US20030224463A1

US20030224463A1 - Compositions and methods relating to DNA mismatch repair genes

Info

Publication number: US20030224463A1
Application number: US10/349,607
Authority: US
Inventors: Robert Liskay; C. Bronner; Sean Baker; Roni Bollag; Richard Kolodner
Original assignee: Individual
Current assignee: Individual
Priority date: 1993-12-17
Filing date: 2003-01-22
Publication date: 2003-12-04
Also published as: DK0760867T3; DE69434765T2; JPH09512702A; AU1442495A; DE69434765D1; JP4101285B2; EP0760867A1; EP0760867B1; US6191268B1; US6538108B1; ES2270424T3; CA2179285A1; WO1995016793A1; US6165713A; ATE330009T1; EP0760867A4

Abstract

Genomic sequences of human mismatch repair genes and gene products are described, as are methods of detecting mutations and/or polymorphisms in those genes. Also described are methods of diagnosing cancer susceptibility in a subject, and methods of identifying and classifying mismatch-repair-defective tumors. In particular, sequences and methods relating to human mutL homologs, hMLH1 and hPMS1 genes and gene products are provided.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation from U.S. patent application Ser. No. 09/265,503 filed Mar. 10, 1999, which is a continuation from U.S. patent application Ser. No. 08/352,902, filed Dec. 4, 1994, which is a continuation-in-part of U.S. patent application Ser. No. 08/209,521, filed Mar. 8, 1994, which is a continuation-in-part from U.S. patent application Ser. No. 08/168,877, filed Dec. 17, 1993. All of the above patent applications are incorporated by reference.[0001]
[0002] This invention was made with government support under Agreement No. GM 32741 and Agreement No. HG00395/GM50006 awarded by the National Institute of Health in the General Sciences Division. The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention involves DNA mismatch repair genes. In particular, the invention relates to identification of mutations and polymorphisms in DNA mismatch repair genes, to identification and characterization of DNA mismatch-repair-defective tumors, and to detection of genetic susceptibility to cancer.

BACKGROUND

In recent years, with the development of powerful cloning and amplification techniques such as the polymerase chain reaction (PCR), in combination with a rapidly accumulating body of information concerning the structure and location of numerous human genes and markers, it has become practical and advisable to collect and analyze samples of DNA or RNA from individuals who are members of families which are identified as exhibiting a high frequency of certain genetically transmitted disorders. For example, screening procedures are routinely used to screen for genes involved in sickle cell anemia, cystic fibrosis, fragile X chromosome syndrome and multiple sclerosis. For some types of disorders, early diagnosis can greatly improve the person's long-term prognosis by, for example, adopting an aggressive diagnostic routine, and/or by making life style changes if appropriate to either prevent or prepare for an anticipated problem.

Once a particular human gene mutation is identified and linked to a disease, development of screening procedures to identify high-risk individuals can be relatively straight forward. For example, after the structure and abnormal phenotypic role of the mutant gene are understood, it is possible to design primers for use in PCR to obtain amplified quantities of the gene from individuals for testing. However, initial discovery of a mutant gene, i.e., its structure, location and linkage with a known inherited health problem, requires substantial experimental effort and creative research strategies.

One approach to discovering the role of a mutant gene in causing a disease begins with clinical studies on individuals who are in families which exhibit a high frequency of the disease. In these studies, the approximate location of the disease-causing locus is determined indirectly by searching for a chromosome marker which tends to segregate with the locus. A principal limitation of this approach is that, although the approximate genomic location of the gene can be determined, it does not generally allow actual isolation or sequencing of the gene. For example, Lindblom et al. ³reported results of linkage analysis studies performed with SSLP (simple sequence length polymorphism) markers on individuals from a family known to exhibit a high incidence of hereditary non-polyposis colon cancer (HNPCC). Lindblom et al. found a “tight linkage” between a polymorphic marker on the short arm of human chromosome 3 (3p21-23) and a disease locus apparently responsible for increasing an individual's risk of developing colon cancer. Even though 3p21-23 is a fairly specific location relative to the entire genome, it represents a huge DNA region relative to the probable size of the mutant gene. The mutant gene could be separated from the markers identifying the locus by millions of bases. At best, such linkage studies have only limited utility for screening purposes because in order to predict one person's risk, genetic analysis must be performed with tightly linked genetic markers on a number of related individuals in the family. It is often impossible to obtain such information, particularly if affected family members are deceased. Also, informative markers may not exist in the family under analysis. Without knowing the gene's structure, it is not possible to sample, amplify, sequence and determine directly whether an individual carries the mutant gene.

Another approach to discovering a disease-causing mutant gene begins with design and trial of PCR primers, based on known information about the disease, for example, theories for disease state mechanisms, related protein structures and function, possible analogous genes in humans or other species, etc. The objective is to isolate and sequence candidate normal genes which are believed to sometimes occur in mutant forms rendering an individual disease prone. This approach is highly dependent on how much is known about the disease at the molecular level, and on the investigator's ability to construct strategies and methods for finding candidate genes. Association of a mutation in a candidate gene with a disease must ultimately be demonstrated by performing tests on members of a family which exhibits a high incidence of the disease. The most direct and definitive way to confirm such linkage in family studies is to use PCR primers which are designed to amplify portions of the candidate gene in samples collected from the family members. The amplified gene products are then sequenced and compared to the normal gene structure for the purpose of finding and characterizing mutations. A given mutation is ultimately implicated by showing that affected individuals have it while unaffected individuals do not, and that the mutation causes a change in protein function which is not simply a polymorphism.

Another way to show a high probability of linkage between a candidate gene mutation and disease is by determining the chromosome location of the gene, then comparing the gene's map location to known regions of disease-linked loci such as the one identified by Lindblom et al. Coincident map location of a candidate gene in the region of a previously identified disease-linked locus may strongly implicate an association between a mutation in the candidate gene and the disease.

There are other ways to show that mutations in a gene candidate may be linked to the disease. For example, artificially produced mutant forms of the gene can be introduced into animals. Incidence of the disease in animals carrying the mutant gene can then be compared to animals with the normal genotype. Significantly elevated incidence of disease in animals with the mutant genotype, relative to animals with the wild-type gene, may support the theory that mutations in the candidate gene are sometimes responsible for occurrence of the disease.

One type of disease which has recently received much attention because of the discovery of disease-linked gene mutations is Hereditary Nonpolyposis Colon Cancer (HNPCC). ^1,2Members of HNPCC families also display increased susceptibility to other cancers including endometrial, ovarian, gastric and breast. Approximately 10% of colorectal cancers are believed to be HNPCC. Tumors from HNPCC patients display an unusual genetic defect in which short, repeated DNA sequences, such as the dinucleotide repeat sequences found in human chromosomal DNA (“microsatellite DNA”), appear to be unstable. This genomic instability of short, repeated DNA sequences, sometimes called the “RER+” phenotype, is also observed in a significant proportion of a wide variety of sporadic tumors, suggesting that many sporadic tumors may have acquired mutations that are similar (or identical) to mutations that are inherited in HNPCC.

Genetic linkage studies have identified two HNPCC loci thought to account for as much as 90% of HNPCC. The loci map to human chromosome 2p 15-16 (2p21) and 3p21-23. Subsequent studies have identified human DNA mismatch repair gene hMSH2 as being the gene on chromosome 2p21, in which mutations account for a significant fraction of HNPCC cancers. ^{1, 2, 12}hMSH2 is one of several genes whose normal function is to identify and correct DNA mispairs including those that follow each round of chromosome replication.

The best defined mismatch repair pathway is the E. coli MutHLS pathway that promotes a long-patch (approximately 3 Kb) excision repair reaction which is dependent on the mutH, mutL, mutS and mutU (uvrD) gene products. The MutHLS pathway appears to be the most active mismatch repair pathway in E. coli and is known to both increase the fidelity of DNA replication and to act on recombination intermediates containing mispaired bases. The system has been reconstituted in vitro, and requires the mutH, mutL, mutS and uvrD (helicase II) proteins along with DNA polymerase III holoenzyme, DNA ligase, single-stranded DNA binding protein (SSB) and one of the single-stranded DNA exonucleases, Exo I, Exo VII or RecJ. hMSH2 is homologous to the bacterial mutS gene. A similar pathway in yeast includes the yeast MSH2 gene and two mutL-like genes referred to as PMS1 and MLH1.

With the knowledge that mutations in a human mutS type gene (hMSH2) sometimes cause cancer, and the discovery that HNPCC tumors exhibit microsatellite DNA instability, interest in other DNA mismatch repair genes and gene products, and their possible roles in HNPCC and/or other cancers, has intensified. It is estimated that as many as 1 in 200 individuals carry a mutation in either the hMSH2 gene or other related genes which encode for other proteins in the same DNA mismatch repair pathway.

An important objective of our work has been to identify human genes which are useful for screening and identifying individuals who are at elevated risk of developing cancer. Other objects are: to determine the sequences of exons and flanking intron structures in such genes; to use the structural information to design testing procedures for the purpose of finding and characterizing mutations which result in an absence of or defect in a gene product which confers cancer susceptibility; and to distinguish such mutations from “harmless” polymorphic variations. Another object is to use the structural information relating to exon and flanking intron sequences of a cancer-linked gene, to diagnose tumor types and prescribe appropriate therapy. Another object is to use the structural information relating to a cancer-linked gene to identify other related candidate human genes for study.

SUMMARY OF THE INVENTION

Based on our knowledge of DNA mismatch repair mechanisms in bacteria and yeast including conservation of mismatch repair genes, we reasoned that human DNA mismatch repair homologs should exist, and that mutations in such homologs affecting protein function, would be likely to cause genetic instability, possibly leading to an increased risk of developing certain forms of human cancer.

We have isolated and sequenced two human genes, hPMS1 and hMLH1 each of which encodes for a protein involved in DNA mismatch repair. hPMS1 and hMLH1 are homologous to mutL genes found in E. coli. Our studies strongly support an association between mutations in DNA mismatch repair genes and susceptibility to HNPCC. Thus, DNA mismatch repair gene sequence information of the present invention, namely, cDNA and genomic structures relating to hMLH1 and hPMS1, make possible a number of useful methods relating to cancer risk determination and diagnosis. The invention also encompasses a large number of nucleotide and protein structures which are useful in such methods.

We mapped the location of hMLH1 to human chromosome 3p21-23. This is a region of the human genome that, based upon family studies, harbors a locus that predisposes individuals to HNPCC. Additionally, we have found a mutation in a conserved region of the hMLH1 cDNA in HNPCC-affected individuals from a Swedish family. The mutation is not found in unaffected individuals from the same family, nor is it a simple polymorphism. We have also found that a homologous mutation in yeast results in a defective DNA mismatch repair protein. We have also found a frameshift mutation in hMLH1 of affected individuals from an English family. Our discovery of a cancer-linked mutations in hMLH1, combined with the gene's map position which is coincident with a previously identified HNPCC-linked locus, plus the likely role of the hMLH1 gene in mutation avoidance makes the hMLH1 gene a prime candidate for underlying one form of common inherited human cancer, and a prime candidate to screen and identify individuals who have an elevated risk of developing cancer.

hMLH1 has 19 exons and 18 introns. We have determined the location of each of the 18 introns relative to hMLH1 cDNA. We have also determined the structure of all intron/exon boundary regions of hMLH1. Knowledge of the intron/exon boundary structures makes possible efficient screening regimes to locate mutations which negatively affect the structure and function of gene products. Further, we have designed complete sets of oligonucleotide primer pairs which can be used in PCR to amplify individual complete exons together with surrounding intron boundary structures.

We mapped the location of HPMS1 to human chromosome 7. Subsequent studies by others³⁹have confirmed our prediction that mutations in this gene are linked to HNPCC.

The most immediate use of the present invention will be in screening tests on human individuals who are members of families which exhibit an unusually high frequency of early onset cancer, for example HNPCC. Accordingly, one aspect of the invention comprises a method of diagnosing cancer susceptibility in a subject by detecting a mutation in a mismatch repair gene or gene product in a tissue from the subject, wherein the mutation is indicative of the subject's susceptibility to cancer. In a preferred embodiment of the invention, the step of detecting comprises detecting a mutation in a human mutL homolog gene, for example, hMLH1 of hPMS1.

The method of diagnosing preferably comprises the steps of: 1) amplifying a segment of the mismatch repair gene or gene product from an isolated nucleic acid; 2) comparing the amplified segment with an analogous segment of a wild-type allele of the mismatch repair gene or gene product; and 3) detecting a difference between the amplified segment and the analogous segment, the difference being indicative of a mutation in the mismatch repair gene or gene product which confers cancer susceptibility.

Another aspect of the invention provides methods of determining whether the difference between the amplified segment and the analogous wild-type segment causes an affected phenotype, i.e., does the sequence alteration affect the individual's ability to repair DNA mispairs.

The method of diagnosing may include the steps of: 1) reverse transcribing all or a portion of an RNA copy of a DNA mismatch repair gene; and 2) amplifying a segment of the DNA produced by reverse transcription. An amplifying step in the present invention may comprise: selecting a pair of oligonucleotide primers capable of hybridizing to opposite strands of the mismatch repair gene, in an opposite orientation; and performing a polymerase chain reaction utilizing the oligonucleotide primers such that nucleic acid of the mismatch repair chain intervening between the primers is amplified to become the amplified segment.

In preferred embodiments of the methods summarized above, the DNA mismatch repair gene is hMLH1 or hPMS1. The segment of DNA corresponds to a unique portion of a nucleotide sequence selected from the group consisting of SEQ ID NOS: 6-24. “First stage” oligonucleotide primers selected from the group consisting of SEQ ID NOS: 44-82 are used in PCR to amplify the DNA segment. The invention also provides a method of using “second stage” nested primers (SEQ ID NOS: 83-122), for use with the first stage primers to allow more specific amplification and conservation of template DNA.

Another aspect of the present invention provides a method of identifying and classifying a DNA mismatch repair defective tumor comprising detecting in a tumor a mutation in a mismatch repair gene or gene product, preferably a mutL homolog (hMLH1 or hPMS1), the mutation being indicative of a defect in a mismatch repair system of the tumor.

The present invention also provides useful nucleotide and protein compositions. One such composition is an isolated nucleotide or protein structure including a segment sequentially corresponding to a unique portion of a human mutL homolog gene or gene product, preferably derived from either hMLH1 or hPMS1.

Other composition aspects of the invention comprise oligonucleotide primers capable of being used together in a polymerase chain reaction to amplify specifically a unique segment of a human mutL homolog gene, preferably hMLH1 or hPMS1.

Another aspect of the present invention provides a probe including a nucleotide sequence capable of binding specifically by Watson/Crick pairing to complementary bases in a portion of a human mutL homolog gene; and a label-moiety attached to the sequence, wherein the label-moiety has a property selected from the group consisting of fluorescent, radioactive and chemiluminescent.

We have also isolated and sequenced mouse MLH1 (mMLH1) and PMS1 (mPMS1) genes. We have used our knowledge of mouse mismatch repair genes to construct animal models for studying cancer. The models will be useful to identify additional oncogenes and to study environmental effects on mutagenesis.

Our knowledge of hMLH1 and hPMS1 gene sequences makes it possible to produce monoclonal and polyclonal antibodies for use in tests that detect the presence or absence of DNA mismatch repair protein in a tumor sample. Protein based testing is receiving significant attention in view of recent research showing that methylation of hMLH1 promoter DNA is the basis for DNA mismatch repair deficiency in some sporadic tumors. In this situation there is usually no detectable mutation in the hMLH1 cDNA. A screen for hMLH1 cDNA mutations would not show any abnormality. However, an immunoassay for hMLH1 protein shows absence of the protein in tumors with inactivation of the hMLH1 gene by mutation or by promotor methylation, and may be the screening test of choice for some applications. The protein structure information has been used to generate monoclonal antibodies that bind specifically to hMLH1 or hPMS1. The antibodies can be conjugated to labels such as fluorescent compounds, and then used as an immunohistochemical stain to detect DNA mismatch repair protein in a tumor sample.

In addition to diagnostic and therapeutic uses for the genes, our knowledge of hMLH1 and hPMS1 can be used to search for other genes of related function which are candidates for playing a role in certain forms of human cancer.

