency transcriptome signature that was obtained by mapping mouse BRCAl deficiency associated breast tumor proteins is novel and could not be obtained by using the published mouse transcriptome data²⁴ as a starting point. To date, there is only one BRCAness gene expression signature reported for ovarian cancer⁶⁰. However, this signature was developed using a publicly available ovarian cancer

transcriptomics dataset and with a pilot study for predictiveness based on only 10 BRCA mutated/reverted samples originating from 6 patients and this signature was not externally evaluated in multiple large (BRCA 1/2 deficient) breast cancer datasets. Together this underscores the utility of the BRCAness transcriptome signature that was obtained by mapping mouse BRCA1 deficiency associated breast tumor proteins.

[0393] References

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Example 2

In silico analysis of BRCA1 -deficiency protein signatures

[0454] Computational analysis

[0455] The Jonsson dataset consists of 359 samples, each with 8,558 gene probes. The dataset was pre-processed as follows: a single quantitative value of each gene was determined by taking the median value of its probes. This resulted in expression values of 8,050 genes. Each of the 359 samples belonged to one of 4 groups: BRCA1 (n = 22), BRCA 2 (n = 32), familial (n = 132), and sporadic (n = 173).

[0456] The centroid classification method was used. Four centroids were created for the four groups by averaging training samples in each group. To classify a new sample, its distances to the four centroids were computed, and subsequently, the new sample was assigned to group of the closest centroid. The Spearman distance was used.

[0457] To evaluate performance, the leave-one-out method was used. Each sample in the dataset was subjected to a classifier built using the remaining samples. In addition, the error in classifying the BRCA 1/2 group versus familial and sporadic combined was considered.

[0458] To evaluate the performance of a particular signature, the genes in the Jonsson dataset were mapped to the signature using symbol matching by name.

[0459] The performance of the 45-protein signature depicted in Fig. 2 demonstrated a 0.34 error rate in classifying BRCA 1/2 versus others, and a 0.26 error rate in classifying BRCA 1 versus others (familial & sporadic).

[0460] Computational search to rank 45-protein signature

[0461] 7-gene signatures taken from the list of 33 genes mapped from the 45-protein signature (Fig. 2) were examined. All of the signatures that performed better than the 45- protein signatures (error < 0.3370474) were recorded. The genes were ranked by their importance defined as the frequency of their presence in the recorded signatures.

[0462] Using this method, the ten 7-protein signatures presented in Table 1 were generated, each having a low error rate.

Table 1

Baseline 45-protein signature 0.3370474 0.2568807

MTAl MSH6 TOP2B RPAl PRPF8 POLDl NCBP1 0.2451253 0.1743119

MSH2 SRCAP RPAl SMC4 PRPF8 POLDl NCBP1 0.2367688 0.204893

MSH2 RPAl PRPF8 DDX21 POLDl SIN3A NCBP1 0.2451253 0.2018349

ARID1A TRIM28 RPAl CSTF3 PRPF8 POLDl SIN3A 0.2423398 0.1896024

SMARCA5 MTAl TOP2B RPAl DDX21 POLDl TOP2A 0.2367688 0.2171254

MSH2 TOP2B RPAl ATM PRPF8 POLDl TRRAP 0.2423398 0.1957187

MSH2 DHX9 TOP2B RPAl PRPF8 TRRAP NCBP1 0.2451253 0.1681957

MSH2 TRIM28 MTAl TOP2B RPAl ATM PRPF8 0.2423398 0.1926606

MSH2 CREBBP RPAl SMC4 PRPF8 POLDl NCBP1 0.2367688 0.1712538

TRIM28 TOP2B RPAl PRPF8 POLDl TRRAP HNRNPF 0.2451253 0.17737

[0463] Table 2 shows the ranking of the genes together with the error rates of the signatures constructed from the first ranked gene up to the each gene.

Table 2

Rank Gene Leave-one- Leave-one- out error out error

BRCAl/2 BRCA1

versus others versus other

1 OGT 1 1

2 PRPF8 0.448468 0.449541

3 POLDl 0.389972 0.397554

4 MSH2 0.395543 0.40367

5 NCBP1 0.259053 0.2263 6 RPAl 0.259053 0.217125

7 SSRPl 0.267409 0.204893

8 T0P2B 0.275766 0.217125

9 MTA1 0.267409 0.207951

10 DDX21 0.261838 0.207951

11 ARID1A 0.264624 0.204893

12 TRIM28 0.275766 0.207951

13 HNRNPF 0.270195 0.214067

14 SIN3A 0.272981 0.220183

15 SMARCA5 0.272981 0.2263

16 MSH6 0.272981 0.223242

17 HCFC1 0.281337 0.220183

18 SMC4 0.281337 0.2263

19 TRRAP 0.289694 0.232416

20 DHX9 0.292479 0.217125

21 ATM 0.281337 0.217125

22 T0P2A 0.300836 0.24159

23 SFRS1 0.314763 0.2263

24 CREBBP 0.309192 0.229358

25 SMC1A 0.309192 0.223242

26 CSTF3 0.320334 0.235474

27 SMARCC1 0.306407 0.232416

28 SMARCA4 0.320334 0.244648

29 PARP1 0.320334 0.247706

30 SRCAP 0.314763 0.247706

31 CSTF1 0.32312 0.244648

32 RSF1 0.334262 0.253823

33 EP400 0.337047 0.256881

[0464] Using this ranking, the protein signatures depicted in Table 3, which comprise 5 to 9 proteins, were generated.

Table 3

[0466] In the same manner, 7-gene signatures taken from the list of 248 genes mapped from the "all up" signature (in total 417 BRCAl deficiency-associated proteins) were examined. All of the protein signatures that performed better than the 45 -protein signatures (error < 0.3370474) were recorded. The genes were ranked by their importance, defined as the frequency of their presence in the recorded signatures.

[0467] Using this method, the ten 7-protein signatures presented in Table 4 were generated, each having a low error rate.

Table 4

CDK9 CUL5 CSTF3 ADD3 DHX30 DDT EIF3G 0.2451253 0.1865443

NUP210 SERPINDl BAX CUL5 BIRC6 KRT78 PDS5A 0.2367688 0.1743119

[0468] Table 5 shows the ranking of the genes together with the error rates signatures constructed from the first ranked gene up to the each gene.