DESCRIPTION OF THE FIGURES

FIG. 1 is a flow chart showing an overview of the sequence of experimental steps we used to isolate, characterize and use human and mouse PMS1 and MLH1 genes. [0032]
FIG. 2 is an alignment of protein sequences for mutL homologs (SEQ ID NOS: 1-3) showing two highly-conserved regions (underlined) which we used to create degenerate PCR oligonucleotides for isolating additional mutL homologs. [0033]
FIG. 3 shows the entire cDNA nucleotide sequence (SEQ ID NO: 4) for the human MLH1 gene, and the corresponding predicted amino acid sequence (SEQ ID NO: 5) for the human MLH1 protein. The underlined DNA sequences are the regions of cDNA that correspond to the degenerate PCR primers that were originally used to amplify a portion of the MLH1 gene (nucleotides 118-135 and 343-359). [0034]
FIG. 4A shows the nucleotide sequences of the 19 exons which collectively correspond to the entire hMLH1 cDNA structure. The exons are flanked by intron boundary structures. Primer sites are underlined. The exons with their flanking intron structures correspond to SEQ ID NOS: 6-24. The exons, shown in non-underlined small case letters, corespond to SEQ ID NOS: 25-43. [0035]
FIG. 4B shows nucleotide sequences of primer pairs which have been used in PCR to amplify the individual exons. The “second stage” amplification primers (SEQ ID NOS: 83-122) are “nested” primers which are used to amplify target exons from the amplification product obtained with corresponding “first stage” amplification primers (SEQ ID NOS: 44-82). The structures in FIG. 4B correspond to the structures in Tables 2 and 3. [0036]
FIG. 5 is an alignment of the predicted amino acid sequences for human and yeast (SEQ ID NOS: 5 and 123, respectively) MLH1 proteins. Amino acid identities are indicated by boxes and gaps are indicated by dashes. [0037]
FIG. 6 is a phylogenetic tree of MutL-related proteins. [0038]
FIG. 7 is a two-panel photograph. The first panel (A) is a metaphase spread showing hybridization of the hMLH1 gene of [0039] chromosome 3. The second panel (B) is a composite of chromosome 3 from multiple metaphase spreads aligned with a human chromosome 3 ideogram. The region of hybridization is indicated in the ideogram by a vertical bar.
FIG. 8 is a comparison of sequence chromatograms from affected and unaffected individuals showing identification of a C to T transition mutation that produces a non-conservative amino acid substitution at [0040] position 44 of the hMLH1 protein.
FIG. 9 is an amino acid sequence alignment (SEQ ID NOS: 124-131) of the highly-conserved region of the MLH family of proteins surrounding the site of the predicted amino acid substitution. Bold type indicates the position of the predicted serine to phenylalanine amino acid substitution in affected individuals. Also highlighted are the serine or alanine residues conserved at this position in MutL-like proteins. Bullets indicate positions of highest amino acid conservation. For the [0041] MLH 1 protein, the dots indicate that the sequence has not been obtained. Sequences were aligned as described below in reference to the phylogenetic tree of FIG. 6.
FIG. 10 shows the entire nucleotide sequence for hPMS1 (SEQ ID NO: 132). [0042]
FIG. 11 is an alignment of the predicted amino acid sequences for human and yeast PMS1 proteins (SEQ ID NOS: 133 and 134, respectively). Amino acid identities are indicated by boxes and gaps are indicated by dashes. [0043]
FIG. 12 is a partial nucleotide sequence (SEQ ID NO: 149) from human MLH1. [0044]
FIG. 13 shows partial nucleotide sequences (SEQ ID NOS: 150 and 151) from human PMS1 cDNA. [0045]
FIG. 14 is a partial nucleotide sequence (SEQ ID NO: 152) from human MLH1. [0046]
FIG. 15 is a partial nucleotide sequence (SEQ ID NO: 153) from human PMS1.[0047]

DEFINITIONS

gene—“Gene” means a nucleotide sequence that contains a complete coding sequence. Generally, “genes” also include nucleotide sequences found upstream (e.g. promoter sequences, enhancers, etc.) or downstream (e.g. transcription termination signals, polyadenylation sites, etc.) of the coding sequence that affect the expression of the encoded polypeptide. [0048]
gene product—A “gene product” is either a DNA or RNA (mRNA) copy of a portion of a gene, or a corresponding amino acid sequence translated from mRNA. [0049]
wild-type—The term “wild-type”, when applied to nucleic acids and proteins of the present invention, means a version of a nucleic acid or protein that functions in a manner indistinguishable from a naturally-occurring, normal version of that nucleic acid or protein (i.e. a nucleic acid or protein with wild-type activity). For example, a “wild-type” allele of a mismatch repair gene is capable of functionally replacing a normal, endogenous copy of the same gene within a host cell without detectably altering mismatch repair in that cell. Different wild-type versions of the same nucleic acid or protein may or may not differ structurally from each other. [0050]
non-wild-type—The term “non-wild-type” when applied to nucleic acids and proteins of the present invention, means a version of a nucleic acid or protein that functions in a manner distinguishable from a naturally-occurring, normal version of that nucleic acid or protein. Non-wild-type alleles of a nucleic acid of the invention may differ structurally from wild-type alleles of the same nucleic acid in any of a variety of ways including, but not limited to, differences in the amino acid sequence of an encoded polypeptide and/or differences in expression levels of an encoded nucleotide transcript of polypeptide product. [0051]
For example, the nucleotide sequence of a non-wild-type allele of a nucleic acid of the invention may differ from that of a wild-type allele by, for example, addition, deletion, substitution, and/or rearrangement of nucleotides. Similarly, the amino acid sequence of a non-wild-type mismatch repair protein may differ from that of a wild-type mismatch repair protein by, for example, addition, substitution, and/or rearrangement of amino acids. [0052]
Particular non-wild-type nucleic acids or proteins that, when introduced into a normal host cell, interfere with the endogenous mismatch repair pathway, are termed “dominant negative” nucleic acids or proteins. [0053]
homologous—The term “homologous” refers to nucleic acids or polypeptides that are highly related at the level of nucleotide or amino acid sequence. Nucleic acids or polypeptides that are homologous to each other are termed “homologues”. [0054]
The term “homologous” necessarily refers to a comparison between two sequences. In accordance with the invention, two nucleotide sequences are considered to be homologous if the polypeptides they encode are at least about 50-60% identical, preferably about 70% identical, for at least one stretch of at least 20 amino acids. Preferably, homologous nucleotide sequences are also characterized by the ability to encode a stretch of at least 4-5 uniquely specified amino acids. Both the identity and the approximate spacing of these amino acids relative to one another must be considered for nucleotide sequences to be considered to be homologous. For nucleotide sequences less than 60 nucleotides in length, homology is determined by the ability to encode a stretch of at least 4-5 uniquely specified amino acids. [0055]
upstream/downstream—The terms “upstream” and “downstream” are art-understood terms referring to the position of an element of nucleotide sequence. “Upstream” signifies an element that is more 5′ than the reference element. “Downstream” refers to an element that is more 3′ than a reference element. [0056]
intron/exon—The terms “exon” and “intron” are art-understood terms referring to various portions of genomic gene sequences. “Exons” are those portions of a genomic gene sequence that encode protein. “Introns” are sequences of nucleotides found between exons in genomic gene sequences. [0057]
affected—The term “affected”, as used herein, refers to those members of a kindred that either have developed a characteristic cancer (e.g. colon cancer in an HNPCC lineage) and/or are predicted, on the basis of, for example, genetic studies, to carry an inherited mutation that confers susceptibility to cancer. [0058]
unique—A “unique” segment, fragment or portion of a gene or protein means a portion of a gene or protein which is different sequentially from any other gene or protein segment in an individual's genome. As a practical matter, a unique segment or fragment of a gene will typically be a nucleotide of at least about 13 bases in length and will be sufficiently different from other gene segments so that oligonucleotide primers may be designed and used to selectively and specifically amplify the segment. A unique segment of a protein is typically an amino acid sequence which can be translated from a unique segment of a gene. [0059]

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DESCRIPTION OF THE INVENTION

We have discovered mammalian genes which are involved in DNA mismatch repair. One of the genes, hPMS1, encodes a protein which is homologous to the yeast DNA mismatch repair protein PMS1. We have mapped the locations of hPMS1 to [0126] human chromosome 7 and the mouse PMS1 gene to mouse chromosome 5, band G. Another gene, hMLH1 (MutL Homolog) encodes a protein which is homologous to the yeast DNA mismatch repair protein MLH1. We have mapped the locations of hMLH1 to human chromosome 3p21.3-23 and to mouse chromosome 9, band E.
Studies[0127] ^1,2have demonstrated involvement of a human DNA mismatch repair gene homolog, hMSH2, on chromosome 2p in HNPCC. Based upon linkage data, a second HNPCC locus has been assigned to chromosome 3p21-23.³Examination of tumor DNA from the chromosome 3-linked kindreds revealed dinucleotide repeat instability similar to that observed for other HNPCC families⁶and several types of sporadic tumors.^7-10Because dinucleotide repeat instability is characteristic of a defect in DNA mismatch repair,^{5, 11, 12}we reasoned that HNPCC linked to chromosome 3p21-23 could result from a mutation in a second DNA mismatch repair gene.
Repair of mismatched DNA in [0128] Escherichia coli requires a number of genes including mutS, mutL and mutH, defects in any one of which result in elevated spontaneous mutation rates.¹³Genetic analysis in the yeast Saccharomyces cerevisiae has identified three DNA mismatch repair genes: a mutS homolog, MSH2,¹⁴and two mutL homologs, PMS1¹⁶and MLH1.⁴Each of these three genes play an indispensable role in DNA replication fidelity, including the stabilization of dinucleotide repeats.⁵
We believe that hMLH1 is the HNPCC gene previously linked to chromosome 3p based upon the similarity of the hMLH1 gene product to the yeast DNA mismatch repair protein, MLH1,[0129] ⁴the coincident location of the hMLH1 gene and the HNPCC locus on chromosome 3, and hMLH1 missense mutations which we found in affected individuals from chromosome 3-linked HNPCC families.
Our knowledge of the human and mouse MLH1 and PMS1 gene structures has many important uses. The gene sequence information can be used to screen individuals for cancer risk. Knowledge of the gene structures makes it possible to easily design PCR primers which can be used to selectively amplify portions of hMLH1 and hPMS1 genes for subsequent comparison to the normal sequence and cancer risk analysis. This type of testing also makes it possible to search for and characterize hMLH1 and hPMS1 cancer-linked mutations for the purpose of eventually focusing the cancer screening effort on specific gene loci. Specific characterization of cancer-linked mutations in hMLH1 and hPMS1 makes possible the production of other valuable diagnostic tools such as allele specific probes which may be used in screening tests to determine the presence or absence of specific gene mutations. [0130]
Additionally, the gene sequence information for hMLH1 and/or hPMS1 can be used, for example, in a two hybrid system, to search for other genes of related function which are candidates for cancer involvement. [0131]
The hMLH1 and hPMS1 gene structures are useful for making proteins which are used to develop antibodies directed to specific portions or the complete hMLH1 and hPMS1 proteins. Such antibodies can then be used to isolate the corresponding protein and possibly related proteins for research and diagnostic purposes. [0132]
The mouse MLH1 and PMS1 gene sequences are useful for producing mice that have mutations in the respective gene. The mutant mice are useful for studying the gene's function, particularly its relationship to cancer. [0133]

Methods for Isolating and Characterizing Mammalian MLH1 and PMS1 Genes

We have isolated and characterized four maimalian genes, i.e., human MLH1 (hMLH1), human PMS1 (hPMS1), mouse MLH1 (mPMS1) and mouse PMS1 (mPMS1). Due to the structural similarity between these genes, the methods we have employed to isolate and characterize them are generally the same. FIG. 1 shows in broad terms, the experimental approach which we used to isolate and characterize the four genes. The following discussion refers to the step-by-step procedure shown in FIG. 1. [0134]
[0135] Step 1 Design of Degenerate Oligonucleotide Pools for PCR
Earlier reports indicated that portions of three MutL-like proteins, two from bacteria, MutL and HexB, and one from yeast, PMS1 are highly conserved.[0136] ^16,18,19After inspection of the amino acid sequences of HexB, MutL and PMS1 proteins, as shown in FIG. 2, we designed pools of degenerate oligonucleotide pairs corresponding to two highly-conserved regions, KELVEN and GFRGEA, of the MutL-like proteins. The sequences (SEQ ID NOS: 139 and 140, respectively) of the degenerate oligonucleotides which we used to isolate the four genes are:

5′-CTTGATTCTAGAGC(T/C)TCNCCNC(T/G)(A/G)AANCC-3′

and

5′-AGCTCGGAGCTCAA(A/G)GA(A/G)(T/C)TNGTNGANAA-3′.
The underlined sequences within the primers are XbaI and SacI restriction endonuclease sites respectively. They were introduced in order to facilitate the cloning of the PCR-amplified fragments. In the design of the oligonucleotides, we took into account the fact that a given amino acid can be coded for by more than one DNA triplet (codon). The degeneracy within these sequences are indicated by multiple nucleotides within parentheses or N, for the presence of any base at that position. [0137]
[0138] Step 2 Reverse Transcription and PCR on Poly A+ Selected mRNA isolated from human cells
We isolated messenger (poly A+ enriched) RNA from cultured human cells, synthesized double-stranded cDNA from the mRNA, and performed PCR with the degenerate oligonucleotides.[0139] ⁴After trying a number of different PCR conditions, for example, adjusting the annealing temperature, we successfully amplified a DNA of the size predicted (˜210 bp) for a MutL-like protein.
[0140] Step 3 Cloning and Sequencing of PCR-Generated Fragments; Identification of Two Gene Fragments Representing Human PMS1 and MLH1
We isolated the PCR amplified material (˜210 bp) from an agarose gel and cloned this material into a plasmid (pUC19). We determined the DNA sequence of several different clones. The amino acid sequence inferred from the DNA sequence of two clones showed strong similarity to other known MutL-like proteins.[0141] ^4,16,18,19The predicted amino acid sequence for one of the clones was most similar to the yeast PMS1 protein. Therefore we named it hPMS1, for human PMS1. The second clone was found to encode a polypeptide that most closely resembles yeast MLH1 protein and was named, hMLH1, for human MLH1.
[0142] Step 4 Isolation of Complete Human and Mouse PMS1 and MLH1 cDNA Clones using the PCR Fragments as Probes
We used the 210 bp PCR-generated fragments of the hMLH1 and hPMS1 cDNAs, as probes to screen both human and mouse cDNA libraries (from Stratagene, or as described in reference 30). A number of cDNAs were isolated that corresponded to these two genes. Many of the cDNAs were truncated at the 5′ end. Where necessary, [0143] PCR techniques 31 were used to obtain the 5′-end of the gene in addition to further screening of cDNA libraries. Complete composite cDNA sequences were used to predict the amino acid sequence of the human and mouse, MLH1 and PMS1 proteins.
[0144] Step 5 Isolation of Human and Mouse, PMS1 and MLH1 Genomic Clones
Information on genomic and cDNA structure of the human MLH1 and PMS1 genes are necessary in order to thoroughly screen for mutations in cancer prone families. We have used human cDNA sequences as probes to isolate the genomic sequences of human PMS1 and MLH1. We have isolated four cosmids and two P1 clones for hPMS1, that together are likely to contain most, if not all, of the cDNA (exon) sequence. For hMLH1 we have isolated four overlapping λ-phage clones containing 5′-MLH1 genomic sequences and four PI clones (two full length clones and two which include the 5′ coding end plus portions of the promoter region) P1 clone. PCR analysis using pairs of oligonucleotides specific to the 5′ and 3′ ends of the hMLH1 cDNA, clearly indicates that the P1 clone contains the complete hMLH1 cDNA information. Similarly, genomic clones for mouse PMS1 and MLH1 genes have been isolated and partially characterized (described in Step 8). [0145]
[0146] Step 6 Chromosome Positional Mapping of the Human and Mouse, PMS1 and MLH1 Genes by Fluorescence In Situ Hybridization
We used genomic clones isolated from human and mouse PMS1 and MLH1 for chromosomal localization by fluorescence in situ hybridization (FISH).[0147] ^20,21We mapped the human MLH1 gene to chromosome 3p21.3-23, shown in FIG. 7 as discussed in more detail below. We mapped the mouse MLH1 gene to chromosome 9 band E, a region of synteny between mouse and human.²²In addition to FISH techniques, we used PCR with a pair of hMLH1-specific oligonucleotides to analyze DNA from a rodent/human somatic cell hybrid mapping panel (Coriell Institute for Medial Research, Camden, N.J.). Our PCR results with the panel clearly indicate that hMLH1 maps to chromosome 3. The position of hMLH1 3p21.3-23 is coincident to a region known to harbor a second locus for HNPCC based upon linkage data.
We mapped the hPMS1 gene, as shown in FIG. 12, to the long (q) arm of chromosome 7 (either 7q11 or 7q22) and the mouse PMS1 to [0148] chromosome 5 band G, two regions of synteny between the human and the mouse.²²We performed PCR using oligonucleotides specific to hPMS1 on DNA from a rodent/human cell panel. In agreement with the FISH data, the location of hPMS1 was confirmed to be on chromosome 7. These observations assure us that our human map position for hPMS1 to chromosome 7 is correct. The physical localization of hPMS1 is useful for the purpose of identifying families which may potentially have a cancer linked mutation in hPMS1.
[0149] Step 7 Using Genomic and cDNA Sequences to Identify Mutations in hPMS1 and hMLH1 Genes from HNPCC Families
We have analyzed samples collected from individuals in HNPCC families for the purpose of identifying mutations in hPMS1 or hMLH1 genes. Our approach is to design PCR primers based on our knowledge of the gene structures, to obtain exon/intron segments which we can compare to the known normal sequences. We refer to this approach as an “exon-screening”. [0150]
Using cDNA sequence information we have designed and are continuing to design hPMS1 and hMLH1 specific oligonucleotides to delineate exon/intron boundaries within genomic sequences. The hPMS1 and hMLH1 specific oligonucleotides were used to probe genomic clones for the presence of exons containing that sequence. Oligonucleotides that hybridized were used as primers for DNA sequencing from the genomic clones. Exon-intron junctions were identified by comparing genomic with cDNA sequences. [0151]
Amplification of specific exons from genomic DNA by PCR and sequencing of the products is one method to screen HNPCC families for mutations.[0152] ^1,2We have identified genomic clones containing hMLH1 cDNA information and have determined the structures of all intron/exon boundary regions which flanks the 19 exons of hMCH1.
We have used the exon-screening approach to examine the MLH1 gene of individuals from HNPCC families showing linkage to [0153] chromosome 3.³As will be discussed in more detail below, we identified a mutation in the MLH1 gene of one such family, consisting of a C to T substitution. We predict that the C to T mutation causes a serine to phenylalanine substitution in a highly-conserved region of the protein. We are continuing to identify HNPCC families from whom we can obtain samples in order to find additional mutations in hMLH1 and hPMS1 genes.
We are also using a second approach to identify mutations in hPMS1 and hMLH1. The approach is to design hPMS1 or hMLH1 specific oligonucleotide primers to produce first-strand cDNA by reverse transcription off RNA. PCR using gene-specific primers will allow us to amplify specific regions from these genes. DNA sequencing of the amplified fragments will allow us to detect mutations. [0154]
[0155] Step 8 Design Targeting Vectors to Disrupt Mouse PMS1 and MLH1 Genes in ES Cells; Study Mice Deficient in Mismatch Repair.
We constructed a gene targeting vector based on our knowledge of the genomic mouse PMS1 DNA structure. We used the vector to disrupt the PMS1 gene in mouse embryonic stem cells.[0156] ³⁶The cells were injected into mouse blastocysts which developed into mice that are chimeric (mixtures) for cells carrying the PMS1 mutation. The chimeric animals will be used to breed mice that are heterozygous and homozygous for the PMS1 mutation. These mice will be useful for studying the role of the PMS1 gene in the whole organism.