Table 5

Rank Gene Leave-one-out Leave-one-out

error BRCAl/2 error BRCA1

versus others versus other

1 CDH3 1 1

2 OGT 0.451253482 0.458715596

3 KIF4A 0.428969359 0.422018349

4 COL14A1 0.409470752 0.360856269

5 ITGB4 0.378830084 0.336391437

6 CUL5 0.348189415 0.327217125

7 NDRG1 0.325905292 0.302752294

8 BYSL 0.309192201 0.275229358

9 COL4A1 0.325905292 0.29969419

10 APOD 0.298050139 0.262996942

11 EIF4A3 0.30362117 0.266055046

12 NUP210 0.300835655 0.266055046

13 LAMB2 0.286908078 0.262996942

14 HMCN 1 0.289693593 0.266055046

15 DDT 0.286908078 0.259938838

16 PBRM1 0.292479109 0.262996942

17 TJP1 0.300835655 0.275229358

18 FAH 0.292479109 0.262996942

19 CSE1L 0.289693593 0.259938838

20 SERPINDl 0.286908078 0.247706422

21 NUP214 0.278551532 0.23853211

22 UBAP2 0.275766017 0.232415902

23 MRPL14 0.286908078 0.241590214

24 COL4A2 0.292479109 0.250764526

25 SCRIB 0.286908078 0.247706422

26 C20orf20 0.284122563 0.247706422

27 MSH2 0.286908078 0.23853211

28 TBL2 0.289693593 0.235474006

29 RAE1 0.284122563 0.23853211

30 FUR 0.292479109 0.244648318

31 LAMC1 0.292479109 0.247706422

32 NCBP1 0.286908078 0.241590214 DOCK1 0.286908078 0.232415902

ALDH1A1 0.275766017 0.23853211

PEC 0.275766017 0.241590214

POLD1 0.278551532 0.232415902

RRP1 0.270194986 0.229357798

OTUD6B 0.278551532 0.235474006

RANBP2 0.270194986 0.22324159

MYH14 0.267409471 0.217125382

MKI67 0.26183844 0.220183486

PSPC1 0.267409471 0.22324159

TP53BP1 0.267409471 0.229357798

TRIP12 0.270194986 0.232415902

TJP2 0.272980501 0.235474006

HNRNPF 0.264623955 0.229357798

MFGE8 0.259052925 0.204892966

FXC1 0.259052925 0.20795107

BID 0.259052925 0.20795107

CIRBP 0.26183844 0.214067278

DDX21 0.256267409 0.217125382

SMC4 0.256267409 0.220183486

LAMA4 0.256267409 0.214067278

THUMPD1 0.26183844 0.22324159

PKP3 0.267409471 0.22324159

PPIF 0.267409471 0.229357798

TST 0.272980501 0.232415902

CDK9 0.270194986 0.229357798

MRPS25 0.267409471 0.226299694

EIF3G 0.270194986 0.229357798

CCDC6 0.270194986 0.229357798

COL18A1 0.270194986 0.22324159

BIRC6 0.267409471 0.22324159

PLCG1 0.267409471 0.22324159

PRPF8 0.270194986 0.22324159

DOCK9 0.270194986 0.217125382

TOP2A 0.272980501 0.226299694

PAPOLA 0.270194986 0.22324159

CD2AP 0.270194986 0.22324159

SLC25A35 0.259052925 0.220183486

JUP 0.267409471 0.226299694

LIN7C 0.267409471 0.22324159

CKAP5 0.267409471 0.22324159

FRYL 0.26183844 0.220183486

ARID1A 0.26183844 0.220183486

SEC24C 0.26183844 0.220183486

PPL 0.259052925 0.217125382

DHRS7B 0.259052925 0.214067278 79 TOP2B 0.26183844 0.217125382

80 PUS1 0.267409471 0.22324159

81 PGP 0.270194986 0.22324159

82 ZFR 0.267409471 0.22324159

83 MRPL4 0.264623955 0.220183486

84 SRRM2 0.264623955 0.22324159

85 AKAP8 0.264623955 0.22324159

86 HCFC1 0.264623955 0.220183486

87 TRIM33 0.264623955 0.22324159

88 SLC25A13 0.26183844 0.22324159

89 USP39 0.26183844 0.22324159

90 GTPBP1 0.26183844 0.220183486

91 BZW2 0.26183844 0.220183486

92 DDX42 0.26183844 0.220183486

93 CREBBP 0.26183844 0.217125382

94 CNN 1 0.26183844 0.217125382

95 DNAJC7 0.26183844 0.217125382

96 CSTF3 0.26183844 0.214067278

97 CPOX 0.26183844 0.214067278

98 ALDOC 0.26183844 0.214067278

99 SSRP1 0.26183844 0.211009174

100 TRA2A 0.26183844 0.211009174

101 PC 0.264623955 0.211009174

102 NF1 0.256267409 0.204892966

103 PTK7 0.259052925 0.211009174

104 BTAF1 0.253481894 0.20795107

105 RNF114 0.253481894 0.20795107

106 SMC1A 0.253481894 0.20795107

107 CNP 0.259052925 0.20795107

108 NSFL1C 0.256267409 0.211009174

109 STIP1 0.26183844 0.217125382

110 EIF2B4 0.26183844 0.217125382

111 DN MT1 0.259052925 0.214067278

112 SIN3A 0.264623955 0.220183486

113 LAMA1 0.259052925 0.214067278

114 MGST1 0.259052925 0.217125382

115 TRIM28 0.26183844 0.214067278

116 RNF20 0.259052925 0.211009174

117 RELL1 0.259052925 0.220183486

118 NCK2 0.256267409 0.214067278

119 CHD8 0.256267409 0.217125382

120 RAVER1 0.256267409 0.211009174

121 RBP4 0.256267409 0.204892966

122 0CIAD1 0.256267409 0.20795107

123 BDH 1 0.259052925 0.211009174

124 DHX30 0.259052925 0.211009174 125 UBTF 0.259052925 0.211009174

126 BCAM 0.256267409 0.20795107

127 ANK D17 0.259052925 0.211009174

128 ADRM 1 0.256267409 0.211009174

129 DSG2 0.259052925 0.217125382

130 MRPL44 0.259052925 0.211009174

131 UXT 0.259052925 0.211009174

132 STAT3 0.259052925 0.217125382

133 CHD4 0.259052925 0.214067278

134 SRCAP 0.259052925 0.217125382

135 SART3 0.256267409 0.211009174

136 ADD3 0.259052925 0.214067278

137 TNKS1BP1 0.256267409 0.20795107

138 GRHPR 0.259052925 0.20795107

139 CAT 0.259052925 0.20795107

140 NID2 0.256267409 0.20795107

141 LUC7L 0.26183844 0.20795107

142 DRG1 0.259052925 0.20795107

143 C0BLL1 0.256267409 0.201834862

144 SFRS1 0.256267409 0.204892966

145 SMARCA5 0.253481894 0.204892966

146 ADO 0.253481894 0.204892966

147 CSTF1 0.253481894 0.204892966

148 RSF1 0.253481894 0.204892966

149 NIPSNAP1 0.26183844 0.204892966

150 ARFGAP2 0.26183844 0.20795107

151 CTNN D1 0.26183844 0.204892966

152 DHX9 0.26183844 0.204892966

153 NSUN2 0.26183844 0.204892966

154 TIM M50 0.264623955 0.211009174

155 LIG3 0.270194986 0.211009174

156 GTF2I 0.270194986 0.20795107

157 FBL 0.270194986 0.20795107

158 TRRAP 0.270194986 0.211009174

159 NUP107 0.264623955 0.20795107

160 PURB 0.264623955 0.20795107

161 BAX 0.267409471 0.211009174

162 HEBP2 0.264623955 0.211009174

163 STAG 2 0.264623955 0.211009174

164 ROMOl 0.267409471 0.20795107

165 RIF1 0.267409471 0.204892966

166 MED12 0.267409471 0.204892966

167 PTGES2 0.270194986 0.20795107

168 SRC 0.267409471 0.20795107

169 TPR 0.267409471 0.20795107

170 UQCRC1 0.264623955 0.20795107 171 DEK 0 264623955 0.201834862

172 PPP5C 0 264623955 0.201834862

173 PDS5A 0 272980501 0.204892966

174 MTA1 0 272980501 0.201834862

175 ATM 0 270194986 0.20795107

176 EP400 0 272980501 0.20795107

177 GCN 1L1 0 272980501 0.20795107

178 LANCL1 0 275766017 0.20795107

179 C5orf24 0 275766017 0.20795107

180 CN0T1 0 272980501 0.20795107

181 MDC1 0 272980501 0.20795107

182 MSH6 0 272980501 0.204892966

183 SMA CA4 0 275766017 0.204892966

184 VPS13A 0 275766017 0.204892966

185 RRP12 0 275766017 0.204892966

186 CTNNB1 0 272980501 0.204892966

187 C17orf49 0 270194986 0.204892966

188 ANK3 0 272980501 0.204892966

189 NUMA1 0 270194986 0.204892966

190 AIM1 0 272980501 0.20795107

191 PARP1 0 272980501 0.20795107

192 LAMB1 0 272980501 0.204892966

193 SMARCC1 0 272980501 0.20795107

194 AGRN 0 272980501 0.204892966

195 WDR43 0 275766017 0.20795107

196 C10orf35 0 275766017 0.20795107

197 KRT78 0 275766017 0.204892966

198 DDX27 0 275766017 0.204892966

199 ADNP 0 270194986 0.201834862

200 PDCD11 0 267409471 0.201834862

201 EZR 0 270194986 0.201834862

202 ILF3 0 270194986 0.201834862

203 PDCD4 0 272980501 0.20795107

204 THUMPD3 0 272980501 0.211009174

205 RPA1 0 272980501 0.211009174

206 CYGB 0 272980501 0.20795107

207 PHLDA3 0 272980501 0.20795107

208 PUS7 0 272980501 0.20795107

209 EPHX1 0 275766017 0.20795107

210 HMGB3 0 281337047 0.211009174

211 MPST 0 275766017 0.211009174

212 TINAGL1 0 275766017 0.211009174

213 NOSIP 0 278551532 0.20795107

214 HK1 0 275766017 0.211009174

215 RAB27A 0 278551532 0.211009174

216 TMEM91 0 284122563 0.211009174 217 ECHDC2 0 284122563 0.214067278

218 KIAA1217 0 284122563 0.214067278

219 LAD1 0 281337047 0.214067278

220 ADD1 0 281337047 0.214067278

221 LAMA5 0 281337047 0.211009174

222 EPCAM 0 281337047 0.214067278

223 PPFIA1 0 284122563 0.214067278

224 FKBP3 0 284122563 0.20795107

225 PYDC1 0 284122563 0.211009174

226 ETV6 0 286908078 0.20795107

227 GTF3C1 0 286908078 0.20795107

228 AQP5 0 281337047 0.198776758

229 PLTP 0 284122563 0.195718654

230 DCPS 0 284122563 0.195718654

231 L C16A 0 286908078 0.198776758

232 MDN1 0 278551532 0.195718654

233 DNAJA3 0 281337047 0.198776758

234 NUDT16L1 0 286908078 0.201834862

235 TRIM29 0 278551532 0.195718654

236 DAK 0 278551532 0.19266055

237 DSP 0 275766017 0.189602446

238 ARFGEF1 0 281337047 0.195718654

239 GSTA4 0 281337047 0.189602446

240 UQCC 0 286908078 0.189602446

241 SNTB1 0 286908078 0.189602446

242 KIT 0 289693593 0.19266055

243 CDH1 0 295264624 0.189602446

244 AP1M2 0 295264624 0.186544343

245 GSTM3 0 289693593 0.189602446

246 FBP1 0 292479109 0.19266055

247 SERPINE2 0 284122563 0.186544343

248 GJA1 0 286908078 0.186544343

[0469] Using this ranking, the protein signatures depicted in Table 6, which comprise 5 to 9 proteins, were generated.

Table 6

Leave-one-out Leave-one-out

Signature error BRCAl/2 error BRCA1

versus others versus other

1 Baseline 45-protein signature 0.3370474 0.2568807 1

I CDH3 OGT KI F4A COL14A1 ITG B4 0.378830084 0.336391437 j

I CDH3 OGT KI F4A COL14A1 ITG B4 CU L5 0.348189415 0.327217125 j CDH3 OGT KIF4A COL14A1 ITGB4 CUL5 NDRG1 0.325905292 0.302752294

CDH3 OGT KIF4A COL14A1 ITGB4 CUL5 NDRG1 0.309192201 0.275229358 BYSL

CDH3 OGT KIF4A COL14A1 ITGB4 CUL5 NDRG1 0.325905292 0.29969419 BYSL COL4A1

[0470] Signatures based on data annotation and integration

[0471] Table 7 depicts protein signatures that displayed high performance using the analysis presented in this Example ("Rank" = overall score).

Table 7

Associate with breast cancer (20 proteins) 0.3370474 0.2691131

DHX9 SMC4 AD21 TOP2A TRIM28 MSH2 RPA1 MSH6

POLD1 CREBBP PCNA ATM MTA1 PARP1 TOPI DDX21

OGT TOP2B ARID1A RSF1

Secretome in BRCA def vs pro (10 proteins) 0.4038997 0.3058104

DHX9 TOP2A TOPI SMC1A SFRS1 SUPT16H SMC3 SFRS3

SSRP1 PRPF8 mRNA BRCAl/2 versus sporadic (16 proteins) 0.3732591 0.3027523

TOP2A SFRS1 SMC4 TRIM28 MSH2 POLD1 C20ORF20

SSRP1 CREBBP ATM OGT TOP2B ARID1A HNRNPF SIN3A

NCBP1

Overlap secretome 10 0.4038997 0.3058104

TOP2A TOPI SUPT16H SSRP1 SMC3 SMC1A SFRS3 SFRS1

PRPF8 DHX9

Overlap secretome 56 0.362117 0.2232416

TOP2A TOPI SUPT16H SSRP1 SMC3 SMC1A SRSF3 SRSF1

PRPF8 DHX9 AGRN AGRN AP1M2 BZW2 CBX3 CDH1 CDH3

CKAP5 CLNS1A COL18A1 CPOX CRIP2 CTNNA1 CTNNB1

DAK DEK DNMT1 FUR FXYD3 GPC4 ILF3 ITGB4 LAMA4

LAMA5 LAMB2 LAMC1 LGALS7 MACF1 NCL NOLC1 NPM3

PKP3 PLTP PTN PURB SART3 SLC3A2 SLC7A5 SSB

THUMPD1 USP39 WDR5 TINAGL1 PTMA LAMB1

HMGB1L1

[0472] Computational analysis - varying random probe sizes

[0473] The length of the protein signatures was varied from 7 to 5, 4, and 3 in further ranking analyses. Table 8 depicts the performance of the ranking with length 5, 4, and 3 signature probes. The ranking with length 7 is depicted in the first block.

Table 8

length 7 Err length 5 err length 4 err length 3 Err

1 OGT 1.00 OGT 1.00 OGT 1.00 PRPF8 1.00

2 PRPF8 0.45 PRPF8 0.45 PRPF8 0.45 POLD1 0.44

3 POLD1 0.39 POLD1 0.39 POLD1 0.39 OGT 0.39 4 MSH2 0.40 MSH2 0.40 MSH2 0.40 HNRNPF 0.28

5 NCBP1 0.26 RPAl 0.41 HNRNPF 0.25 MSH2 0.25

6 RPAl 0.26 T0P2B 0.30 RPAl 0.26 RPAl 0.26

7 SSRP1 0.27 NCBP1 0.27 T0P2B 0.27 T0P2B 0.27

8 T0P2B 0.28 HNRNPF 0.26 T0P2A 0.31 TRIM28 0.28

9 MTA1 0.27 DDX21 0.25 SMC4 0.31 DDX21 0.26

10 DDX21 0.26 TRIM28 0.26 TRIM28 0.32 T0P2A 0.30

11 ARID1A 0.26 ARID1A 0.25 ARID1A 0.31 SSRP1 0.28

12 TRIM28 0.28 MTA1 0.25 DDX21 0.30 NCBP1 0.27

13 HNRNPF 0.27 SSRP1 0.27 NCBP1 0.29 ATM 0.28

14 SIN3A 0.27 T0P2A 0.29 MTA1 0.29 ARID1A 0.29

15 SMARCA5 0.27 SMC4 0.29 SSRP1 0.29 SIN3A 0.28

16 MSH6 0.27 SIN3A 0.30 MSH6 0.28 CSTF3 0.28

17 HCFC1 0.28 SMARCA5 0.29 SIN3A 0.30 MSH6 0.28

18 SMC4 0.28 HCFC1 0.28 HCFC1 0.29 SMC4 0.30

19 TRRAP 0.29 MSH6 0.29 SMARCA5 0.29 SMARCA4 0.30

20 DHX9 0.29 CREBBP 0.28 CREBBP 0.28 SMARCA5 0.30

21 ATM 0.28 TRRAP 0.29 SMARCC1 0.31 HCFC1 0.31

22 T0P2A 0.30 DHX9 0.30 CSTF3 0.31 MTA1 0.31

23 SFRS1 0.31 ATM 0.30 TRRAP 0.30 CREBBP 0.31

24 CREBBP 0.31 SMARCC1 0.31 DHX9 0.31 SMARCC1 0.31

25 SMC1A 0.31 CSTF3 0.31 SMARCA4 0.31 TRRAP 0.32

26 CSTF3 0.32 SFRS1 0.33 ATM 0.32 PARP1 0.31

27 SMARCC1 0.31 SMC1A 0.31 SMC1A 0.31 SMC1A 0.31

28 SMARCA4 0.32 SMARCA4 0.32 SFRS1 0.32 SRCAP 0.31

29 PARP1 0.32 PARP1 0.32 PARP1 0.32 DHX9 0.31

30 SRCAP 0.31 SRCAP 0.31 SRCAP 0.31 SFRS1 0.31

31 CSTF1 0.32 CSTF1 0.32 RSF1 0.34 EP400 0.33

32 RSF1 0.33 RSF1 0.33 CSTF1 0.33 RSF1 0.33

33 EP400 0.34 EP400 0.34 EP400 0.34 CSTF1 0.34

[0474] The results show that the proteins OGT, PRPF8 and POLDl were consistent in all analyses. Thus, proteins signatures comprising these 3 proteins gave strong results.