Human MLH1

The following discussion is a more detailed explanation of our experimental work relating to hMLH1. As mentioned above, to clone mammalian MLH genes, we used PCR techniques like those used to identify the yeast MSH1, MSH2 and MLH1 genes and the human MSH2 gene.[0157] ^{1, 2, 4, 14}As template in the PCR, we used double-stranded cDNA synthesized from poly (A+) enriched RNA prepared from cultured primary human fibroblasts. The degenerate oligonucleotides were targeted at the N-terminal amino acid sequences KELVEN and GFRGEA (see FIG. 3), two of the most conserved regions of the MutL family of proteins previously described for bacteria and yeast.^16,18,19Two PCR products of the predicted size were identified, cloned and shown to encode a predicted amino acid sequence with homology to MutL-like proteins. These two fragments generated by PCR were used to isolate human cDNA and genomic DNA clones.
The oligonueleotide primers which we used to amplify human MutL-related sequences were 5′-CTTGATTCTAGAGC(T/C)TCNCCNC(T/G)(A/G)AANCC-3′ (SEQ ID NO: 139) and 5′-AGGTCGGAGCTCAA(A/G)GA(A/G)(T/C)TNGTNGANAA-3′ (SEQ ID NO: 140). PCR was carried out in 50 μL reactions containing cDNA template, 1.0 μM each primer, 5 IU of Taq polymerase (C) 50 mM KCl, 10 mM Tris buffer pH 7.5 and 1.5 mM MgCl. PCR was carried out for 35 cycles of 1 minute at 94 C.°, 1 minute at 43 C.° and 1.5 minutes at 62 C.°. Fragments of the expected size, approximately 212 bp, were cloned into [0158] pUC 19 and sequenced. The cloned MLH1 PCR products were labeled with a random primer labeling kit (RadPrime, Gibco BRL) and used to probe human cDNA and genomic cosmid libraries by standard procedures. DNA sequencing of double-stranded plasmid DNAs was performed as previously described.
The hMLH1 cDNA nucleotide sequence as shown in FIG. 3 encodes an open reading frame of 2268 bp. Also shown in FIG. 3 is the predicted protein sequence encoded for by the hMLH1 cDNA. The underlined DNA sequences are the regions of cDNA that correspond to the degenerate PCR primers that were originally used to amplify a portion of the MLH1 gene (nucleotides 118-135 and 343-359). [0159]
FIG. 4A shows 19 nucleotide sequences corresponding to portions of hMLH1. Each sequence includes one of the 19 exons, in its entirety, surrounded by flanking intron sequences. Target PCR primer cites are underlined. More details relating to the derivation and uses of the sequences shown in FIG. 4A, are set forth below. [0160]
As shown in FIG. 5, the hMLH1 protein is comprised of 756 amino acids and [0161] shares 41% identity with the protein product of the yeast DNA mismatch repair gene, MLH1.⁴The regions of the hMLH1 protein most similar to yeast MLH1 correspond to amino acids 11 through 317, showing 55% identity, and the last 13 amino acids which are identical between the two proteins. FIG. 5 shows an alignment of the predicted human MLH1 and S. cerevisiae MLH1 protein sequences. Amino acid identities are indicated by boxes, and gaps are indicated by dashes. The pair wise protein sequence alignment was performed with DNAStar MegAlign using the clustal method.²⁷Pair wise alignment parameters were a ktuple of 1, gap penalty of 3, window of 5 and diagonals of 5. Furthermore, as shown in FIG. 13, the predicted amino acid sequences of the human and mouse MLH1 proteins show at least 74% identity.
FIG. 6 shows a phylogenetic tree of MutL-related proteins. The phylogenetic tree was constructed using the predicted amino acid sequences of 7 MutL-related proteins: human MLH1; mouse MLH1; [0162] S. cerevisiae MLH1; S. cerevisiae PMS1; E. coli; MutL; S. typhimurium MutL and S. pneumoniae HexB. Required sequences were obtained from GenBank release 7.3. The phylogenetic tree was generated with the PILEUP program of the Genetics Computer Group software using a gap penalty of 3 and a length penalty of 0.1. The recorded DNA sequences of hMLH1 and hPMS1 have been submitted to GenBank.

hMLH1 Intron Location and Intron/Exon Boundary Structures

In our previous U.S. patent application Ser. No. 08/209,521, we described the nucleotide sequence of a complimentary DNA (cDNA) clone of a human gene, hMLH1. The cDNA sequence of hMLH1 (SEQ ID NO: 4) is presented in this application in FIG. 3. We note that there may be some variability between individuals hMLH1 cDNA structures, resulting from polymorphisms within the human population, and the degeneracy of the genetic code. [0163]
In the present application, we report the results of our genomic sequencing studies. Specifically, we have cloned the human genomic region that includes the hMLH1 gene, with specific focus on individual exons and surrounding intron/exon boundary structures. Toward the ultimate goal of designing a comprehensive and efficient approach to identify and characterize mutations which confer susceptibility to cancer, we believe it is important to know the wild-type sequences of intron structures which flank exons in the hMLH1 gene. One advantage of knowing the sequence of introns near the exon boundaries, is that it makes it possible to design primer pairs for selectively amplifying entire individual exons. More importantly, it is also possible that a mutation in an intron region, which, for example, may cause a mRNA splicing error, could result in a defective gene product, i.e., susceptibility to cancer, without showing any abnormality in an exon region of the gene. We believe a comprehensive screening approach requires searching for mutations, not only in the exon or cDNA, but also in the intron structures which flank the exon boundaries. [0164]
We have cloned the human genomic region that includes hMLH1 using approaches which are known in the art, and other known approaches could have been used. We used PCR to screen a P1 human genomic library for the hMLH1 gene. We obtained four clones, two that contained the whole gene and two which lacked the C-terminus. We characterized one of the full length clones by cycle sequencing, which resulted in our definition of all intron/exon junction sequences for both sides of the 19 hMLH1 exons. We then designed multiple sets of PCR primers to amplify each individual exon (first stage primers) and verified the sequence of each exon and flanking intron sequence by amplifying several different genomic DNA samples and sequencing the resulting fragments using an [0165] ABI 373 sequencer. In addition, we have determined the sizes of each hMLH1 exon using PCR methods. Finally, we devised a set of nested PCR primers (second stage primers) for reamplification of individual exons. We have used the second stage primers in a multi-plex method for analyzing HNPCC families and tumors for hMLH1 mutations. Generally, in the nested PCR primer approach, we perform a first multi-plex amplification with four to eight sets of “first stage” primers, each directed to a different exon. We then reamplify individual exons from the product of the first amplification step, using a single set of second stage primers. Examples and further details relating to our use of the first and second stage primers are set forth below.

Through our genomic sequencing studies, we have identified all nineteen exons within the hMLH1 gene, and have mapped the intron/exon boundaries. One aspect of the invention, therefore, is the individual exons of the hMLH1 gene. Table 1 presents the nucleotide coordinates (i.e., the point of insertion of each intron within the coding region of the gene) of the hMLH1 exons (SEQ ID NOS: 25-43). The presented coordinates are based on the hMLH1 cDNA sequence, assigning position “1” to the “A” of the start “ATG” (which A is nucleotide 1 in SEQ ID NO: 4.

	TABLE 1


	Intron Number	cDNA Sequence Coordinates

	intron 1	116 & 117
	intron 2	207 & 208
	intron 3	306 & 307
	intron 4	380 & 381
	intron 5	453 & 454
	intron 6	545 & 546
	intron 7	592 & 593
	intron 8	677 & 678
	intron 9	790 & 791
	intron 10	884 & 885
	intron 11	1038 & 1039
	intron 12	1409 & 1410
	intron 13	1558 & 1559
	intron 14	1667 & 1668
	intron 15	1731 & 1732
	intron 16	1896 & 1897
	intron 17	1989 & 1990
	intron 18	2103 & 2104

We have also determined the nucleotide sequence of intron regions which flank exons of the hMLH1 gene. SEQ ID NOS: 6-24 are individual exon sequences bounded by their respective upstream and downstream intron sequences. The same nucleotide structures are shown in FIG. 4A, where the exons are numbered from N-terminus to C-terminus with respect to the chromosomal locus. The 5-digit numbers indicate the primers used to amplify the exon. All sequences are numbered assuming the A of the ATG codon is [0167] nucleotide 1. The numbers in ( ) are the nucleotide coordinates of the coding sequence found in the indicated exon. Uppercase is intron. Lowercase is exon or non-translated sequences found in the mRNA/cDNA clone. Lowercase and underlined sequences correspond to primers. The stop codon at 2269-2271 is in italics and underlined.

Table 2 presents the sequences of primer pairs (“first stage” primers) which we have used to amplify individual exons together with flanking intron structures.

TABLE 2


	PRIMER		PRIMER
EXON NO.	LOCATION	PRIMER NO.	SEQ ID NO	PRIMER NUCLEOTIDE SEQUENCE

1	upstream	18442	44	5′ aggcactgaggtgattggc
1	downstream	19109	45	5′ tcgtagcccttaagtgagc

2	upstream	19689	46	5′ taatatgtacattagagtagttg
2	downstream	19688	47	5′ cagagaaaggtcctgactc

3	upstream	19687	48	5′ agagatttggaaaatgagtaac
3	downstream	19786	49	5′ acaatgtcatcacaggagg

4	upstream	18492	50	5′ aacctttccctttggtgagg
4	downstream	18421	51	5′ gattactctgagacctaggc

5	upstream	18313	52	5′ gattttctcttttccccttggg
5	downstream	18179	53	5′ caaacaaagcttcaacaatttac

6	upstream	18318	54	5′ gggttttattttcaagtacttctatg
6	downstream	18317	55	5′ gctcagcaactgttcaatgtatgagc

7	upstream	19009	56	5′ ctagtgtgtgtttttggc
7	downstream	19135	57	5′ cataaccttatctccacc

8	upstream	18197	58	5′ ctcagccatgagacaataaatcc
8	downstream	18924	59	5′ ggttcccaaataatgtgatgg

9	upstream	18765	60	5′ caaaagcttcagaatctc
9	downstream	18198	61	5′ ctgtgggtgtttcctgtgagtgg

10	upstream	18305	62	5′ catgactttgtgtgaatgtacacc
10	downstream	18306	63	5′ gaggagagcctgatagaacatctg

11	upstream	18182	64	5′ gggctttttctccccctcec
11	downstream	19041	6S	5′ aaaatctgggctctcaeg

12	upstream	18579	66	5′ aattatacctcatactagc
12	downstream	18178	67	5′ gttttattacagaataaaggagg
12	downstream	19070	68	5′ aagccaaagttagaaggca

13	upstream	18420	69	5′ tgcaacccacaaaatttggc
13	downstream	18443	70	5′ ctttctceatttccaaaacc

14	upstream	19028	71	5′ tggtgtctctagttctgg
14	downstream	18897	72	5′ cattgttgtagtagctctgc

15	upstream	19025	73	5′ cccatttgtcccaaetgg
15	downstream	18575	74	5′ cggtcagttgaaatgtcag

16	upstream	18184	75	5′ catttggatgctccgttaaagc
16	downstream	18314	76	5′ cacccggctggaaattttatttg

17	upstream	18429	77	5′ ggaaaggcactggagaaatggg
17	downstream	18315	78	5′ ccctccagcaeacatgcatgtaccg

18	upstream	18444	79	5′ taagtagtctgtgatctccg
18	downstream	18581	80	5′ atgtatgaggtcctgtcc

19	upstream	18638	81	5′ gacaccagtgtatgttgg
19	downstream	18637	82	5′ tgagaaagaagaacacatccc

Additionally, we have designed a set of “second stage” amplification primers, the structures of which are shown below in Table 3. We use the second stage primers in conjunction with the first stage primers in a nested amplification protocol, as described below.