[0475] The results also show that OGT, PRPF8, POLDl and MSH2 were consistent in 3 analyses, with MSH2 ranked number 5 in the last analysis. Thus, protein signatures comprising MSH2 also gave strong results.

[0476] The data provided in Table 8 show that the following 5-protein signature performed well, in 2 out of 3 new analyses (length 4 & length 3): OGT, PRPF8, POLDl, MSH2 and HNRNPF. The error rate was 0.25.

[0477] The following 6-protein and 7-protein signatures also performed consistently well in two analyses (length 4 & length 3):

[0478] OGT, PRPF8, POLDl, MSH2, HNRNPF and RPAl (error rate 0.26); and

[0479] OGT, PRPF8, POLDl, MSH2, HNRNPF, RPAl and TOP2B (error rate 0.27). [0480] Finally, the following 7-protein signature (length 5 probe) also performed well:

[0481] OGT, PRPF8, POLD1, MSH2, RPA1, TOP2B and NCBP1 (error rate 0.27).

Example 3

Immuno-histochemical analysis of selected BRCAness signature candidates in tissue microarrays

[0482] In silico data mining of the 45 -protein BRCAness signature (Fig. 2) showed the potential of the DNA repair and chromatin remodeling proteins to identify human BRCAl mutation-related tumors at the transcriptome level (after mapping mouse proteins to human RNA; see Warmoes et al., MCP 2012). To validate selected signature proteins in human BRCA mutation related breast cancer at the protein level, immunohistochemistry of tissue microarrays was performed. To this end, the signature proteins were ranked based on annotations, among others for concordant changes at the transcriptome and genome level, whether the protein was a known BRCAl interactor, and whether a link with breast cancer was found in PubMed. The top 10 proteins that results from the ranking included TOP2A, TOPI, MSH2 and MSH6, for which antibodies and staining protocols were readily available. These proteins were selected for follow-up for immunohistochemical analysis in tissue microarrays.

[0483] The study group comprised 201 cases of human invasive breast cancer, 95 of which contained a known BRCAl germline mutation and 106 of which had an unknown BRCA mutation status (and were referred to as sporadic breast cancer cases). Tissue microarrays were constructed and stained for TOPI, TOP2A, MSH2, MSH6 and CDH3 (P- cadherin, abundant in the BRCAl deficient cell line secretome) by immunohistochemistry. Scoring was performed by a single observer, who was blinded as to the origin of the tumors. For all the markers the percentage of positive nuclei was scored, except for CDH3 for which any cytoplasmic expression was scored positive. Associations between expression of these proteins were tested by Chi-square analysis.

[0484] Most of the tumors were of ductal type and high grade (Table 9). The mean age of the sporadic cases was 57 and for the BRCAl mutation related cases 42. Preliminary statistical analysis of the immunohistochemical analysis of the 6 proteins confirmed previously published data on high protein expression of P-cadherin in 80% (68/85) of the BRCAl mutation-related cases and is significantly different from expression frequencies of P- cadherin in non-BRCA mutation-related cases 23%(19/81) (p<0.001). TOPI expression was mostly seen in BRCAl mutation-related cases 61% (51/83) compared to only 37% (26/71) in the non-BRCA mutation-related cases (p=0.002). TOP2A expression was present in 88% (68/77) of the BRCAl mutation-related cases, which was significantly different compared to the expression of 27% (17/99) seen in the non-BRCA mutation-related cases (p<0.001).

Expression of MSH2 was present in 60% (51/85) of the non-BRCA mutation-related cases and seen in 55% (47/85) and of the BRCAl mutation-related cases. No significant differences in the expression patterns of marker MSH2 between the two groups was observed (p=0.535). Expression of MSH6 was observed in 75% (61/81) of the BRCAl mutation-related cases, significantly different compared to the expression in only 23% (19/81) seen in the non-BRCA mutation-related cases (p<0.001) (Table 9).

[0485] Preliminary subgroup analysis of BRCAl TNBC cases versus triple negative controls revealed that TOP2A and MSH6 retained statistical significance.

[0486] In summary, expression of TOPI, TOP2A and MSH6 is increased in BRCAl (and in BRCA2, data not shown) deficient breast tumors in comparison to the expression of these markers in non-BRCA mutation-related breast tumors, especially in comparison with relevant sporadic control groups (triple negative for BRCAl, luminal for BRCA2). These results therefore confirm the predictive potential of these proteins, which can be used in retro- and prospective trials using DNA damaging agents and for early detection in biofluids.

Table 9 - Expression patterns of TOPI, TOP2A, MSH2, MSH6 and P-cadh in invasive breast cancer of non-BRCA and BRCAl mutation carriers.

[0487] Finally, it should be noted that there are alternative ways of implementing the embodiments disclosed herein. Accordingly, the present embodiments are to be considered as illustrative and not restrictive. Furthermore, the claims are not to be limited to the details given herein, and are entitled their full scope and equivalents thereof.

Claims

Claims What is claimed is:

1. A BRC A-deficiency signature comprising at least 5 proteins selected from: TRRAP, BAZIB, SMC3, NCAPD2, RPAl, SIN3A, POLDl, SNRNP200, SMCIA, TOP2A, SMARCCl, TOP2B, HCFCl, PCNA, RSFl, CSNK2A1, CDC5L, TOPI, OGT, EP400, MSH6, TRIM28, SFRSl, SRCAP, PARPl, SMARCA4, CREBBP, ATM, RAD21, PRPF8, C20ORF20, CSTFl, MTAl, DDX21, HNRNPF, NCBP1, SMARCA5, MSH2, SFRS3, DHX9, SUPT16H, CSTF3, SSRP1, SMC4 and ARID 1 A,

wherein the proteins are up-regulated in BRCA-deficient tumors.

2. A BRC A-deficiency signature according to claim 1, wherein 3 of the proteins are OGT, PRPF8 and POLDl.

3. A BRC A-deficiency signature according to claim 1 or claim 2, wherein 4 of the proteins are OGT, PRPF8, POLDl and MSH2.

4. A BRCA-deficiency signature according to any one of claims 1-3, comprising OGT, PRPF8, POLDl, MSH2 and HNRNPF.

5. A BRCA-deficiency signature according to any one of claims 1-4, comprising OGT, PRPF8, POLDl, MSH2, HNRNPF and RPAl.

6. A BRCA-deficiency signature according to any one of claims 1-5, comprising OGT, PRPF8, POLDl, MSH2, HNRNPF, RPAl and TOP2B.

7. A BRCA-deficiency signature according to any one of claims 1-3, comprising OGT, PRPF8, POLDl, MSH2, RPAl, TOP2B and NCBP1.

8. A BRCA-deficiency signature according to any one of claims 1-3, comprising OGT, PRPF8, POLDl, MSH2 and NCBP1.

9. A BRCA-deficiency signature according to any one of claims 1-3 or 8, comprising OGT, PRPF8, POLDl, MSH2, NCBP1 and RPAl.

10. A BRCA-deficiency signature according to any one of claims 1-3, 8 or 9, comprising OGT, PRPF8, POLDl, MSH2, NCBP1, RPAl and SSRP1.

11. A BRCA-deficiency signature according to any one of claims 1-3 or 8-10, comprising OGT, PRPF8, POLDl, MSH2, NCBPl, RPAl, SSRPl and TOP2B.

12. A BRCA-deficiency signature according to any one of claims 1-3 or 8-11, comprising OGT, PRPF8, POLDl, MSH2, NCBPl, RPAl, SSRPl, TOP2B and MTAl.