TABLE 3


	PRIMER		PRIMER
EXON NO.	LOCATION	PRIMER NO.	SEQ ID NO	PRIMER NUCLEOTIDE SEQUENCE

1	upstream	19295	83	5′ tgtaaaacgacggccagtcactgaggtgattggctgaa
1	downstream	19446	84	*5′ tagcccttaagtgagcccg

2	upstream	18685	85	5′ tgtaaaacgacggccagttacattagagtagttgcaga
2	downstream	19067	86	*5′ aggtcctgactcttccatg

3	upstream	18687	87	5′ tgtaaaacgaeggccagtttggaaaatgagtaacatgatt
3	downstream	19068	88	*5′ tgtcatcacaggaggatat

4	upstream	19294	89	5′ tgtaaaacgacggccagtctttccctttggtgaggtga
4	downstream	19077	90	*5′ tactctgagacctaggccca

5	upstream	19301	91	5′ tgtaaaacgacggccagttctcttttccccttgggattag
5	downstream	19046	92	*5′ acaaagcttcaacaatttactct

6	upstream	19711	93	5′ tgtaaaacgacggccagtgttttattttcaagtacttctatgaatt
6	downstream	19079	94	*5′ cagcaaetgttcaatgtatgagcact

7	upstream	19293	95 5′ tgtaaaaegacggccagtgtgtgtgtttttggcaac
7	downstream	19435	96	*5′ aaccttatctccaccagc

8	upstream	19329	97	5′ tgtaaaacgacggccagtagccatgagacaataaatccttg
8	downstream	19450	98	*5′ tcccaaataatgtgatggaatg

9	upstream	19608	99	5′ tgtaaaacgacggccagtaagcttcagaatctctttt
9	downstream	19449	100	*5′ tgggtgtttcctgtgagtggatt

10	upstream	19297	101	5′ tgtaaaacgacggccagtactttgtgtgaatgtacacctgtg
10	downstream	19081	102	*5′ gagagcctgatagaacatctgttg

11	upstream	19486	103	5′ tgtaaaaegacggccagtctttttctccccctcccacta
11	downstream	19455	104	*5′ tctgggctctcacgtct

12	upstream	20546	105	*5′ cttattctgagtctctcc
12	downstream	20002	106	5′ tgtaaaacgacggccagtgtttgctcagaggctgc
12	upstream	19829	107	*5′ gatggttcgtacagattcccg
12	downstream	19385	108	5′ tgtaaaacgacggccagtttattacagaataaaggaggtag

13	upstream	19300	109	5′ tgtaaaacgacggccagtaacccacaaaatttggctaag
13	downstream	19078	110	*5′ tctccatttccaaaaccttg

14	upstream	19456	111	*5′ tgtctctagttctggtgc
14	downstream	19472	112	5′ tgtaaaacgacggccagttgttgtagtagctctgcttg

15	upstream	19697	113	*5′ atttgtcccaactggttgta
15	downstream	19466	114	5′ tgtaaaacgacggccagttcagttgaaatgtcagaaagtg

16	upstream	19269	115	5′ tgtaaaacgacggccagt
16	downstream	19047	116	*5′ ccggctggaaattttatttggag

17	upstream	19298	117	5′ tgtaaaacgacggccagtaggcactggagaaatgggatttg
17	downstream	19080	118	*5′ tccagcacacatgcatgtaccgaaat

18	upstream	19436	119	*5′ gtagtctgtgatctccgttt
18	downstream	19471	120	5′ tgtaaaacgacggccagttatgaggtcctgtcctag

19	upstream	19447	121	*5′ accagtgtatgttgggatg
19	downstream	19330	122	5′ tgtaaaacgacggccagtgaaagaagaacacatcccaca

In Table 3 an asteric (*) indicates that the 5′ nucleotide is biotinylated. Exons 1-7, 10, 13 and 16-19 can be specifically amplified in PCR reactions containing either 1.5 mM or 3 mM MgCl[0170] ₂. Exons 11 and 14 can only be specifically amplified in PCR reactions containing 1.5 mM MgCl₂and exons 8, 9, 12 and 15 can only be specifically amplified in PCR reactions containing 3 mM MgCl₂. With respect to exon 12, the second stage amplification primers have been designed so that exon 12 is reamplified in two halves. The 20546 and 20002 primer set amplifies the N-terminal half. The primer set 19829 and 19835 amplifies the C-terminal half. An alternate primer for 18178 is 19070.
The hMLH1 sequence information provided by our studies and disclosed in this application and preceding related applications, may be used to design a large number of different oligonucleotide primers for use in identifying hMLH1 mutations that correlate with cancer susceptibility and/or with tumor development in an individual, including primers that will amplify more than one exon (and/or flanking intron sequences) in a single product band. [0171]
One of ordinary skill in the art would be familiar with considerations important to the design of PCR primers for use to amplify the desired fragment or gene.[0172] ³⁷These considerations may be similar, though not necessarily identical to those involved in design of sequencing primers, as discussed above. Generally it is important that primers hybridize relatively specifically (i.e. have a T_mof greater than about 55-degrees° C., and preferably around 60-degrees° C.). For most cases, primers between about 17 and 25 nucleotides in length work well. Longer primers can be useful for amplifying longer fragments. In all cases, it is desirable to avoid using primers that are complementary to more than one sequence in the human genome, so that each pair of PCR primers amplifies only a single, correct fragment. Nevertheless, it is only absolutely necessary that the correct band be distinguishable from other product bands in the PCR reaction.
The exact PCR conditions (e.g. salt concentration, number of cycles, type of DNA polymerase, etc.) can be varied as known in the art to improve, for example, yield or specificity of the reaction. In particular, we have found it valuable to use nested primers in PCR reactions in order to reduce the amount of required DNA substrate and to improve amplification specificity. [0173]
Two examples follow. The first example illustrates use of a first stage primer pair (SEQ ID NOS: 69 and 70) to amplify intron/exon segment (SEQ ID NO: 18). The second example illustrates use of second stage primers to amplify a target intron/exon segment from the product of a first PCR amplification step employing first stage primers. [0174]

EXAMPLE 1

Amplification of hMLH1 Genomic Clones from a P1 Phage Library

25 ng genomic DNA (or 1 ng of a P1 phage can be used) was used in PCR reactions including: [0175]
0.05 mM dNTPs [0176]
50 mM KCl [0177]
3 mM Mg [0178]
10 mM Tris-HCl pH 8.5 [0179]
[0180] 0.01% gelatin
5 μM primers [0181]
Reactions were performed on a Perkin-Elmer Cetus model 9600 thermal cycler. Reactions were incubated at 95-degrees° C. for 5 minutes, followed by 35 cycles (30 cycles from a PI phage) of: [0182]
94-degrees° C. for 30 seconds [0183]
55-degrees° C. for 30 seconds [0184]
72-degrees° C. for 1 minute. [0185]
A final 7 minute extension reaction was then performed at 72′-degrees C. Desirable P1 clones were those from which an approximately bp product band was produced. [0186]

EXAMPLE 2

Amplification of hMLH1 Sequences from Genomic DNA Using Nested PCR Primers

We performed two-step PCR amplification of hMLH1 sequences from genomic DNA as follows. Typically, the first amplification was performed in a 25 microliter reaction including: [0187]
25 ng of chromosomal DNA [0188]
Perkin-Elmer PCR buffer II (any suitable buffer could be used) [0189]
3 mM MgCl[0190] ₂
50 μM each dNTP [0191]
Taq DNA polymerase [0192]
5 μM primers (SEQ ID NOS: 69, 70) [0193]
and incubated at 95-degrees° C. for 5 minutes, followed by 20 cycles of: [0194]
94-degrees° C. for 30 seconds [0195]
55-degrees° C. for 30 seconds. [0196]
The product band was typically small enough (less than an approximately 500 bp) that separate extension steps were not performed as part of each cycle. Rather, a single extension step was performed, at 72-degrees° C. for 7 minutes, after the 20 cycles were completed. Reaction products were stored at 4-degrees° C. [0197]
The second amplification reaction, usually 25 or 50 microliters in volume, included: [0198]
1 or 2 microliters (depending on the volume of the reaction) of the first amplification reaction product [0199]
Perkin-Elmer PCR buffer II (any suitable buffer could be used) [0200]
3 mM or MgCl[0201] ₂
50 μM each dNTP [0202]
Taq DNA polymerase [0203]
5 μM nested primers (SEQ ID NOS: 109, 110), [0204]
and was incubated at 95-degrees° C. for 5 minutes, followed by 20-25 cycles of: [0205]
94-degrees° C. for 30 seconds [0206]
55-degrees° C. for 30 seconds [0207]
a single extension step was performed, at 72-degrees° C. for 7 minutes, after the cycles were completed. Reaction products were stored at 4-degrees° C. [0208]
Any set of primers capable of amplifying a target hMLH1 sequence can be used in the first amplification reaction. We have used each of the primer sets presented in Table 2 to amplify an individual hMLH1 exon in the first amplification reaction. We have also used combinations of those primer sets, thereby amplifying multiple individual hMLH1 exons in the first amplification reaction. [0209]
The nested primers used in the first amplification step were designed relative to the primers used in the first amplification reaction. That is, where a single set of primers is used in the first amplification reaction, the primers used in the second amplification reaction should be identical to the primers used in the first reaction except that the primers used in the second reaction should not include the 5′-most nucleotides of the first amplification reaction primers, and should extend sufficiently more at the 3′ end that the T[0210] _mof the second amplification primers is approximately the same as the T_mof the first amplification reaction primers. Our second reaction primers typically lacked the 3 5′-most nucleotides of the first amplification reaction primers, and extended approximately 3-6 nucleotides farther on the 3′ end. SEQ ID NOS: 109, 110 are examples of nested primer pairs that could be used in a second amplification reaction when SEQ ID NOS: 69 and 70 were used in the first amplification reaction.
We have also found that it can be valuable to include a standard sequence at the 5′ end of one of the second amplification reaction primers to prime sequencing reactions. Additionally, we have found it useful to biotinylate that last nucleotide of one or both of the second amplification reaction primers so that the product band can easily be purified using magnetic beads[0211] ⁴⁰and then sequencing reactions can be performed directly on the bead-associated products.^41-45
For additional discussion of multiplex amplification and sequencing methods, see References by Zu et al. and Espelund et al.[0212] ^46,47

hMLH1 Link to Cancer

As a first step to determine whether hMLH1 was a candidate for the 1HNPCC locus on human chromosome 3p21-23,[0213] ³we mapped hMLH1 by fluorescence in situ hybridization (FISH).^20,21We used two separate genomic fragments (data not shown) of the hMLH1 gene in FISH analysis. Examination of several metaphase chromosome spreads localized hMLH1 to chromosome 3p21.3-23.
Panel A of FIG. 7 shows hybridization of hMLH1 probes in a metaphase spread. Biotinylated hMLH1 genomic probes were hybridized to banded human metaphase chromosomes as previously described.[0214] ^20,21Detection was performed with fluorescein isothiocyanate (FITC)-conjugated avidin (green signal); chromosomes, shown in blue, were counterstained with 4′6-diamino-2-phenylindole (DAPI). Images were obtained with a cooled CCD camera, enhanced, pseudocoloured and merged with the following programs: CCD Image Capture; NIH Image 1.4; Adobe Photoshop and Genejoin Maxpix respectively. Panel B of FIG. 7 shows a composite of chromosome 3 from multiple metaphase spreads aligned with the human chromosome 3 ideogram. Region of hybridization (distal portion of 3p21.3-23) is indicated in the ideogram by a vertical bar.
As independent confirmation of the location of hMLH1 on [0215] chromosome 3, we used both PCR with a pair of hMLH1-specific oligonucleotides and Southern blotting with a hMLH1-specific probe to analyze DNA from the NIGMS2 rodent/human cell panel (Coriell Inst. for Med. Res., Camden, N.J., USA). Results of both techniques indicated chromosome 3 linkage. We also mapped the mouse MLH1 gene by FISH to chromosome 9 band E. This is a position of synteny to human chromosome 3p.²²Therefore, the hMLH1 gene localizes to 3p21.3-23, within the genomic region implicated in chromosome 3-linked HNPCC families.³
Next, we analyzed blood samples from affected and unaffected individuals from two chromosome-3 candidate HNPCC families [0216] ³for mutations. One family, Family 1, showed significant linkage (lod score=3.01 at recombination fraction of 0) between HNPCC and a marker on 3p. For the second family, Family 2, the reported lod score (1.02) was below the commonly accepted level of significance, and thus only suggested linkage to the same marker on 3p. Subsequent linkage analysis of Family 2 with the microsatellite marker D3S1298 on 3p21.3 gave a more significant lod score of 1.88 at a recombination fraction of 0. Initially, we screened for mutations in two PCR-amplified exons of the hMLH1 gene by direct DNA sequencing (FIG. 4). We examined these two exons from three affected individuals of Family 1, and did not detect any differences from the expected sequence. In Family 2, we observed that four individuals affected with colon cancer are heterozygous for a C to T substitution in an exon encoding amino acids 41-69, which corresponds to a highly-conserved region of the protein (FIG. 9). For one affected individual, we screened PCR-amplified cDNA for additional sequence differences. The combined sequence information obtained from the two exons and cDNA of this one affected individual represents 95% (i.e. all but the first 116 bp) of the open reading frame. We observed no nucleotide changes other than the C to T substitution. In addition, four individuals from Family 2, predicted to be carriers based upon linkage data, and as yet unaffected with colon cancer, were found to be heterozygous for the same C to T substitution. Two of these predicted carriers are below and two are above the mean age of onset (50 years) in this particular family. Two unaffected individuals examined from this same family, both predicted by linkage data to be non carriers, showed the expected normal sequence at this position. Linkage analysis that includes the C to T substitution in Family 2 gives a lod score of 2.23 at a recombination fraction 0. Using low stringency cancer diagnostic criteria, we calculated a lod score of 2.53. These data indicate the C to T substitution shows significant linkage to the HNPCC in Family 2.
FIG. 8 shows sequence chromatograms indicating a C to T transition mutation that produces a non-conservative amino acid substitution at [0217] position 44 of the hMLH1 protein. Sequence analysis of one unaffected (top panels, plus and minus strands) and one affected individual (lower panels, plus and minus strands) is presented. The position of the heterozygous nucleotide is indicated by an arrow. Analysis of the sequence chromatographs indicates that there is sufficient T signal in the C peak and enough A signal in the G peak for the affected individuals to be heterozygous at this site.
To determine whether this C to T substitution was a polymorphism, we sequenced this same exon amplified from the genomic DNA from 48 unrelated individuals and observed only the normal sequence. We have examined an additional 26 unrelated individuals using allele specific oligonucleotide (ASO) hybridization analysis.[0218] ³³The ASO sequences (SEQ ID NOS: 141 and 142, respectively) which we used are:
5′-ACTTGTGGATTTTGC-3′ and 5′-ACTTGTGAATTTTGC-3′. [0219]
Based upon direct DNA sequencing and ASO analysis, none of these 74 unrelated individuals carry the C to T substitution. Therefore, the C to T substitution observed in [0220] Family 2 individuals is not likely to be a polymorphism. As mentioned above, we did not detect this same C to T substitution in affected individuals from a second chromosome 3-linked family, Family 1.3 We are continuing to study individuals of Family 1 for mutations in hMLH1.

Table 4 below summarizes our experimental analysis of blood samples from affected and unaffected individuals from Family 2 and unrelated individuals.

TABLE 4


		Number of Individuals with
		C to T Mutation/
FAMILY 2	Status	Number of Individuals Tested

	Affected	4/4
	Predicted Carriers	4/4
	Predicted Non-carriers	0/2
	Unrelated Individuals	0/74

Based on several criteria, we suggest that the observed C to T substitution in the coding region of hMLH1 represents the mutation that is the basis for HNPCC in [0222] Family 2.³First, DNA sequence and ASO analysis did not detect the C to T substitution in 74 unrelated individuals. Thus, the C to T substitution is not simply a polymorphism. Second, the observed C to T substitution is expected to produce a serine to phenylalanine change at position 44 (See FIG. 9). This amino acid substitution is a non-conservative change in a conserved region of the protein (FIGS. 3 and 9). Secondary structure predictions using Chou-Fasman parameters suggest a helix-turn-beta sheet structure with position 44 located in the turn. The observed Ser to Phe substitution, at position 44 lowers the prediction for this turn considerably, suggesting that the predicted amino acid substitution alters the conformation of the hMLH1 protein. The suggestion that the Ser to Phe substitution is a mutation which confers cancer susceptibility is further supported by our experiments which show that an analogous substitution (alanine to phenylalanine) in a yeast MLH1 gene results in a nonfunctional mismatch repair protein. In bacteria and yeast, a mutation affecting DNA mismatch repair causes comparable increases in the rate of spontaneous mutation including additions and deletions within dinucleotide repeats.^{4,5,11,13,14,15,16}In humans, mutation of hMSH2 is the basis of chromosome-2 HNPCC,^1,2tumors which show microsatellite instability and an apparent defect in mismatch repair.¹²Chromosome 3-linked HNPCC is also associated with instability of dinucleotide repeats.³Combined with these observations, the high degree of conservation between the human MLH1 protein and the yeast DNA mismatch repair protein MLH1 suggests that hMLH1 is likely to function in DNA mismatch repair. During isolation of the hMLH1 gene, we identified the hPMS1 gene. This observation suggests that mammalian DNA mismatch repair, like that in yeast,⁴may require at least two MutL-like proteins.
It should be noted that it appears that different HNPCC families show different mutations in the MLH1 gene. As explained above, affected individuals in [0223] Family 1 showed “tight linkage” between HNPCC and a locus in the region of 3p21-23. However, affected individuals in Family 1 do not have the C to T mutation found in Family 2. It appears that the affected individuals in Family 1 have a different mutation in their MLH1 gene. Further, we have used the structure information and methods described in this application to find and characterize another hMLH1 mutation which apparently confers cancer susceptibility in heterozygous carriers of the mutant gene in a large English HNPCC family. The hMLH1 mutation in the English family is a +1 T frameshift which is predicted to lead to the synthesis of a truncated hMLH1 proteiri. Unlike, for example, sickle cell anemia, in which essentially all known affected individuals have the same mutation multiple hMLH1 mutations have been discovered and linked to cancer. Therefore, knowledge of the entire cDNA sequence for hMLH1 (and probably hPMS1), as well as genomic sequences particularly those that surround exons, will be useful and important for characterizing mutations in families identified as exhibiting a high frequency of cancer.
Subsequent to our discovery of a cancer conferring mutation in hMLH1, studies by others have resulted in the characterization of at least 5 additional mutations in hMLH1, each of which appears to have conferred cancer susceptibility to individuals in at least one HNPCC family. For example, Papadopoulos et al. indentified such as a mutation, characterized by an in-frame deletion of 165 base pairs between codons 578 to 632. In another family, Papadopoulos et al. observed an hMLH1 mutation, characterized by a frame shift and substitution of new amino acids, namely, a 4 base pair deletion between codons 727 and 728. Papadopoulos et al. also reports an hMLH1 cancer linked mutation, characterized by an extension of the COOH terminus, namely, a 4 base pair insertion between [0224] codons 755 and 756.³⁸
In summary, we have shown that DNA mismatch repair gene hMLH1 which is likely to be the hereditary nonpolyposis colon cancer gene previously localized by linkage analysis to chromosome 3p21-23.[0225] ³Availability of the hMLH1 gene sequence will facilitate the screening of HNPCC families for cancer-linked mutations. In addition, although loss of heterozygosity (LOH) of linked markers is not a feature of either the 2p or 3p forms of HNPCC,^3,6LOH involving the 3p21.3-23 region has been observed in several human cancers.^24,26This suggests the possibility that hMLH1 mutation may play some role in these tumors.