13. A BRCA-deficiency signature according to claim 1, comprising MTAl, MSH6, TOP2B, RPAl, PRPF8, POLDl and NCBPl.

14. A BRCA-deficiency signature according to claim 1, comprising MSH2, SRCAP, RPAl, SMC4, PRPF8, POLDl and NCBPl.

15. A BRCA-deficiency signature according to claim 1, comprising MSH2, RPAl, PRPF8, DDX21, POLDl, SIN3A and NCBPl.

16. A BRCA-deficiency signature according to claim 1, comprising ARID1A, TRIM28, RPAl, CSTF3, PRPF8, POLDl and SIN3A.

17. A BRCA-deficiency signature according to claim 1, comprising SMARCA5, MTAl, TOP2B, RPAl, DDX21, POLDl and TOP2A.

18. A BRCA-deficiency signature according to claim 1, comprising MSH2, TOP2B, RPAl, ATM, PRPF8, POLDl and TRRAP.

19. A BRCA-deficiency signature according to claim 1, comprising MSH2, DHX9, TOP2B, RPAl, PRPF8, TRRAP and NCBPl.

20. A BRCA-deficiency signature according to claim 1, comprising MSH2, TRIM28, MTAl, TOP2B, RPAl, ATM and PRPF8.

21. A BRCA-deficiency signature according to claim 1, comprising MSH2, CREBBP, RPAl, SMC4, PRPF8, POLDl and NCBPl.

22. A BRCA-deficiency signature according to claim 1, comprising TRIM28, TOP2B, RPAl, PRPF8, POLDl, TRRAP and HNRNPF.

23. A BRCA-deficiency signature according to claim 1, comprising TOP2A, TRIM28,MSH2, DHX9, SMC4, RPAl, MSH6, POLDl, TRRAP, CREBBP, PCNA, ATM, MTA1, PARPl, TOPI, DDX21, SMC1A, SFRSl, C20ORF20, RAD21, CSTF1, OGT, TOP2B, ARIDIA, RSFl, CSNK2A1, SMARCA4, SMARCCl, SUPT16H, SMC3, SFRS3, SSRP1, PRPF8, HCFC1, NCAPD2 and CDC5L.

24. A BRCA-deficiency signature according to claim 1, comprising TOP2A, TRIM28, MSH2, DHX9, SMC4, RPAl, MSH6, POLDl, TRRAP, CREBBP, PCNA, ATM, MTA1, PARPl, TOPI, DDX21, SMC1A, SFRSl, C20ORF20, RAD21 and CSTF1.

25. A BRCA-deficiency signature according to claim 1, comprising TOP2A, TRIM28, MSH2, DHX9, SMC4, RPAl, MSH6, POLDl and TRRAP.

26. A BRCA-deficiency signature according to claim 1, comprising DHX9, SMC4, TRRAP, RAD21, CSTF1, NCAPD2 and CDC5L.

27. A BRCA-deficiency signature according to claim 1, comprising DHX9, SMC4, RAD21, TOP2A, TRIM28, MSH2, RPAl, MSH6, POLDl, CREBBP, PCNA, ATM, MTA1, PARPl, TOPI, DDX21, OGT, TOP2B, ARIDIA.

28. A BRCA-deficiency signature according to claim 1, comprising DHX9, TOP2A, TOPI, SMC1A, SFRSl, SUPT16H, SMC3, SFRS3, SSRP1 and PRPF8.

29. A BRCA-deficiency signature according to claim 1, comprising TOP2A, TOPI, SUPT16H, SSRP1, SMC3, SMC1A, SFRS3, SFRSl, PRPF8 and DHX9.

30. A BRCA-deficiency signature according to claim 1, comprising TRRAP, BAZ1B, SMC3, NCAPD2, RPAl, SIN3A, POLDl, SNRNP200, SMC1A, TOP2A, SMARCCl, TOP2B, HCFC1, PCNA, RSFl, CSNK2A1, CDC5L, TOPI, OGT, EP400, MSH6, TRIM28, SFRSl, SRCAP, PARPl, SMARCA4, CREBBP, ATM, RAD21, PRPF8, C20ORF20, CSTF1, MTA1, DDX21, HNRNPF, NCBP1, SMARCA5, MSH2, SFRS3, DHX9, SUPT16H, CSTF3, SSRP1, SMC4 and ARIDIA.

31. A kit, comprising:

a BRCA-deficiency signature according to any one of claims 1-30; and

instructions for using the BRCA-deficiency signature to identify BRCA-deficiency in a subject.

32. A kit according to claim 31, wherein the BRCA-deficiency is BRCA1- deficiency.

33. A kit according to claim 31, wherein the BRCA-deficiency is BRCA2- deficiency.

34. A kit according to claim 31, wherein the BRCA-deficiency is both BRCA1- deficiency and BRCA2-deficiency.

35. A method of identifying BRCA-deficiency in a tumor, comprising:

isolating the proteome of the tumor;

measuring the expression level of one or more of the proteins in the proteome; and comparing the expression level of the proteome to a BRCA-deficiency signature according to any one of claims 1-30;

wherein the proteins comprising the BRCA-deficiency signature are up-regulated in BRCA-deficient tumors; and

wherein the tumor is BRCA-deficient when the expression level of the one or more proteins of the proteome is similar to the expression level of the proteins of the BRCA- deficiency signature.

36. A method according to claim 35, wherein the BRCA-deficiency is BRCA1- deficiency.

37. A method according to claim 35, wherein the BRCA-deficiency is BRCA2- deficiency.

38. A method of optimizing anti-cancer therapy in a subject, comprising:

isolating the proteome from a tumor obtained from the subject;

measuring the expression level of one or more proteins in the proteome;

comparing the expression level of the one or more proteins of the proteome to a

BRCA-deficiency signature according to any one of claims 1-30; and

administering anti-cancer therapy to the patient when the expression level of the proteome is similar to the expression level of the proteins comprising the BRCA-deficiency signature; wherein the proteins comprising the BRCA-deficiency signature are up-regulated in BRCA-deficient tumors.

39. A BRCA-deficiency signature comprising at least 5 amino acid sequences selected from: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID NO: 45,

wherein the amino acid sequences correspond to proteins that are up-regulated in BRCA-deficient tumors.

40. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 7, SEQ ID NO: 38 and SEQ ID NO: 36.

41. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 7, SEQ ID NO: 38, SEQ ID NO: 36 and SEQ ID NO: 5.

42. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 7, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 5 and SEQ ID NO: 43.

43. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 7, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 5, SEQ ID NO: 43 and SEQ ID NO: 12.

44. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 19, SEQ ID NO: 30, SEQ ID NO: 7, SEQ ID NO: 38, SEQ ID NO: 36, SEQ ID NO: 5, SEQ ID NO: 43, SEQ ID NO: 12 and SEQ ID NO: 33.

45. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 33, SEQ ID NO: 21, SEQ ID NO: 12, SEQ ID NO: 5, SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 36.

46. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 38, SEQ ID NO: 24, SEQ ID NO: 5, SEQ ID NO: 44, SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 36.

47. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 38, SEQ ID NO: 5, SEQ ID NO: 30, SEQ ID NO: 34, SEQ ID NO: 7, SEQ ID NO: 6 and SEQ ID NO: 36.

48. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 45, SEQ ID NO: 22, SEQ ID NO: 5, SEQ ID NO: 42, SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 6.

49. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO:

37, SEQ ID NO: 33, SEQ ID NO: 12, SEQ ID NO: 5, SEQ ID NO: 34, SEQ ID NO: 7 and SEQ ID NO: 10.

50. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO:

38, SEQ ID NO: 12, SEQ ID NO: 5, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 1.

51. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 12, SEQ ID NO: 5, SEQ ID NO: 30, SEQ ID NO: 1 and SEQ ID NO: 36.

52. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 38, SEQ ID NO: 22, SEQ ID NO: 33, SEQ ID NO: 12, SEQ ID NO: 5, SEQ ID NO: 28 and SEQ ID NO: 30.

53. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 38, SEQ ID NO: 27, SEQ ID NO: 5, SEQ ID NO: 44, SEQ ID NO: 30, SEQ ID NO: 7 and SEQ ID NO: 36.

54. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 22, SEQ ID NO: 12, SEQ ID NO: 5, SEQ ID NO: 30, SEQ ID NO: 7, SEQ ID NO: 1 and SEQ ID NO: 35.

55. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 10, SEQ ID NO: 22, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 5, SEQ ID NO: 21, SEQ ID NO: 7, SEQ ID NO: 1, SEQ ID NO: 27, SEQ ID NO: 14, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 25, SEQ ID NO: 18, SEQ ID NO: 34, SEQ ID NO: 9, SEQ ID NO: 23, SEQ ID NO: 31, SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 19, SEQ ID NO: 12, SEQ ID NO: 45, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 26, SEQ ID NO: 11, SEQ ID NO: 41, SEQ ID NO: 3, SEQ ID NO: 39, SEQ ID NO: 43, SEQ ID NO: 30, SEQ ID NO: 13, SEQ ID NO: 4 and SEQ ID NO: 17.

56. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 10, SEQ ID NO: 22, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 5, SEQ ID NO: 21, SEQ ID NO: 7, SEQ ID NO: 1, SEQ ID NO: 27, SEQ ID NO: 14, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 25, SEQ ID NO: 18, SEQ ID NO: 34, SEQ ID NO: 9, SEQ ID NO: 23, SEQ ID NO: 31, SEQ ID NO: 29 and SEQ ID NO: 32.

57. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 10, SEQ ID NO: 22, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 5, SEQ ID NO: 21, SEQ ID NO: 7 and SEQ ID NO: 1.

58. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 1, SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 4 and SEQ ID NO: 17.

59. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 40, SEQ ID NO: 44, SEQ ID NO: 29, SEQ ID NO: 10, SEQ ID NO: 22, SEQ ID NO: 38, SEQ ID NO: 5, SEQ ID NO: 21, SEQ ID NO: 7, SEQ ID NO: 27, SEQ ID NO: 14, SEQ ID NO: 28, SEQ ID NO: 33, SEQ ID NO: 25, SEQ ID NO: 18, SEQ ID NO: 34, SEQ ID NO: 19, SEQ ID NO: 12, SEQ ID NO: 45 and SEQ ID NO: 15.

60. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 40, SEQ ID NO: 10, SEQ ID NO: 18, SEQ ID NO: 9, SEQ ID NO: 23, SEQ ID NO: 41, SEQ ID NO: 3, SEQ ID NO: 39, SEQ ID NO: 43 and SEQ ID NO: 30.

61. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 10, SEQ ID NO: 18, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 3, SEQ ID NO: 9, SEQ ID NO: 39, SEQ ID NO: 23, SEQ ID NO: 30 and SEQ ID NO: 40.

62. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 21, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 38, and SEQ ID NO: 44.

63. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 21, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 38, and SEQ ID NO: 44.

64. A BRCA-deficiency signature according to claim 39, comprising SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID NO: 45.

65. A kit, comprising:

a BRCA-deficiency signature according to any one of claims 39-64; and

66. A kit according to claim 65, wherein the BRCA-deficiency is BRCA1- deficiency.

67. A kit according to claim 65, wherein the BRCA-deficiency is BRCA2- deficiency.

68. A kit according to claim 65, wherein the BRCA-deficiency is both BRCA1- deficiency and BRCA2-deficiency.

69. A method of identifying BRCA-deficiency in a tumor, comprising:

isolating the proteome of the tumor;

measuring the expression level of one or more of the proteins in the proteome; and comparing the expression level of the proteome to a BRCA-deficiency signature according to any one of claims 39-64;

70. A method according to claim 69, wherein the BRCA-deficiency is BRCA1- deficiency.

71. A method according to claim 69, wherein the BRCA-deficiency is BRCA2- deficiency.

72. A method of optimizing anti-cancer therapy in a subject, comprising:

isolating the proteome from a tumor obtained from the subject;

measuring the expression level of one or more proteins in the proteome;

comparing the expression level of the one or more proteins of the proteome to a BRCA-deficiency signature according to any one of claims 39-64; and

administering anti-cancer therapy to the patient when the expression level of the proteome is similar to the expression level of the proteins comprising the BRCA-deficiency signature;

wherein the proteins comprising the BRCA-deficiency signature are up-regulated in BRCA-deficient tumors.

73. A BRCA-deficiency signature comprising at least 5 proteins selected from: Tacstdl, Lamal, 2610018G03Rik, Thumpdl, Mfge8, Serpine2, 1110067D22Rik, Nipsnapl, Fxyd3, Beam, Hlfx, Myhl4, Mafg, Cul5, Aldhlal, Pnptl, 1600014C10Rik, Rifl, Fl lr, Heatr2, Add3, Slc25a35, Trim33, Chd8, Gtf3cl, F12, Aqp5, Trim29, Ladl, Ppfial, Rsfl, Mrps25, Pdcd4, Otud6b, Pdzdl l, Dock9, Zfr, Kifl l, Agrn, Zfand6, Cdk9, Phlda3, Pbrml, Eif2b4, Dhxl6, Sntbl, 1500005K14Rik, B230219D22Rik, Acyl, Bysl, Gdpdl, Gemin5, Ank3, Rnf20, Dnmt3a, Vpsl3a, Epm2aipl, Coblll, Uxt, LOC100043597, Etv6, Lcmtl, Atplbl, Crym, Kctdl4, Bdhl, Lamb2, Scrib, StardlO, Gcat, Gyk, Cldn3, Dak, Azgpl, Btafl, Aldh4al, Tnn, Tcfap2c, Rab27a, 2010107G23Rik, D0HXS9928E, Ppl, Bptf, Lrrcl6, Relll, Ccdc44, Dnaja3, Ponl, Fbpl, Rtn4ipl, Hiplr, 1190003J15Rik, Ckmtl, Ccdc6, Cnnl, Ptn, Cdh3, Krt6b, Dsg2, Ephxl, Etl4, Stiml, Itgal, Txndcl4, Nudcd3, Pltp, AW549877, Trp63, Padi3, 1600027N09Rik, Mrpl44, Serpindl, Tubb3, Thumpd3, Nck2, Cstfl, Gjal, Echdc2, Mdcl, Lig3, Mtal, Cpn2, Plekha7, Fxcl, ENSMUSG00000073624, Papola, Kit, Cnp, Ppl, Aiml, Mki67, Dsp, Lama2, Nup210, Jup, Aldoc, Lama5, Dhx30, Arfgefl, Lancll, Mki67, Sin3a, Ahctfl, Fryl, Adnp, Gpc4, Tst, Itgb4, Bckdha, Gm237, Apod, NatlO, Pkp3, Acotl, Wbpl l, Agrn, Nfl, Tinagl, Mest, Aplm2, Slc7a5, Trp53bpl, Plcgl, Ubap2,

0610010K14Rik, Ep400, Ankrdl7, Addl, Tfam, Wdrl2, Gstt3, 2610528E23Rik, Poldl, Trrap, Tjp2, Bat2d, Srrm2, Akap8, Cd2ap, Ptk7, Rrpl, LOC68280, Acoxl, Peer, Cpox, Myol8a, Hebp2, Adrml, Msh6, Klkbl, Mrpl47, Fatl, Krtl4, Gtf2i, Ddx42, Cstf3, Rpal, Zfp289, Kif4, Chchd4, Mrpl4, Lgals7, Nupl07, Atm, Medl2, Nosip, Ptma, Hist3h2bb, Ppif, Ubtf, Gsttl, 1700012G19Rik, Crebbp, Pspcl, Tbl2, Slc25al3, Pds5a, Cdhl, Tmeml76b, Gsta4, Nup214, Pesl, Ctnnbl, Ncapd2, Wdr5, Pusl, Ddx27, Slc9a3rl, Rbm7, Dockl, Ndrgl, Saa4, Asfla, Dnmtl, Aqr, Usp39, Wdr43, Mllt4, Bazlb, Top2a, Nid2, Bzw2, Aridla, Ogt, Stag2, Ranbp2, Rael, Rrplb, Src, Clnsla, 492151 lH13Rik, Hint2, Dhrs7b, Ddx46, Dnajc7, Rbp4, Hcfcl, Mdnl, C330023M02Rik, Tjpl, Shmtl, Prep, Sfn, Supt5h, Lamcl, Zfp313, Raverl, Bat2, 2410003P15Rik, Numal, Fenl, Hmgb3, Tnkslbpl, H47, Cygb, Smcla, 2010100O12Rik, Ssrpl, Cdc51, Parpl, Rad21, Col4al, Nudtl611, Pcx, Smarccl, Crip2, Rps271, Msh2, Ppp5c, Ociadl, Col4a2, Grhpr, Cbr3, Nudt5, Rrpl2, Gtpbpl, Npm3, Ppmel, Tripl2, Dcps, Pus7, Smul, Ptges2, Mrpll4, Itga6, Cirbp, Apip, Drgl, 130000110 IRik, Ctnnal, Smchdl, Mgstl, Coll8al, Lin7c, Macfl, Isynal, Stat3, Huwel, Ppig, Aprin, Oat, Lama4, Sec24c, Tra2a, Csnk2al, Smc4, Ldhb, Eif4g2, Smc3, Cbxl, Acadl, Timm50, Dek, Fah, Smarca4, Ighg, Hkl, Ilf3, Ctnndl, Ddx21, 2610301G19Rik, Nasp, Albg, Dut, Topi, Bid, Son, Sart3, Suptl6h, Cat, Ddx6, Pdcdl l, Abcfl, Slc3a2, Luc71, Top2b, Nolcl, Eif3s4, Pycard, Vil2, Ilf2, Purb, Tpr, Esl, D10Jhu81e, Fkbp3, Hnrpul2, Mpst, Ncbpl, Lambl-1, Trim28, LOC100047252, Bat3, Eif4a3, Coll4al, Ckap5, Cnotl, Gcnlll, Fkbp4, Pcna, Gstm5, Nsun2, Chd4, Bax, Atplal, Csell, Birc6, Fabp5, Batla, Dkcl, Ddt, Ahcy, Fbl, Ascc311, Nol5a, Rab6, Nsfllc, Anp32b, Ddbl, Prpf8, Idh3a, Ssb, Hnrpd, Stipl, Sfrsl, Cbx3, Smarca5, Hmgbl, Hnrpf, Hnrpl, Uqcrcl, Sfrs3, Tufm, Dhx9, Hnrpa2bl, Ncl, and Hspdl, wherein the proteins are significantly differentially regulated in BRCA-deficient tumors.

74. A BRCA-deficiency signature according to claim 73, comprising CDH3, OGT, KIF4A, COL14A1 and ITGB4.

75. A BRCA-deficiency signature according to claim 73, comprising CDH3, OGT, KIF4A, COL14A1, ITGB4 and CUL5.

76. A BRCA-deficiency signature according to claim 73, comprising CDH3, OGT, KIF4A, COL14A1, ITGB4, CUL5 and NDRG1.

77. A BRCA-deficiency signature according to claim 73, comprising CDH3, OGT, KIF4A, COL14A1, ITGB4, CUL5, NDRG1 and BYSL.

78. A BRCA-deficiency signature according to claim 73, comprising CDH3, OGT, KIF4A, COL14A1, ITGB4, CUL5, NDRG1, BYSL and COL4A1.

79. A BRCA-deficiency signature according to claim 73, comprising TBL2, UQCRC1, CUL5, ITGB4, FBL, VPS 13 A and TJP2.

80. A BRCA-deficiency signature according to claim 73, comprising PSPC1, CDK9, KIF4A, FUR, PECR, SMARCA4 and UBAP2.

81. A BRCA-deficiency signature according to claim 73, comprising BZW2, NUP210, SCRIB, RSF1, OTUD6B, DHRS7B and CDH3.

82. A BRCA-deficiency signature according to claim 73, comprising CCDC6, TRIP12, CUL5, AKAP8, NUP214, UXT and COL4A1.

83. A BRCA-deficiency signature according to claim 73, comprising SERPIND1, SART3, CUL5, LIN7C, ADD3, DDT and PDS5A.

84. A BRCA-deficiency signature according to claim 73, comprising SMARCA5, NUP210, TRIP12, CUL5, OGT, POLD1 and NF1.

85. A BRCA-deficiency signature according to claim 73, comprising SMARCA5, DHX9, CSTF1, TRIP12, BYSL, CUL5 and JUP.

86. A BRCA-deficiency signature according to claim 73, comprising TP53BP1, DRG1, COL14A1, FRYL, HNRNPF, ROMOl and DOCK1.

87. A BRCA-deficiency signature according to claim 73, comprising CDK9, CUL5, CSTF3, ADD3, DHX30, DDT and EIF3G.

88. A BRCA-deficiency signature according to claim 73, comprising NUP210, SERPIND1, BAX, CUL5, BIRC6, KRT78 and PDS5A.

89. A BRCA-deficiency signature according to claim 73, comprising TOP2A, TOPI, SUPT16H, SSRPl, SMC3, SMCIA, SRSF3, SRSFl, PRPF8, DHX9, AGRN, AGRN, AP1M2, BZW2, CBX3, CDH1, CDH3, CKAP5, CLNS1A, COL18A1, CPOX, CRIP2, CTNNAl, CTNNBl, DAK, DEK, DNMTl, FUR, FXYD3, GPC4, ILF3, ITGB4, LAMA4, LAMA5, LAMB2, LAMCl, LGALS7, MACFl, NCL, NOLCl, NPM3, PKP3, PLTP, PTN, PURB, SART3, SLC3A2, SLC7A5, SSB, THUMPDl, USP39, WDR5, TINAGLl, PTMA, LAMB1 and HMGB1L1.

90. A BRCA-deficiency signature according to claim 73, comprising Tacstdl, Lamal, 2610018G03Rik, Thumpdl, Mfge8, Serpine2, 1110067D22Rik, Nipsnapl, Fxyd3, Beam, Hlfx, Myhl4, Mafg, Cul5, Aldhlal, Pnptl, 1600014C10Rik, Rifl, Fl lr, Heatr2, Add3, Slc25a35, Trim33, Chd8, Gtf3cl, F12, Aqp5, Trim29, Ladl, Ppfial, Rsfl, Mrps25, Pdcd4, Otud6b, Pdzdl 1 , Dock9, Zfr, Kif 11 , Agrn, Zfand6, Cdk9, Phlda3, Pbrml , Eif2b4, Dhxl6, Sntbl, 1500005K14Rik, B230219D22Rik, Acyl, Bysl, Gdpdl, Gemin5, Ank3, Rnf20, Dnmt3a, Vpsl3a, Epm2aipl, Coblll, Uxt, LOC100043597, Etv6, Lcmtl, Atplbl, Crym, Kctdl4, Bdhl, Lamb2, Scrib, StardlO, Gcat, Gyk, Cldn3, Dak, Azgpl, Btafl, Aldh4al, Tnn, Tcfap2c, Rab27a, 2010107G23Rik, D0HXS9928E, Ppl, Bptf, Lrrcl6, Relll, Ccdc44, Dnaja3, Ponl, Fbpl, Rtn4ipl, Hiplr, 1190003J15Rik, Ckmtl, Ccdc6, Cnnl, Ptn, Cdh3, Krt6b, Dsg2, Ephxl, Etl4, Stiml, Itgal, Txndcl4, Nudcd3, Pltp, AW549877, Trp63, Padi3, 1600027N09Rik, Mrpl44, Serpindl, Tubb3, Thumpd3, Nck2, Cstfl, Gjal, Echdc2, Mdcl, Lig3, Mtal, Cpn2, Plekha7, Fxcl, ENSMUSG00000073624, Papola, Kit, Cnp, Ppl, Aiml, Mki67, Dsp, Lama2, Nup210, Jup, Aldoc, Lama5, Dhx30, Arfgefl, Lancll, Mki67, Sin3a, Ahctfl, Fryl, Adnp, Gpc4, Tst, Itgb4, Bckdha, Gm237, Apod, NatlO, Pkp3, Acotl, Wbpl l, Agrn, Nfl, Tinagl, Mest, Aplm2, Slc7a5, Trp53bpl, Plcgl, Ubap2,