Human PMS1

Human PMS1 was isolated using the procedures discussed with reference to FIG. 1. FIG. 10 shows the entire hPMS1 cDNA nucleotide sequence. FIG. 11 shows an alignment of the predicted human and yeast PMS1 protein sequences. We determined by FISH analysis that human PMS1 is located on [0226] chromosome 7. Subsequent to our discovery of hPMS1, others have identified mutations in the gene which appear to confer HNPCC susceptibility.³⁹

Mouse MLH1

Using the procedure outlined above with reference to FIG. 1, we have determined a partial nucleotide sequence of mouse MLH1 cDNA, as shown in FIG. 12 (SEQ ID NO: 135). FIG. 13 shows the corresponding predicted amino acid sequence for mMLH1 protein (SEQ ID NO: 136) in comparison to the predicted hMLH1 protein sequence (SEQ ID NO: 5). Comparison of the mouse and human MLH1 proteins as well as the comparison of hMLH1 with yeast MLH1 proteins, as shown in FIG. 9, indicate a high degree of conservation. [0227]

Mouse PMS1

Using the procedures discussed above with reference to FIG. 1, we isolated and sequenced the mouse PMS1 gene, as shown in FIG. 14 (SEQ ID NO: 137). This cDNA sequence encodes a predicted protein of 864 amino acids (SEQ ID NO: 138), as shown in FIG. 15, where it is compared to the predicted amino acid sequence for hPMS1 (SEQ ID NO: 133). The degree of identity between the predicted mouse and human PMS1 proteins is high, as would be expected between two mammals. Similarly, as noted above, there is a strong similarity between the human PMS1 protein and the yeast DNA mismatch repair protein PMS1, as shown in FIG. 11. The fact that yeast PMS1 and MLH1 function in yeast to repair DNA mismatches, strongly suggests that human and mice PMS1 and [0228] MLH 1 are also mismatch repair proteins.

Uses for Mouse MLH1 and PMS1

We believe our isolation and characterization of mMLH1 and mPMS1 genes will have many research applications. For example, as already discussed above, we have used our knowledge of the mPMS1 gene to produce antibodies which react specifically with hPMS1. We have already explained that antibodies directed to the human proteins, MLH1 or PMS1 may be used for both research purposes as well as diagnostic purposes. [0229]
We also believe that our knowledge of mPMS1 and mMLH1 will be useful for constructing mouse models in order to study the consequences of DNA mismatch repair defects. We expect that mPMS1 or mMLH1 defective mice will be highly prone to cancer because chromosome 2p and 3p-associated HNPCC are each due to a defect in a mismatch repair gene.[0230] ^1,2As noted above, we have already produced chimeric mice which carry an mPMS1 defective gene. We are currently constructing mice heterozygous for mPMS1 or mMLH1 mutation. These heterozygous mice should provide useful animal models for studying human cancer, in particular HNPCC. The mice will be useful for analysis of both intrinsic and extrinsic factors that determine cancer risk and progression. Also, cancers associated with mismatch repair deficiency may respond differently to conventional therapy in comparison to other cancers. Such animal models will be useful for determining if differences exist, and allow the development of regimes for the effective treatment of these types of tumors. Such animal models may also be used to study the relationship between hereditary versus dietary factors in carcinogenesis.

Distinguishing Mutations From Polymorphisms

For studies of cancer susceptibility and for tumor identification and characterization, it is important to distinguish “mutations” from “polymorphisms”. A “mutation” produces a “non-wild-type allele” of a gene. A non-wild-type allele of a gene produces a transcript and/or a protein product that does not function normally within a cell. “Mutations” can be any alteration in nucleotide sequence including insertions, deletions, substitutions, and rearrangements. [0231]
“Polymorphisms”, on the other hand, are sequence differences that are found within the population of normally-functioning (i.e., “wild-type”) genes. Some polymorphisms result from the degeneracy of the nucleic acid code. That is, given that most amino acids are encoded by more than one triplet codon, many different nucleotide sequences can encode the same polypeptide. Other polymorphisms are simply sequence differences that do not have a significant effect on the function of the gene or encoded polypeptide. For example, polypeptides can often tolerate small insertions or deletions, or “conservative” substitutions in their amino acid sequence without significantly altering function of the polypeptide. [0232]
“Conservative” substitutions are those in which a particular amino acid is substituted by another amino acid of similar chemical characteristics. For example, the amino acids are often characterized as “non-polar (hydrophobic)” including alanine, leucine, isoleucine, valine, proline, phenylaline, tryptophan, and methionine; “polar neutral”, including glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; “positively charged (basic)”, including arginine, lysine, and histidine; and “negatively charged (acidic)”, including aspartic acid and glutamic acid. A substitution of one amino acid for another amino acid in the same group is generally considered to be “conservative”, particularly if the side groups of the two relevant amino acids are of a similar size. [0233]
The first step in identifying a mutation or polymorphism in a mismatch repair gene sequence involves identification, using available techniques including those described herein, of a mismatch repair gene, (or gene fragment) sequence that differs from a known, normal (e.g. wild-type) sequence of the same mismatch repair gene (or gene fragment). For example, a hMLH1 gene (or gene fragment) sequence could be identified that differs in at least one nucleotide position from a known normal (e.g. wild-type) hMLH1 sequence such as any of SEQ ID NOS: 6-24. [0234]
Mutations can be distinguished from polymorphisms using any of a variety of methods, perhaps the most direct of which is data collection and correlation with tumor development. That is, for example, a subject might be identified whose hMLH1 gene sequence differs from a sequence reported in SEQ ID. NOS: 6-24, but who does not have cancer and has no family history of cancer. Particularly if other, preferably senior, members of that subject's family have hMLH1 gene sequences that differ from SEQ ID NOS: 6-24 in the same way(s), it is likely that subject's hMLH1 gene sequence could be categorized as a “polymorphism”. If other, unrelated individuals are identified with the same hMLH1 gene sequence and no family history of cancer, the categorization may be confirmed. [0235]
Mutations that are responsible for conferring genetic susceptibility to cancer can be identified because, among other things, such mutations are likely to be present in all tissues of an affected individual and in the germ line of at least one of that individual's parents, and are not likely to be found in unrelated families with no history of cancer. [0236]
When distinguishing mutations from polymorphisms, it can sometimes be valuable to evaluate a particular sequence difference in the presence of at least one known mismatch repair gene mutation. In some instances, a particular sequence change will not have a detectable effect (i.e., will appear to be a polymorphism) when assayed alone, but will, for example, increase the penetrance of a known mutation, such that individuals carrying both the apparent polymorphism difference and a known mutation have higher probability of developing cancer than do individuals carrying only the mutation. Sequence differences that have such an effect are properly considered to be mutations, albeit weak ones. [0237]
As discussed above and previously (U.S. patent application Ser. Nos. 08/168,877 and 08/209,521), mutations in mismatch repair genes or gene products produced non-wild-type versions of those genes or gene products. Some mutations can therefore be distinguished from polymorphisms by their functional characteristics in in vivo or in vitro mismatch repair assays. Any available mismatch repair assay can be used to analyze these characteristics.[0238] ^49-63It is generally desirable to utilize more than one mismatch repair assay before classifying a sequence change as a polymorphism, since some mutations will have effects that will not be observed in all assays.
For example, a mismatch repair gene containing a mutation would not be expected to be able to replace an endogenous copy of the same gene in a host cell without detectably affecting mismatch repair in that cell; whereas a mismatch repair gene containing a sequence polymorphism would be expected to be able to replace an endogenous copy of the same gene in a host cell without detectably affecting mismatch repair in that cell. We note that for such “replacement” studies, it is generally desirable to introduce the gene to be tested into a host cell of the same (or at least closely related) species as the cell from which the test gene was derived, to avoid complications due to, for example, the inability of a gene product from one species to interact with other mismatch repair gene products from another species. Similarly, a mutant mismatch repair protein would not be expected to function normally in an in vitro mismatch repair system (preferably from a related organism); whereas a polymorphic mismatch repair protein would be expected to function normally. [0239]
The methods described herein and previously allow identification of different kinds of mismatch repair gene mutations. The following examples illustrate protocols for distinguishing mutations from polymorphisms in DNA mismatch repair genes. [0240]

EXAMPLE 3

We have developed a system for testing in yeast, [0241] S. cerevisiae the functional significance of mutations found in either the hMLH1 or hPMS1 genes. The system is described in this application using as an example, the serine (SER) to phenylalanine (PHE) causing mutation in hMLH1 that we found in a family with HNPCC, as described above. We have derived a yeast strain that it is essentially deleted for its MLH1 gene and hence is a strong mutator (i.e., 1000 fold above the normal rate in a simple genetic marker assay involving reversion from growth dependence on a given amino acid to independence (reversion of the hom3-10 allele, Prolla, Christie and Liskay, Mol Cell Biol, 14:407-415, 1994). When we placed the normal yeast MLH1 gene (complete with all known control regions) on a yeast plasma that is stably maintained as a single copy into the MLH1-deleted strain, the mutator phenotype is fully corrected using the reversion to amino acid independence assay. However, if we introduce a deleted copy of the yeast MLH1 there is no correction. We next tested the mutation that in the HNPCC family caused a SER to PHE alteration. We found that the resultant mutant yeast protein cannot correct the mutator phenotype, strongly suggesting that the alteration from the wild-type gene sequence probably confers cancer susceptibility, and is therefore classified as a mutation, not a polymorphism. We subsequently tested proteins engineered to contain other amino acids at the “serene” position and found that most changes result in a fully mutant, or at least partially mutant phenotype.
As other “point” mutations in MLH1 and PMS1 genes are found in cancer families, they can be engineered into the appropriate yeast homolog gene and their consequence on protein function studied. In addition, we have identified a number of highly conserved amino acids in both the MLH1 and PMS1 genes. We also have evidence that hMLH1 interacts with yeast PMS1. This finding raises the possibility that mutations observed in the hMLH1 gene can be more directly tested in the yeast system. We plan to systematically make mutations that will alter the amino acid at these conserved positions and determine what amino acid substitutions are tolerated and which are not. By collecting mutation information relating to hMLH1 and hPMS1, both by determining and documenting actual found mutations in HNPCC families, and by artificially synthesizing mutants for testing in experimental systems, it may be eventually possible to practice a cancer susceptibility testing protocol which, once the individuals hMLH1 or hPMS1 structure is determined, only requires comparison of that structure to known mutation versus polymorphism data. [0242]

EXAMPLE 4

Another method which we have employed to study physical interactions between hMLH1 and hPMS1, can also be used to study whether a particular alteration in a gene product results in a change in the degree of protein-protein interaction. Information concerning changes in protein-protein interaction may demonstrate or confirm whether a particular genomic variation is a mutation or a polymorphism. Following our labs findings on the interaction between yeast MLH1 and PMS1 proteins in vitro and in vivo, (U.S. patent application Ser. No. 08/168,877), the interaction between the human counterparts of these two DNA mismatch repair proteins was tested. The human MLH1 and human PMS1 proteins were tested for in vitro interaction using maltose binding protein (MBP) affinity chromatography. hMLH1 protein was prepared as an MBP fusion protein, immobilized on an amylose resin column via the MBP, and tested for binding to hPMS1, synthesized in vitro. The hPMS1 protein bound to the MBP-hMLH1 matrix, whereas control proteins showed no affinity for the matrix. When the hMLH1 protein, translated in vitro, was passed over an MBP-hPMS1 fusion protein matrix, the hMLH1 protein bound to the MBP-hPMS1 matrix, whereas control proteins did not. [0243]
Potential in vivo interactions between hMLH1 and HPMS1 were tested using the yeast “two hybrid” system.[0244] ²⁸Our initial results indicate that hMLH1 and hPMS1 interact in vivo in yeast. The same system can also be used to detect changes in protein-protein interaction which result from changes in gene or gene product structure and which have yet to be classified as either a polymorphism or a mutation which confers cancer susceptibility.

Detection of HNPCC Families and Their Mutation(s)

It has been estimated that approximately 1,000,000 individuals in the United States carry (are heterozygous for) an HNPCC mutant gene.[0245] ²⁹Furthermore, estimates suggest that 50-60% of HNPCC families segregate mutations in the MSH2 gene that resides on chromosome 2p.^1,2Another significant fraction appear to be associated with the HNPCC gene that maps to chromosome 3p21-22, presumably due to hMLH1 mutations such as the C to T transition discussed above. Identification of families that segregate mutant alleles of either the hMSH2 or hMLH1 gene, and the determination of which individuals in these families actually have the mutation will be of great utility in the early intervention into the disease. Such early intervention will likely include early detection through screening and aggressive follow-up treatment of affected individuals. In addition, determination of the genetic basis for both familial and sporadic tumors could direct the method of therapy in the primary tumor, or in recurrences.
Initially, HNPCC candidate families will be diagnosed partly through the study of family histories, most likely at the local level, e.g., by hospital oncologists. One criterion for HNPCC is the observation of microsatellite instability in individual's tumors.[0246] ^3,6The presenting patient would be tested for mutations in hMSH2, hMLH1, hPMS1 and other genes involved in DNA mismatch repair as they are identified. This is most easily done by sampling blood from the individual. Also highly useful would be freshly frozen tumor tissue. It is important to note for the screening procedure, that affected individuals are heterozygous for the offending mutation in their normal tissues.
The available tissues, e.g., blood and tumor, are worked up for PCR-based mutation analysis using one or both of the following procedures: [0247]
1) Linkage Analysis with a Microsatellite Marker Tightly Linked to the hMLH1 Gene. [0248]
One approach to identify cancer prone families with a hMLH1 mutation is to perform linkage analysis with a highly polymorphic marker located within or tightly linked to hMLH1. Microsatellites are highly polymorphic and therefore are very useful as markers in linkage analysis. Because we possess the hMLH1 gene on a single large genomic fragment in a P1 phage clone (˜100 kbp), it is very likely that one or more microsatellites, e.g., tracts of dinucleotide repeats, exist within, or very close to, the hMLH1 gene. At least one such microsatellite has been reported.[0249] ³⁸Once such markers have been identified, PCR primers will be designed to amplify the stretches of DNA containing the microsatellites. DNA of affected and unaffected individuals from a family with a high frequency of cancer will be screened to determine the segregation of the MLH1 markers and the presence of cancer. The resulting data can be used to calculate a lod score and hence determine the likelihood of linkage between hMLH1 and the occurrence of cancer. Once linkage is established in a given family, the same polymorphic marker can be used to test other members of the kindred for the likelihood of their carrying the hMLH1 mutation.
2) Sequencing of Reverse Transcribed cDNA. [0250]
a) RNA from affected individuals, unaffected and unrelated individuals is reverse transcribed (RT'd), followed by PCR to amplify the cDNA in 4-5 overlapping portions.[0251] ^34,37It should be noted that for the purposes of PCR, many different oligonucleotide primer pair sequences may potentially be used to amplify relevant portions of an individual's hMLH1 or hPMS1 gene for genetic screening purposes. With the knowledge of the cDNA structures for the genes, it is a straight-forward exercise to construct primer pairs which are likely to be effective for specifically amplifying selected portions of the gene. While primer sequences are typically between 20 to 30 bases long, it may be possible to use shorter primers, potentially as small as approximately 13 bases, to amplify specifically selected gene segments. The principal limitation on how small a primer sequence may be is that it must be long enough to hybridize specifically to the targeted gene segment. Specificity of PCR is generally improved by lengthening primers and/or employing nested pairs of primers.
The PCR products, in total representing the entire cDNA, are then sequenced and compared to known wild-type sequences. In most cases a mutation will be observed in the affected individual. Ideally, the nature of mutation will indicate that it is likely to inactivate the gene product. Otherwise, the possibility that the alteration is not simply a polymorphism must be determined. [0252]
b) Certain mutations, e.g., those affecting splicing or resulting in translation stop codons, can destabilize the messenger RNA produced from the mutant gene and hence comprise the normal RT-based mutation detection method. One recently reported technique can circumvent this problem by testing whether the mutant cDNA can direct the synthesis of normal length protein in a coupled in vitro transcription/translation system.[0253] ³²
3) Direct Sequencing of Genomic DNA. [0254]
A second route to detect mutations relies on examining the exons and the intron/exon boundaries by PCR cycle sequencing directly off a DNA template.[0255] ^1,2This method requires the use of oligonucleotide pairs, such as those described in Tables 2 and 3 above, that amplify individual exons for direct PCR cycle sequencing. The method depends upon genomic DNA sequence information at each intron/exon boundary (50 bp, or greater, for each boundary). The advantage of the technique is two fold. First, because DNA is more stable than RNA, the condition of the material used for PCR is not as important as it is for RNA-based protocols. Second, most any mutation within the actual transcribed region of the gene, including those in an intron affecting splicing, will be detectable.
For each candidate gene, mutation detection may require knowledge of both the entire cDNA structure, and all intron/exon boundaries of the genomic structure. With such information, the type of causal mutation in a particular family can be determined. In turn, a more specific and efficient mutation detection scheme can be adapted for the particular family. Screening for the disease (HNPCC) is complex because it has a genetically heterogeneous basis in the sense that more than one gene is involved, and for each gene, multiple types of mutations are involved.[0256] ²Any given family is highly likely to segregate one particular mutation. However, as the nature of the mutation in multiple families is determined, the spectrum of the most prevalent mutations in the population will be determined. In general, determination of the most frequent mutations will direct and streamline mutation detection.
Because HNPCC is so prevalent in the human population, carrier detection at birth could become part of standardized neonatal testing. Families at risk can be identified and all members not previously tested can be tested. Eventually, all affected kindreds could be determined. [0257]