0610010K14Rik, Ep400, Ankrdl7, Addl, Tfam, Wdrl2, Gstt3, 2610528E23Rik, Poldl, Trrap, Tjp2, Bat2d, Srnn2, Akap8, Cd2ap, Ptk7, Rrpl, LOC68280, Acoxl, Peer, Cpox, Myol8a, Hebp2, Adrml, Msh6, Klkbl, Mrpl47, Fatl, Krtl4, Gtf2i, Ddx42, Cstf3, Rpal, Zfp289, Kif4, Chchd4, Mrpl4, Lgals7, Nupl07, Atm, Medl2, Nosip, Ptma, Hist3h2bb, Ppif, Ubtf, Gsttl, 1700012G19Rik, Crebbp, Pspcl, Tbl2, Slc25al3, Pds5a, Cdhl, Tmeml76b, Gsta4, Nup214, Pesl, Ctnnbl, Ncapd2, Wdr5, Pusl, Ddx27, Slc9a3rl, Rbm7, Dockl, Ndrgl, Saa4, Asfla, Dnmtl, Aqr, Usp39, Wdr43, Mllt4, Bazlb, Top2a, Nid2, Bzw2, Aridla, Ogt, Stag2, Ranbp2, Rael, Rrplb, Src, Clnsla, 492151 lH13Rik, Hint2, Dhrs7b, Ddx46, Dnajc7, Rbp4, Hcfcl, Mdnl, C330023M02Rik, Tjpl, Shmtl, Prep, Sfn, Supt5h, Lamcl, Zfp313, Raverl, Bat2, 2410003P15Rik, Numal, Fenl, Hmgb3, Tnkslbpl, H47, Cygb, Smcla, 2010100O12Rik, Ssrpl, Cdc51, Parpl, Rad21, Col4al, Nudtl611, Pcx, Smarccl, Crip2, Rps271, Msh2, Ppp5c, Ociadl, Col4a2, Grhpr, Cbr3, Nudt5, Rrpl2, Gtpbpl, Npm3, Ppmel, Tripl2, Dcps, Pus7, Smul, Ptges2, Mrpll4, Itga6, Cirbp, Apip, Drgl, 130000110 IRik, Ctnnal, Smchdl, Mgstl, Coll8al, Lin7c, Macfl, Isynal, Stat3, Huwel, Ppig, Aprin, Oat, Lama4, Sec24c, Tra2a, Csnk2al, Smc4, Ldhb, Eif4g2, Smc3, Cbxl, Acadl, Timm50, Dek, Fah, Smarca4, Ighg, Hkl, Ilf3, Ctnndl, Ddx21, 2610301G19Rik, Nasp, Albg, Dut, Topi, Bid, Son, Sart3, Suptl6h, Cat, Ddx6, Pdcdl l, Abcfl, Slc3a2, Luc71, Top2b, Nolcl, Eif3s4, Pycard, Vil2, Ilf2, Purb, Tpr, Esl, D10Jhu81e, Fkbp3, Hnrpul2, Mpst, Ncbpl, Lambl-1, Trim28, LOC100047252, Bat3, Eif4a3, Coll4al, Ckap5, Cnotl, Gcnlll, Fkbp4, Pcna, Gstm5, Nsun2, Chd4, Bax, Atplal, Csell, Birc6, Fabp5, Batla, Dkcl, Ddt, Ahcy, Fbl, Ascc311, Nol5a, Rab6, Nsfllc, Anp32b, Ddbl, Prpf8, Idh3a, Ssb, Hnrpd, Stipl, Sfrsl, Cbx3, Smarca5, Hmgbl, Hnrpf, Hnrpl, Uqcrcl, Sfrs3, Tufm, Dhx9, Hnrpa2bl, Ncl, and Hspdl.

91. A kit, comprising:

a BRCA-deficiency signature according to any one of claims 73-90; and

92. A kit according to claim 91, wherein the BRCA-deficiency is BRCA1- deficiency.

93. A kit according to claim 91, wherein the BRCA-deficiency is BRCA2- deficiency.

94. A kit according to claim 91, wherein the BRCA-deficiency is both BRCA1- deficiency and BRCA2-deficiency.

95. A method of identifying BRCA-deficiency in a tumor, comprising:

isolating the proteome of the tumor;

measuring the expression level of one or more of the proteins in the proteome; and comparing the expression level of the proteome to a BRCA-deficiency signature according to any one of claims 73-90;

wherein the proteins comprising the BRCA-deficiency signature are significantly differentially regulated in BRCA-deficient tumors; and

96. A method according to claim 95, wherein the BRCA-deficiency is BRCA1- deficiency.

97. A method according to claim 95, wherein the BRCA-deficiency is BRCA2- deficiency.

98. A method of optimizing anti-cancer therapy in a subject, comprising:

isolating the proteome from a tumor obtained from the subject;

measuring the expression level of one or more proteins in the proteome;

comparing the expression level of the one or more proteins of the proteome to a BRCA-deficiency signature according to any one of claims 73-90; and

wherein the proteins comprising the BRCA-deficiency signature are significantly differentially regulated in BRCA-deficient tumors.

99. A BRCA-deficiency signature comprising at least 5 nucleic acid sequences selected from: SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90,

wherein the nucleic acid sequences code for proteins that are up-regulated in BRCA- deficient tumors.

100. A BRCA-deficiency signature according to claim 99, comprising SEQ ID NO: 55, SEQ ID NO: 68, SEQ ID NO: 89, SEQ ID NO: 67, SEQ ID NO: 83, SEQ ID NO: 52, SEQ ID NO: 76, SEQ ID NO: 88, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 64, SEQ ID NO: 57, SEQ ID NO: 90, SEQ ID NO: 80, SEQ ID NO: 51 and SEQ ID NO: 81.

101. A BRCA-deficiency signature according to claim 99, comprising SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 66, SEQ ID NO: 70, SEQ ID NO: 73, SEQ ID NO: 83 and SEQ ID NO: 89.

102. A BRCA-deficiency signature according to claim 99, comprising SEQ ID NO: 46, SEQ ID NO: 49, SEQ ID NO: 62, SEQ ID NO: 74, SEQ ID NO: 85, SEQ ID NO: 87 and SEQ ID NO: 89.

103. A BRCA-deficiency signature according to claim 99, comprising SEQ ID NO: 46, SEQ ID NO: 49, SEQ ID NO: 55, SEQ ID NO: 62, SEQ ID NO: 74, SEQ ID NO: 85, SEQ ID NO: 87 and SEQ ID NO: 89.

104. A BRCA-deficiency signature according to claim 99, comprising SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90.

105. A BRCA-deficiency signature according to claim 99, comprising SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89 and SEQ ID NO: 90.

106. A kit, comprising:

a BRCA-deficiency signature according to any one of claims 99-105; and

107. A kit according to claim 106, wherein the BRCA-deficiency is BRCA1- deficiency.

108. A kit according to claim 106, wherein the BRCA-deficiency is BRCA2- deficiency.

109. A kit according to claim 106, wherein the BRCA-deficiency is both BRCA1- deficiency and BRCA2-deficiency.

110. A method of identifying BRCA-deficiency in a tumor, comprising:

isolating nucleic acids from the tumor;

measuring the expression level of one or more of the isolated nucleic acids; and comparing the expression level of the one or more of the isolated nucleic acids to a BRCA-deficiency signature according to any one of claims 99-105;

wherein the nucleic acids comprising the BRCA-deficiency signature code for proteins that are up-regulated in BRCA-deficient tumors; and wherein the tumor is BRCA-deficient when the expression level of the one or more of the isolated nucleic acids is similar to the expression level of the nucleic acids of the BRCA- deficiency signature.

111. A method according to claim 110, wherein the BRCA-deficiency is BRCA1- deficiency.

112. A method according to claim 110, wherein the BRCA-deficiency is BRCA2- deficiency.

113. A method of optimizing anti-cancer therapy in a subject, comprising:

isolating nucleic acids from a tumor obtained from the subject;

measuring the expression level of one or more of the isolated nucleic acids;

comparing the expression level of the one or more isolated nucleic acids to a BRCA- deficiency signature according to any one of claims 99-105; and

administering anti-cancer therapy to the patient when the expression level of the one or more isolated nucleic acids is similar to the expression level of the nucleic acids comprising the BRCA-deficiency signature;

wherein the nucleic acids comprising the BRCA-deficiency signature code for proteins that are up-regulated in BRCA-deficient tumors.