Mode of Mutation Screening and Testing

DNA-Based Testing [0258]
Initial testing, including identifying likely HNPCC families by standard diagnosis and family history study, will likely be done in local and smaller DNA diagnosis laboratories. However, large scale testing of multiple family members, and certainly population wide testing, will ultimately require large efficient centralized commercial facilities. [0259]
Tests will be developed based on the determination of the most common mutations for the major genes underlying HNPCC, including at least the hMSH2 gene on chromosome 2p and the MLH1 gene on chromosome 3p. A variety of tests are likely to be developed. For example, one possibility is a set of tests employing oligonucleotide hybridizations that distinguish the normal vs. mutant alleles.[0260] ³³As already noted, our knowledge of the nucleotide structures for hMLH1, hPMS1 and hMSH2 genes makes possible the design of numerous oligonucleotide primer pairs which may be used to amplify specific portions of an individual's mismatch repair gene for genetic screening and cancer risk analysis. Our knowledge of the genes' structures also makes possible the design of labeled probes which can be quickly used to determine the presence or absence of all or a portion of one of the DNA mismatch repair genes. For example, allele-specific oligomer probes (ASO) may be designed to distinguish between alleles. ASOs are short DNA segments that are identical in sequence except for a single base difference that reflects the difference between normal and mutant alleles. Under the appropriate DNA hybridization conditions, these probes can recognize a single base difference between two otherwise identical DNA sequences. Probes can be labeled radioactively or with a variety of non-radioactive reporter molecules, for example, fluorescent or chemiluminescent moieties. Labeled probes are then used to analyze the PCR sample for the presence of the disease-causing allele. The presence or absence of several different disease-causing genes can readily be determined in a single sample. The length of the probe must be long enough to avoid non-specific binding to nucleotide sequences other than the target. All tests will depend ultimately on accurate and complete structural information relating to hMLH1, hMSH2, hPMS1 and other DNA mismatch repair genes implicated in HNPCC.
Protein Detection-Based Screening [0261]
Tests based on the functionality of the protein product, per se, may also be used. The protein-examining tests will most likely utilize antibody reagents specific to either the hMLH1, hPMS1 or hMSH2 proteins or other related “cancer” gene products as they are identified. [0262]
For example, a frozen tumor specimen can be sectioned and prepared for antibody staining using indirect fluorescence techniques. Certain gene mutations are expected to alter or destabilize the protein structure sufficiently such as to give an altered or reduced signal after antibody staining. It is likely that such tests will be performed in cases where gene involvement in a family's cancer has yet to be established. Monoclonal antibodies are developed against the human MLH1 and PMS1 proteins. MLH1 and PMS1 human proteins are overexpressed in bacteria. Proteins are purified and injected into mice. Protein specific monoclonal antibodies are derived which can be used for diagnostic and research purposes. For example, two different monoclonal antibodies directed to hMLH1 are now available from PharMingen under catalog #13271A, clone: G168-15 and #13291A, clone: G168-728. Both of PharMingen's monoclonal antibodies were generated based on purified, recombinant hMLH1 protein, that was provided by applicants to PharMingen in the form of a fusion to bacterial protein. [0263]
Recent research suggests that methylation of hMLH1 promoter DNA is involved in mismatch repair gene inactivation in some sporadic tumors. 64, 65 In this situation, there is usually no detectable mutation in the hMLH1 cDNA. A screening test for hMLH1 cDNA mutations would not show any abnormality. However, an immunoassay for hMLH1 protein will show presence or absence of the protein. It is believed that 90-percent or more of sporadic colon tumors and endometrial tumors that are DNA mismatch repair defective, do not have mutations in any known gene, but instead are MLH1 protein deficient due to methylation of the promotor region of the gene. It appears that the most reliable method for detecting absence of hMLH1 in sporadic tumors is to use labeled antibodies in an immunohistochemical staining procedure of tumor sections. It is likely that immunohistochemical staining of tumor tissue sections with monoclonal antibodies directed to hMLH1 protein will become a standard diagnostic method at least for colon and endometrial tumors. [0264]

Identification and Characterization of DNA Mismatch Repair Tumors

In addition to their usefulness in diagnosing cancer susceptibility in a subject, nucleotide sequences that are homologous to a bacterial mismatch repair gene can be valuable for, among other things, use in the identification and characterization of mismatch-repair-defective tumors. Such identification and characterization is valuable because mismatch-repair-defective tumors may respond better to particular therapy regimens. For example, mismatch-repair-defective tumors might be sensitive to DNA damaging agents, especially when administered in combination with other therapeutic agents. [0265]
Defects in mismatch repair genes need not be present throughout an individual's tissues to contribute to tumor formation in that individual. Spontaneous mutation of a mismatch repair gene in a particular cell or tissue can contribute to tumor formation in that tissue. In fact, at least in some cases, a single mutation in a mismatch repair gene is not sufficient for tumor development. In such instances, an individual with a single mutation in a mismatch repair gene is susceptible to cancer, but will not develop a tumor until a secondary mutation occurs. Additionally, in some instances, the same mismatch repair gene mutation that is strictly tumor-associated in an individual will be responsible for conferring cancer susceptibility in a family with a hereditary predisposition to cancer development. [0266]
In yet another aspect of the invention, the sequence information we have provided can be used with methods known in the art to analyze tumors (or tumor cell lines) and to identify tumor-associated mutations in mismatch repair genes. Preferably, it is possible to demonstrate that these tumor-associated mutations are not present in non-tumor tissues from the same individual. The information described in this application is particularly useful for the identification of mismatch repair gene mutations within tumors (or tumor cell lines) that display genomic instability of short repeated DNA elements. [0267]
The sequence information and testing protocols of the present invention can also be used to determine whether two tumors are related, i.e., whether a second tumor is the result of metastasis from an earlier found first tumor which exhibits a particular DNA mismatch repair gene mutation. [0268]

Isolating Additional Genes of Related Function

Proteins that interact physically with either hMLH1 and/or hPMS1, are likely to be involved in DNA mismatch repair. By analogy to hMLH1 and hMSH2, mutations in the genes which encode for such proteins would be strong candidates for potential cancer linkage. A powerful molecular genetic approach using yeast, referred to as a “two-hybrid system”, allows the relatively rapid detection and isolation of genes encoding proteins that interact with a gene product of interest, e.g., hMLH1.[0269] ²⁸
The two-hybrid system involves two plasmid vectors each intended to encode a fusion protein. Each of the two vectors contains a portion, or domain, of a transcription activator. The yeast cell used in the detection scheme contains a “reporter” gene. The activator alone cannot activate transcription. However, if the two domains are brought into close proximity then transcription may occur. The cDNA for the protein of interest, e.g., hMLH1 is inserted within a reading frame in one of the vectors. This is termed the “bait”. A library of human cDNAs, inserted into a second plasmid vector so as to make fusions with the other domain of the transcriptional activator, is introduced into the yeast cells harboring the “bait” vector. If a particular yeast cell receives a library member that contains a human cDNA encoding a protein that interacts with hMLH1 protein, this interaction will bring the two domains of the transcriptional activator into close proximity, activate transcription of the reporter gene and the yeast cell will turn blue. Next, the insert is sequenced to determine whether it is related to any sequence in the data base. The same procedure can be used to identify yeast proteins in DNA mismatch repair or a related process. Performing the yeast and human “hunts” in parallel has certain advantages. The function of novel yeast homologs can be quickly determined in yeast by gene disruption and subsequent examination of the genetic consequences of being defective in the new found gene. These yeast studies will help guide the analysis of novel human “hMLH1-or hPMS1-interacting” proteins in much the same way that the yeast studies on PMS1 and MLH1 have influenced our studies of the human MLH1 and PMS1 genes. [0270]

Production of Antibodies

By using our knowledge of the DNA sequences for hMLH1 and hPMS1, we can synthesize all or portions of the predicted protein structures for the purpose of producing antibodies. One important use for antibodies directed to hMLH1 and hPMS1 proteins will be for capturing other proteins which may be involved in DNA mismatch repair. For example, by employing coimmuno-precipitation techniques, antibodies directed to either hMLH1 or hPMS1 may be precipitated along with other associated proteins which are functionally and/or physically related. Another important use for antibodies will be for the purpose of isolating hMLH1 and hPMS1 proteins from tumor tissue. The hMLH1 and hPMS1 proteins from tumors can then be characterized for the purpose of determining appropriate treatment strategies. [0271]
We are in the process of developing monoclonal antibodies directed to the hMLH1 and hPMS1 proteins. [0272]

EXAMPLE 5

We have also used the following procedure to produce polyclonal antibodies directed to the human and mouse forms of PMS1 protein. [0273]
We inserted a 3′ fragment of the mouse PMS1 cDNA in the bacterial expression plasmid vector, pET (Novagen, Madison, Wis.). The expected expressed portion of the mouse PMS1 protein corresponds to a region of approximately 200 amino acids at the end of the PMS1 protein. This portion of the mPMS1 is conserved with yeast PMS1 but is not conserved with either the human or the mouse MLH1 proteins. One reason that we selected this portion of the PMS1 protein for producing antibodies is that we did not want the resulting antibodies to cross-react with MLH1. The mouse PMS1 protein fragment was highly expressed in [0274] E. coli., purified from a polyacrylamide gel and the eluted protein was then prepared for animal injections. Approximately 2 mg of the PMS1 protein fragment was sent to the Pocono Rabbit Farm (PA) for injections into rabbits. Sera from rabbits multiple times was tittered against the PMS1 antigen using standard ELISA techniques. Rabbit antibodies specific to mouse PMS1 protein were affinity-purified using columns containing immobilized mouse PMS1 protein. The affinity-purified polyclonal antibody preparation was tested further using Western blotting and dot blotting. We found that the polyclonal antibodies recognized, not only the mouse PMS1 protein, but also the human PMS1 protein which is very similar. Based upon the Western blots, there is no indication that other proteins were recognized strongly by our antibody, including either the human or mouse MLH1 proteins.

DNA Mismatch Repair Defective Mice

EXAMPLE 6

In order to create a experimental model system for studying DNA mismatch repair defects and resultant cancer in a whole animal system we have derived DNA mismatch repair defective mice using embryonic stem (ES) cell technology. Using genomic DNA containing a portion of the mPMS1 gene we constructed a vector that upon homologous recombination causes disruption of the chromosomal mPMS1 gene. Mouse ES cells from the 129 mouse strain were confirmed to contain a disrupted mPMS1 allele. The ES cells were injected into C57/BL6 host blastocysts to produce animals that were chimeric or a mixture of 129 and C57/BL6 cells. The incorporation of the ES cells was determined by the presence of patches of agouti coat coloring (indicative of ES cell contribution). All male chimeras were bred with C57/BL6 female mice. [0275]
Subsequently, twelve offspring (F[0276] ₂) were born in which the agouti coat color was detected indicating the germline transmission of genetic material from the ES cells. Analysis of DNA extracted from the tail tips of the twelve offspring indicated that six of the animals were heterozygous (contained one wild-type and one mutant allele) for the mPMS1 mutation. Of the six heterozygous animals, three were female, (animals F₂-8, F₂-11 and F₂-12) and three were males (F₂, F₂-10 and F₂-13). Four breeding pens were set up to obtain mice that were homozygous for mPMS1 mutation, and additional heterozygous mice. Breeding pen #1 which contained animals F₂-11 and F₂-10, yielded a total of thirteen mice in three litters, four of which have been genotyped. Breeding pen #2 (animals F₂-8 and F₂-13) gave twenty-two animals and three litters, three of which have been genotyped. Of the seven animals genotyped, three homozygous female animals have been identified. One animal died at six weeks of age from unknown causes. The remaining homozygous females are alive and healthy at twelve weeks of age. The results indicate that mPMS1 homozygous defective mice are viable.
Breeding pens #3 and #4 were used to backcross the mPMS1 mutation into the C57/BL6 background. Breeding pen #3 (animal F[0277] ₂-12 crossed to a C57/BL6 mouse) produced twenty-one animals in two litters, nine of which have been genotyped. Breeding pen #4 (animal F₂-6 crossed with a C57/BL6 mouse) gave eight mice. In addition, the original male chimera (breeding pen #5) has produced thirty-one additional offspring.

To genotype the animals, a series of PCR primers have been developed that are used to identify mutant and wild-type mPMS1 genes. They are: (SEQ ID NOS: 143-148, respectively)


	Primer 1:	5′ TTCGGTGACAGATFFTGTAAATG-3′

	Primer 2:	5′ TTTACGGAGCCCTGGC-3′

	Primer 3:	5′ TCACCATAAAAATAGTTTCCCG-3′

	Primer 4:	5′ TCCTGGATCATATTTTCTGAGC-3′

	Primer 5:	5′ TTTCAGGTATGTCCTGTTACCC-3′

	Primer 6:	5′ TGAGGCAGCTTTTAAGAAACTC-3′

	Primers
1 @ 2	(5′ targeted)

	Primers 1 @ 3	(5′ untargeted)

	Primers 4 @ 5	(3′ targeted)

	Primers 4 @ 6	(3′ untargeted)

The mice we have developed provide an animal model system for studying the consequences of defects in DNA mismatch repair and resultant HNPCC. The long term survival of mice homozygous and heterozygous for the mPMS1 mutation and the types and timing of tumors in these mice will be determined. The mice will be screened daily for any indication of cancer onset as indicated by a hunched appearance in combination with deterioration in coat condition. These mice carrying mPMS1 mutation will be used to test the effects of other factors, environmental and genetic, on tumor formation. For example, the effect of diet on colon and other type of tumors can be compared for normal mice versus those carrying mPMS1 mutation either in the heterozygous or homozygous genotype. In addition, the mPMS1 mutation can be put into different genetic backgrounds to learn about interactions between genes of the mismatch repair pathway and other genes involved in human cancer, for example, p53. Mice carrying mPMS1 mutations will also be useful for testing the efficacy of somatic gene therapy on the cancers that arise in mice, for example, the expected colon cancers. Further, isogenic fibroblast cell lines from the homozygous and heterozygous mPMS1 mice can be established for use in various cellular studies, including the determination of spontaneous mutation rates. [0279]
We are currently constructing a vector for disrupting the mouse mMLH1 gene to derive mice carrying mutation in mMLH1. We will compare mice carrying defects in mPMS1 to mice carrying defects in mMLH1. In addition, we will construct mice that carry mutations in both genes to see whether there is a synergistic effect of having mutations in two HNPCC genes. Other studies on the mMLH1 mutant mice will be as described above for the mPMS1 mutant mice. [0280]
While the present invention has been particularly shown and described with reference to the foregoing preferred embodiments, those skilled in the art will understand that many variations may be made therein without departing from the spirit and scope of the invention as defined in the following claims. The description of the invention should be understood to include all novel and non-obvious combinations of elements described herein, and claims may be presented in this or a later application to any novel and non-obvious combination of these elements. Where the claims recite “a” or “a first” element or the equivalent thereof, such claims should be understood to include incorporation of one or more such elements, neither requiring nor excluding two or more such elements. [0281]
1 153 1 361 PRT Salmonella typhimurium 1 Met Pro Ile Gln Val Leu Pro Pro Gln Leu Ala Asn Gln Ile Ala Ala 1 5 10 15 Gly Glu Val Val Glu Arg Pro Ala Ser Val Val Lys Glu Leu Val Glu 20 25 30 Asn Ser Leu Asp Ala Gly Ala Thr Arg Val Asp Ile Asp Ile Glu Arg 35 40 45 Gly Gly Ala Lys Leu Ile Arg Ile Arg Asp Asn Gly Cys Gly Ile Lys 50 55 60 Lys Glu Glu Leu Ala Leu Ala Leu Ala Arg His Ala Thr Ser Lys Ile 65 70 75 80 Ala Ser Leu Asp Asp Leu Glu Ala Ile Ile Ser Leu Gly Phe Arg Gly 85 90 95 Glu Ala Leu Ala Ser Ile Ser Ser Val Ser Arg Leu Thr Leu Thr Ser 100 105 110 Arg Thr Ala Glu Gln Ala Glu Ala Trp Gln Ala Tyr Ala Glu Gly Arg 115 120 125 Asp Met Asp Val Thr Val Lys Pro Ala Ala His Pro Val Gly Thr Thr 130 135 140 Leu Glu Val Leu Asp Leu Phe Tyr Asn Thr Pro Ala Arg Arg Lys Phe 145 150 155 160 Met Arg Thr Glu Lys Thr Glu Phe Asn His Ile Asp Glu Ile Ile Arg 165 170 175 Arg Ile Ala Leu Ala Arg Phe Asp Val Thr Leu Asn Leu Ser His Asn 180 185 190 Gly Lys Leu Val Arg Gln Tyr Arg Ala Val Ala Lys Asp Gly Gln Lys 195 200 205 Glu Arg Arg Leu Gly Ala Ile Cys Gly Thr Pro Phe Leu Glu Gln Ala 210 215 220 Leu Ala Ile Glu Trp Gln His Gly Asp Lys Thr Lys Arg Gly Trp Val 225 230 235 240 Ala Asp Pro Asn His Thr Thr Thr Ala Leu Thr Glu Ile Gln Tyr Cys 245 250 255 Tyr Val Asn Gly Arg Met Met Arg Asp Arg Leu Ile Asn His Ala Ile 260 265 270 Arg Gln Ala Cys Glu Asp Lys Leu Gly Ala Asp Gln Gln Pro Ala Phe 275 280 285 Val Leu Tyr Leu Glu Ile Asp Pro His Gln Val Asp Val Asn Val His 290 295 300 Pro Ala Lys His Glu Val Arg Phe His Gln Ser Arg Leu Val His Asp 305 310 315 320 Phe Ile Tyr Gln Gly Val Leu Ser Val Leu Gln Gln Gln Thr Glu Thr 325 330 335 Ala Leu Pro Leu Glu Glu Ile Ala Pro Ala Pro Arg His Val Gln Glu 340 345 350 Asn Arg Ile Ala Ala Gly Arg Asn His 355 360 2 538 PRT Streptococcus pneumoniae 2 Met Ser His Ile Ile Glu Leu Pro Glu Met Leu Ala Asn Gln Ile Ala 1 5 10 15 Ala Gly Glu Val Ile Glu Arg Pro Ala Ser Val Cys Lys Glu Leu Val 20 25 30 Glu Asn Ala Ile Asp Ala Gly Ser Ser Gln Ile Ile Ile Glu Ile Glu 35 40 45 Glu Ala Gly Leu Lys Lys Val Gln Ile Thr Asp Asn Gly His Gly Ile 50 55 60 Ala His Asp Glu Val Glu Leu Ala Leu Arg Arg His Ala Thr Ser Lys 65 70 75 80 Ile Lys Asn Gln Ala Asp Leu Phe Arg Ile Arg Thr Leu Gly Phe Arg 85 90 95 Gly Glu Ala Leu Pro Ser Ile Ala Ser Val Ser Val Leu Thr Leu Leu 100 105 110 Thr Ala Val Asp Gly Ala Ser His Gly Thr Lys Leu Val Ala Arg Gly 115 120 125 Gly Glu Val Glu Glu Val Ile Pro Ala Thr Ser Pro Val Gly Thr Lys 130 135 140 Val Cys Val Glu Asp Leu Phe Phe Asn Thr Pro Ala Arg Leu Lys Tyr 145 150 155 160 Met Lys Ser Gln Gln Ala Glu Leu Ser His Ile Ile Asp Ile Val Asn 165 170 175 Arg Leu Gly Leu Ala His Pro Glu Ile Ser Phe Ser Leu Ile Ser Asp 180 185 190 Gly Lys Glu Met Thr Arg Thr Ala Gly Thr Gly Gln Leu Arg Gln Ala 195 200 205 Ile Ala Gly Ile Tyr Gly Leu Val Ser Ala Lys Lys Met Ile Glu Ile 210 215 220 Glu Asn Ser Asp Leu Asp Phe Glu Ile Ser Gly Phe Val Ser Leu Pro 225 230 235 240 Glu Leu Thr Arg Ala Asn Arg Asn Tyr Ile Ser Leu Phe Ile Asn Gly 245 250 255 Arg Tyr Ile Lys Asn Phe Leu Leu Asn Arg Ala Ile Leu Asp Gly Phe 260 265 270 Gly Ser Lys Leu Met Val Gly Arg Phe Pro Leu Ala Val Ile His Ile 275 280 285 His Ile Asp Pro Tyr Leu Ala Asp Val Asn Val His Pro Thr Lys Gln 290 295 300 Glu Val Arg Ile Ser Lys Glu Lys Glu Leu Met Thr Leu Val Ser Glu 305 310 315 320 Ala Ile Ala Asn Ser Leu Lys Glu Gln Thr Leu Ile Pro Asp Ala Leu 325 330 335 Glu Asn Leu Ala Lys Ser Thr Val Arg Asn Arg Glu Lys Val Glu Gln 340 345 350 Thr Ile Leu Pro Leu Ser Phe Pro Glu Leu Glu Phe Phe Gly Gln Met 355 360 365 His Gly Thr Tyr Leu Phe Ala Gln Gly Arg Asp Gly Leu Tyr Ile Ile 370 375 380 Asp Gln His Ala Ala Gln Glu Arg Val Lys Tyr Glu Glu Tyr Arg Glu 385 390 395 400 Ser Ile Gly Asn Val Asp Gln Ser Gln Gln Gln Leu Leu Val Pro Tyr 405 410 415 Ile Phe Glu Phe Pro Ala Asp Asp Ala Leu Arg Leu Lys Glu Arg Met 420 425 430 Pro Leu Leu Glu Glu Val Gly Val Phe Leu Ala Glu Tyr Gly Glu Asn 435 440 445 Gln Phe Ile Leu Arg Glu His Pro Ile Trp Met Ala Glu Glu Glu Ile 450 455 460 Glu Ser Gly Ile Tyr Glu Met Cys Asp Met Leu Leu Leu Thr Lys Glu 465 470 475 480 Val Ser Ile Lys Lys Tyr Arg Ala Glu Leu Ala Ile Met Met Ser Cys 485 490 495 Lys Arg Ser Ile Lys Ala Asn His Arg Ile Asp Asp His Ser Ala Arg 500 505 510 Gln Leu Leu Tyr Gln Leu Ser Gln Cys Asp Asn Pro Tyr Asn Cys Pro 515 520 525 His Gly Arg Pro Val Leu Val His Phe Thr 530 535 3 607 PRT Saccharomyces cerevisiae 3 Met Phe His His Ile Glu Asn Leu Leu Ile Glu Thr Glu Lys Arg Cys 1 5 10 15 Lys Gln Lys Glu Gln Arg Tyr Ile Pro Val Lys Tyr Leu Phe Ser Met 20 25 30 Thr Gln Ile His Gln Ile Asn Asp Ile Asp Val His Arg Ile Thr Ser 35 40 45 Gly Gln Val Ile Thr Asp Leu Thr Thr Ala Val Lys Glu Leu Val Asp 50 55 60 Asn Ser Ile Asp Ala Asn Ala Asn Gln Ile Glu Ile Ile Phe Lys Asp 65 70 75 80 Tyr Gly Leu Glu Ser Ile Glu Cys Ser Asp Asn Gly Asp Gly Ile Asp 85 90 95 Pro Ser Asn Tyr Glu Phe Leu Ala Leu Lys His Tyr Thr Ser Lys Ile 100 105 110 Ala Lys Phe Gln Asp Val Ala Lys Val Gln Thr Leu Gly Phe Arg Gly 115 120 125 Glu Ala Leu Ser Ser Leu Cys Gly Ile Ala Lys Leu Ser Val Ile Thr 130 135 140 Thr Thr Ser Pro Pro Lys Ala Asp Lys Glu Leu Tyr Asp Met Val Gly 145 150 155 160 His Ile Thr Ser Lys Thr Thr Thr Ser Arg Asn Lys Gly Thr Thr Val 165 170 175 Leu Val Ser Gln Leu Phe His Asn Leu Pro Val Arg Gln Lys Glu Phe 180 185 190 Ser Lys Thr Phe Lys Arg Gln Phe Thr Lys Cys Leu Thr Val Ile Gln 195 200 205 Gly Tyr Ala Ile Ile Asn Ala Ala Ile Lys Phe Ser Val Trp Asn Ile 210 215 220 Thr Pro Lys Gly Lys Lys Asn Leu Ile Leu Ser Thr Met Arg Asn Ser 225 230 235 240 Ser Met Arg Lys Asn Ile Ser Ser Val Phe Gly Ala Gly Gly Met Arg 245 250 255 Gly Glu Leu Glu Val Asp Leu Val Leu Asp Leu Asn Pro Phe Lys Asn 260 265 270 Arg Met Leu Gly Lys Tyr Thr Asp Asp Pro Asp Phe Leu Asp Leu Asp 275 280 285 Tyr Lys Ile Arg Val Lys Gly Tyr Ile Ser Gln Asn Ser Phe Gly Cys 290 295 300 Gly Arg Asn Ser Lys Asp Arg Gln Phe Ile Tyr Val Asn Lys Arg Pro 305 310 315 320 Val Glu Tyr Ser Thr Leu Leu Lys Cys Cys Asn Glu Val Tyr Lys Thr 325 330 335 Phe Asn Asn Val Gln Phe Pro Ala Val Phe Leu Asn Leu Glu Leu Pro 340 345 350 Met Ser Leu Ile Asp Val Asn Val Thr Pro Asp Lys Arg Val Ile Leu 355 360 365 Leu His Asn Glu Arg Ala Val Ile Asp Ile Phe Lys Thr Thr Leu Ser 370 375 380 Asp Tyr Tyr Asn Arg Gln Glu Leu Ala Leu Pro Lys Arg Met Cys Ser 385 390 395 400 Gln Ser Glu Gln Gln Ala Gln Lys Arg Leu Leu Thr Glu Val Phe Asp 405 410 415 Asp Asp Phe Lys Lys Met Glu Val Val Gly Gln Phe Asn Leu Gly Phe 420 425 430 Ile Ile Val Thr Arg Lys Val Asp Asn Lys Ser Asp Leu Phe Ile Val 435 440 445 Asp Gln His Ala Ser Asp Glu Lys Tyr Asn Phe Glu Thr Leu Gln Ala 450 455 460 Val Thr Val Phe Lys Ser Gln Lys Leu Ile Ile Pro Gln Pro Val Glu 465 470 475 480 Leu Ser Val Ile Asp Glu Leu Val Val Leu Asp Asn Leu Pro Val Phe 485 490 495 Glu Lys Asn Gly Phe Lys Leu Lys Ile Asp Glu Glu Glu Glu Phe Gly 500 505 510 Ser Arg Val Lys Leu Leu Ser Leu Pro Thr Ser Lys Gln Thr Leu Phe 515 520 525 Asp Leu Gly Asp Phe Asn Glu Leu Ile His Leu Ile Lys Glu Asp Gly 530 535 540 Gly Leu Arg Arg Asp Asn Ile Arg Cys Ser Lys Ile Arg Ser Met Phe 545 550 555 560 Ala Met Arg Ala Cys Arg Ser Ser Ile Met Ile Gly Lys Pro Leu Asn 565 570 575 Lys Lys Thr Met Thr Arg Val Val His Asn Leu Ser Glu Leu Asp Lys 580 585 590 Pro Trp Asn Cys Pro His Gly Arg Pro Thr Met Arg His Leu Met 595 600 605 4 2484 DNA Homo sapiens 4 cttggctctt ctggcgccaa aatgtcgttc gtggcagggg ttattcggcg gctggacgag 60 acagtggtga accgcatcgc ggcgggggaa gttatccagc ggccagctaa tgctatcaaa 120 gagatgattg agaactgttt agatgcaaaa tccacaagta ttcaagtgat tgttaaagag 180 ggaggcctga agttgattca gatccaagac aatggcaccg ggatcaggaa agaagatctg 240 gatattgtat gtgaaaggtt cactactagt aaactgcagt cctttgagga tttagccagt 300 atttctacct atggctttcg aggtgaggct ttggccagca taagccatgt ggctcatgtt 360 actattacaa cgaaaacagc tgatggaaag tgtgcataca gagcaagtta ctcagatgga 420 aaactgaaag cccctcctaa accatgtgct ggcaatcaag ggacccagat cacggtggag 480 gacctttttt acaacatagc cacgaggaga aaagctttaa aaaatccaag tgaagaatat 540 gggaaaattt tggaagttgt tggcaggtat tcagtacaca atgcaggcat tagtttctca 600 gttaaaaaac aaggagagac agtagctgat gttaggacac tacccaatgc ctcaaccgtg 660 gacaatattc gctccatctt tggaaatgct gttagtcgag aactgataga aattggatgt 720 gaggataaaa ccctagcctt caaaatgaat ggttacatat ccaatgcaaa ctactcagtg 780 aagaagtgca tcttcttact cttcatcaac catcgtctgg tagaatcaac ttccttgaga 840 aaagccatag aaacagtgta tgcagcctat ttgcccaaaa acacacaccc attcctgtac 900 ctcagtttag aaatcagtcc ccagaatgtg gatgttaatg tgcaccccac aaagcatgaa 960 gttcacttcc tgcacgagga gagcatcctg gagcgggtgc agcagcacat cgagagcaag 1020 ctcctgggct ccaattcctc caggatgtac ttcacccaga ctttgctacc aggacttgct 1080 ggcccctctg gggagatggt taaatccaca acaagtctga cctcgtcttc tacttctgga 1140 agtagtgata aggtctatgc ccaccagatg gttcgtacag attcccggga acagaagctt 1200 gatgcatttc tgcagcctct gagcaaaccc ctgtccagtc agccccaggc cattgtcaca 1260 gaggataaga cagatatttc tagtggcagg gctaggcagc aagatgagga gatgcttgaa 1320 ctcccagccc ctgctgaagt ggctgccaaa aatcagagct tggaggggga tacaacaaag 1380 gggacttcag aaatgtcaga gaagagagga cctacttcca gcaaccccag aaagagacat 1440 cgggaagatt ctgatgtgga aatggtggaa gatgattccc gaaaggaaat gactgcagct 1500 tgtacccccc ggagaaggat cattaacctc actagtgttt tgagtctcca ggaagaaatt 1560 aatgagcagg gacatgaggt tctccgggag atgttgcata accactcctt cgtgggctgt 1620 gtgaatcctc agtgggcctt ggcacagcat caaaccaagt tataccttct caacaccacc 1680 aagcttagtg aagaactgtt ctaccagata ctcatttatg attttgccaa ttttggtgtt 1740 ctcaggttat cggagccagc accgctcttt gaccttgcca tgcttgcctt agatagtcca 1800 gagagtggct ggacagagga agatggtccc aaagaaggac ttgctgaata cattgttgag 1860 tttctgaaga agaaggctga gatgcttgca gactatttct ctttggaaat tgatgaggaa 1920 gggaacctga ttggattacc ccttctgatt gacaactatg tgcccccttt ggagggactg 1980 cctatcttca ttcttcgact agccactgag gtgaattggg acgaagaaaa ggaatgtttt 2040 gaaagcctca gtaaagaatg cgctatgttc tattccatcc ggaagcagta catatctgag 2100 gagtcgaccc tctcaggcca gcagagtgaa gtgcctggct ccattccaaa ctcctggaag 2160 tggactgtgg aacacattgt ctataaagcc ttgcgctcac acattctgcc tcctaaacat 2220 ttcacagaag atggaaatat cctgcagctt gctaacctgc ctgatctata caaagtcttt 2280 gagaggtgtt aaatatggtt atttatgcac tgtgggatgt gttcttcttt ctctgtattc 2340 cgatacaaag tgttgtatca aagtgtgata tacaaagtgt accaacataa gtgttggtag 2400 cacttaagac ttatacttgc cttctgatag tattccttta tacacagtgg attgattata 2460 aataaataga tgtgtcttaa cata 2484 5 756 PRT Homo sapiens 5 Met Ser Phe Val Ala Gly Val Ile Arg Arg Leu Asp Glu Thr Val Val 1 5 10 15 Asn Arg Ile Ala Ala Gly Glu Val Ile Gln Arg Pro Ala Asn Ala Ile 20 25 30 Lys Glu Met Ile Glu Asn Cys Leu Asp Ala Lys Ser Thr Ser Ile Gln 35 40 45 Val Ile Val Lys Glu Gly Gly Leu Lys Leu Ile Gln Ile Gln Asp Asn 50 55 60 Gly Thr Gly Ile Arg Lys Glu Asp Leu Asp Ile Val Cys Glu Arg Phe 65 70 75 80 Thr Thr Ser Lys Leu Gln Ser Phe Glu Asp Leu Ala Ser Ile Ser Thr 85 90 95 Tyr Gly Phe Arg Gly Glu Ala Leu Ala Ser Ile Ser His Val Ala His 100 105 110 Val Thr Ile Thr Thr Lys Thr Ala Asp Gly Lys Cys Ala Tyr Arg Ala 115 120 125 Ser Tyr Ser Asp Gly Lys Leu Lys Ala Pro Pro Lys Pro Cys Ala Gly 130 135 140 Asn Gln Gly Thr Gln Ile Thr Val Glu Asp Leu Phe Tyr Asn Ile Ala 145 150 155 160 Thr Arg Arg Lys Ala Leu Lys Asn Pro Ser Glu Glu Tyr Gly Lys Ile 165 170 175 Leu Glu Val Val Gly Arg Tyr Ser Val His Asn Ala Gly Ile Ser Phe 180 185 190 Ser Val Lys Lys Gln Gly Glu Thr Val Ala Asp Val Arg Thr Leu Pro 195 200 205 Asn Ala Ser Thr Val Asp Asn Ile Arg Ser Ile Phe Gly Asn Ala Val 210 215 220 Ser Arg Glu Leu Ile Glu Ile Gly Cys Glu Asp Lys Thr Leu Ala Phe 225 230 235 240 Lys Met Asn Gly Tyr Ile Ser Asn Ala Asn Tyr Ser Val Lys Lys Cys 245 250 255 Ile Phe Leu Leu Phe Ile Asn His Arg Leu Val Glu Ser Thr Ser Leu 260 265 270 Arg Lys Ala Ile Glu Thr Val Tyr Ala Ala Tyr Leu Pro Lys Asn Thr 275 280 285 His Pro Phe Leu Tyr Leu Ser Leu Glu Ile Ser Pro Gln Asn Val Asp 290 295 300 Val Asn Val His Pro Thr Lys His Glu Val His Phe Leu His Glu Glu 305 310 315 320 Ser Ile Leu Glu Arg Val Gln Gln His Ile Glu Ser Lys Leu Leu Gly 325 330 335 Ser Asn Ser Ser Arg Met Tyr Phe Thr Gln Thr Leu Leu Pro Gly Leu 340 345 350 Ala Gly Pro Ser Gly Glu Met Val Lys Ser Thr Thr Ser Leu Thr Ser 355 360 365 Ser Ser Thr Ser Gly Ser Ser Asp Lys Val Tyr Ala His Gln Met Val 370 375 380 Arg Thr Asp Ser Arg Glu Gln Lys Leu Asp Ala Phe Leu Gln Pro Leu 385 390 395 400 Ser Lys Pro Leu Ser Ser Gln Pro Gln Ala Ile Val Thr Glu Asp Lys 405 410 415 Thr Asp Ile Ser Ser Gly Arg Ala Arg Gln Gln Asp Glu Glu Met Leu 420 425 430 Glu Leu Pro Ala Pro Ala Glu Val Ala Ala Lys Asn Gln Ser Leu Glu 435 440 445 Gly Asp Thr Thr Lys Gly Thr Ser Glu Met Ser Glu Lys Arg Gly Pro 450 455 460 Thr Ser Ser Asn Pro Arg Lys Arg His Arg Glu Asp Ser Asp Val Glu 465 470 475 480 Met Val Glu Asp Asp Ser Arg Lys Glu Met Thr Ala Ala Cys Thr Pro 485 490 495 Arg Arg Arg Ile Ile Asn Leu Thr Ser Val Leu Ser Leu Gln Glu Glu 500 505 510 Ile Asn Glu Gln Gly His Glu Val Leu Arg Glu Met Leu His Asn His 515 520 525 Ser Phe Val Gly Cys Val Asn Pro Gln Trp Ala Leu Ala Gln His Gln 530 535 540 Thr Lys Leu Tyr Leu Leu Asn Thr Thr Lys Leu Ser Glu Glu Leu Phe 545 550 555 560 Tyr Gln Ile Leu Ile Tyr Asp Phe Ala Asn Phe Gly Val Leu Arg Leu 565 570 575 Ser Glu Pro Ala Pro Leu Phe Asp Leu Ala Met Leu Ala Leu Asp Ser 580 585 590 Pro Glu Ser Gly Trp Thr Glu Glu Asp Gly Pro Lys Glu Gly Leu Ala 595 600 605 Glu Tyr Ile Val Glu Phe Leu Lys Lys Lys Ala Glu Met Leu Ala Asp 610 615 620 Tyr Phe Ser Leu Glu Ile Asp Glu Glu Gly Asn Leu Ile Gly Leu Pro 625 630 635 640 Leu Leu Ile Asp Asn Tyr Val Pro Pro Leu Glu Gly Leu Pro Ile Phe 645 650 655 Ile Leu Arg Leu Ala Thr Glu Val Asn Trp Asp Glu Glu Lys Glu Cys 660 665 670 Phe Glu Ser Leu Ser Lys Glu Cys Ala Met Phe Tyr Ser Ile Arg Lys 675 680 685 Gln Tyr Ile Ser Glu Glu Ser Thr Leu Ser Gly Gln Gln Ser Glu Val 690 695 700 Pro Gly Ser Ile Pro Asn Ser Trp Lys Trp Thr Val Glu His Ile Val 705 710 715 720 Tyr Lys Ala Leu Arg Ser His Ile Leu Pro Pro Lys His Phe Thr Glu 725 730 735 Asp Gly Asn Ile Leu Gln Leu Ala Asn Leu Pro Asp Leu Tyr Lys Val 740 745 750 Phe Glu Arg Cys 755 6 397 DNA Homo sapiens 6 tggctggatg ctaagctaca gctgaaggaa gaacgtgagc acgaggcact gaggtgattg 60 gctgaaggca cttccgttga gcatctagac gtttccttgg ctcttctggc gccaaaatgt 120 cgttcgtggc aggggttatt cggcggctgg acgagacagt ggtgaaccgc atcgcggcgg 180 gggaagttat ccagcggcca gctaatgcta tcaaagagat gattgagaac tggtacggag 240 ggagtcgagc cgggctcact taagggctac gacttaacgg gccgcgtcac tcaatggcgc 300 ggacacgcct ctttccccgg gcagaggcat gtacagcgca tgcccacaac ggcggaggcc 360 gccgggttcc ctacgtgcca taagccttct ccttttc 397 7 393 DNA Homo sapiens 7 aaacacgtta atgaggcact attgtttgta tttggagttt gttatcattg cttggctcat 60 attaaaatat gtacattaga gtagttgcag actgataaat tattttctgt ttgatttgcc 120 agtttagatg caaaatccac aagtattcaa gtgattgtta aagagggagg cctgaagttg 180 attcagatcc aagacaatgg caccgggatc agggtaagta aaacctcaaa gtagcaggat 240 gtttgtgcgc ttcatggaag agtcaggacc tttctctgtt ctggaaacta ggcttttgca 300 gatgggattt tttcactgaa aaattcaaca ccaacaataa atatttattg agtacctatt 360 atttgcgggg cactgttcag gggatgtgtc agt 393 8 352 DNA Homo sapiens 8 tttcctggat taatcaagaa atggaattca aagagatttg gaaaatgagt aacatgatta 60 tttactcatc tttttggtat ctaacagaaa gaagatctgg atattgtatg tgaaaggttc 120 actactagta aactgcagtc ctttgaggat ttagccagta tttctaccta tggctttcga 180 ggtgaggtaa gctaaagatt caagaaatgt gtaaaatatc ctcctgtgat gacattgtct 240 gtcatttgtt agtatgtatt tctcaacata gataaataag gtttggtacc ttttacttgt 300 taaatgtatg caaatctgag caaacttaat gaactttaac tttcaaagac tg 352 9 287 DNA Homo sapiens 9 tggaagcagc agcagataac ctttcccttt ggtgaggtga cagtgggtga cccagcagtg 60 agtttttctt tcagtctatt ttcttttctt ccttaggctt tggccagcat aagccatgtg 120 gctcatgtta ctattacaac gaaaacagct gatggaaagt gtgcatacag gtatagtgct 180 gacttctttt actcatatat attcattctg aaatgtattt tgggcctagg tctcagagta 240 atcctgtctc aacaccagtg ttatctttgg cagagatctt gagtacg 287 10 336 DNA Homo sapiens 10 ttgatatgat tttctctttt ccccttggga ttagtatcta tctctctact ggatattaat 60 ttgttatatt ttctcattag agcaagttac tcagatggaa aactgaaagc ccctcctaaa 120 ccatgtgctg gcaatcaagg gacccagatc acggtaagaa tggtacatgg gagagtaaat 180 tgttgaagct ttgtttgtat aaatattgga ataaaaaata aaattgcttc taagttttca 240 gggtaataat aaaatgaatt tgcactagtt aatggaggtc ccaagatatc ctctaagcaa 300 gataaatgac tattggcttt ttggcatggc agcctg 336 11 275 DNA Homo sapiens 11 gcttttgcca ggaccatctt gggttttatt ttcaagtact tctatgaatt tacaagaaaa 60 atcaatcttc tgttcaggtg gaggaccttt tttacaacat agccacgagg agaaaagctt 120 taaaaaatcc aagtgaagaa tatgggaaaa ttttggaagt tgttggcagg tacagtccaa 180 aatctgggag tgggtctctg agatttgtca tcaaagtaat gtgttctagt gctcatacat 240 tgaacagttg ctgagctaga tggtgaaaag taaaa 275 12 389 DNA Homo sapiens 12 cagcaaccta taaaagtaga gaggagtctg tgttttgacg cagcaccttt agcattttta 60 tttggatgaa gtttctgctg gtttattttt ctgtgggtaa aatattaata ggctgtatgg 120 agatattttt ctttatatgt acctttgttt agattactca actccactaa tttatttaac 180 taaaaggggg ctctgacatc tagtgtgtgt ttttggcaac tcttttctta ctcttttgtt 240 tttcttttcc aggtattcag tacacaatgc aggcattagt ttctcagtta aaaaagtaag 300 ttcttggttt atgggggatg gttttgtttt atgaaaagaa aaaaggggat ttttaatagt 360 ttgctggtgg agataaggtt atgatgttt 389 13 381 DNA Homo sapiens 13 atgtttcagt ctcagccatg agacaataaa tccttgtgtc ttctgctgtt tgtttatcag 60 caaggagaga cagtagctga tgttaggaca ctacccaatg cctcaaccgt ggacaatatt 120 cgctccatct ttggaaatgc tgttagtcgg tatgtcgata acctatataa aaaaatcttt 180 tacatttatt atcttggttt atcattccat cacattattt gggaaccttt caagatatta 240 tgtgtgttaa gagtttgctt tagtcaaata cacaggcttg ttttatgctt cagatttgtt 300 aatggagttc ttatttcacg taatcaacac tttctaggtg tatgtaatct cctagattct 360 gtggcgtgaa tcatgtgttc t 381 14 526 DNA Homo sapiens 14 actgagtagg gtaggtgggt gagtgggtgg gtgggtgggt gggtggatgg atggatggga 60 ggatgggtgg gtgaatgggt gaacagacaa atggatggat gaatggacag gcacaggagg 120 acctcaaatg gaccaagtct tcggggccct catttcacaa agttagttta tgggaaggaa 180 ccttgtgttt ttaaattctg attcttttgt aatgtttgag ttttgagtat tttcaaaagc 240 ttcagaatct cttttctaat agagaactga tagaaattgg atgtgaggat aaaaccctag 300 ccttcaaaat gaatggttac atatccaatg caaactactc agtgaagaag tgcatcttct 360 tactcttcat caaccgtaag ttaaaaagaa ccacatggga aatccactca caggaaacac 420 ccacagggaa ttttatggga ccatggaaaa atttctgagt ccataggttt gattaaacat 480 ggagaaacct catggcaaag tttggtttta ttgggaagca tgtata 526 15 434 DNA Homo sapiens 15 atagtgggct ggaaagtggc cacaggtaaa ggtgcacctt tcttcctggg gatgtgatgt 60 gcatatcact acagaaatgt ctttcctgag gtgatgtcat gactttgtgt gaatgtacac 120 ctgtgacctc acccctcagg acagttttga actggttgct ttctttttat tgtttagatc 180 gtctggtaga atcaacttcc ttgagaaaag ccatagaaac agtgtatgca gcctatttgc 240 ccaaaaacac acacccattc ctgtacctca ggtaatgtag caccaaactc ctcaaccaag 300 actcacaagg aacagatgtt ctatcaggct ctcctctttg aaagagatga gcatgctaat 360 agtacaatca gagtgaatcc catacaccac tggcaaaagg atgttctgtc ccttcttaca 420 ggtacaaggc acag 434 16 458 DNA Homo sapiens 16 cttacgcaaa gctacacagc tcttaagtag cagtgccaat atttgaacac actcagactc 60 gagcctgagg ttttgaccac tgtgtcatct ggcctcaaat cttctggcca ccacatacac 120 catatgtggg ctttttctcc ccctcccact atctaaggta attgttctct cttattttcc 180 tgacagttta gaaatcagtc cccagaatgt ggatgttaat gtgcacccca caaagcatga 240 agttcacttc ctgcacgagg agagcatcct ggagcgggtg cagcagcaca tcgagagcaa 300 gctcctgggc tccaattcct ccaggatgta cttcacccag gtcagggcgc ttctcatcca 360 gctacttctc tggggccttt gaaatgtgcc cggccagacg tgagagccca gatttttgct 420 gttatttagg aacttttttt gaagtattac ctggatag 458 17 618 DNA Homo sapiens 17 gataattata cctcatacta gcttctttct tagtactgct ccatttgggg acctgtatat 60 ctatacttct tattctgagt ctctccacta tatatatata tatatatata tttttttttt 120 tttttttttt taatacagac tttgctacca ggacttgctg gcccctctgg ggagatggtt 180 aaatccacaa caagtctgac ctcgtcttct acttctggaa gtagtgataa ggtctatgcc 240 caccagatgg ttcgtacaga ttcccgggaa cagaagcttg atgcatttct gcagcctctg 300 agcaaacccc tgtccagtca gccccaggcc attgtcacag aggataagac agatatttct 360 agtggcaggg ctaggcagca agatgaggag atgcttgaac tcccagcccc tgctgaagtg 420 gctgccaaaa atcagagctt ggagggggat acaacaaagg ggacttcaga aatgtcagag 480 aagagaggac ctacttccag caaccccagg tatggccttt tgggaaaagt acagcctacc 540 tcctttattc tgtaataaaa ctgccttcta actttggctt ttcatgaatc acttgcatct 600 tctctctgcc gacttccc 618 18 478 DNA Homo sapiens 18 ctgtgctcca gcacaggtca tccagctctg tagaccagcg cagagaagtt gcttgctccc 60 aaatgcaacc cacaaaattt ggctaagttt aaaaacaaga ataataatga tctgcacttc 120 cttttcttca ttgcagaaag agacatcggg aagattctga tgtggaaatg gtggaagatg 180 attcccgaaa ggaaatgact gcagcttgta ccccccggag aaggatcatt aacctcacta 240 gtgttttgag tctccaggaa gaaattaatg agcagggaca tgagggtacg taaacgctgt 300 ggcctgcctg ggatgcatag ggcctcaact gccaaggttt tggaaatgga gaaagcagtc 360 atgttgtcag agtggcacta cagttttgat gggcaagctc ctcttccttt actaacccac 420 aatagcatca gcttaaagac aatttttgat tgggagaaaa gggagaaaat aatctctg 478 19 377 DNA Homo sapiens 19 cagttttcac caggaggctc aaatcaggcc tttgcttact tggtgtctct agttctggtg 60 cctggtgctt tggtcaatga agtggggttg gtaggattct attacttacc tgttttttgg 120 ttttattttt tgttttgcag ttctccggga gatgttgcat aaccactcct tcgtgggctg 180 tgtgaatcct cagtgggcct tggcacagca tcaaaccaag ttataccttc tcaacaccac 240 caagcttagg taaatcagct gagtgtgtga acaagcagag ctactacaac aatggtccag 300 ggagcacagg cacaaaagct aaggagagca gcatgaaggt agttgggaag ggcacaggct 360 ttggagtcag cacatgt 377 20 325 DNA Homo sapiens 20 cccctggttg aagcgttgga atcccactct ttggaagatt gtgttagact gttaaccaga 60 ttccacagcc aggcagaact atgtctgtct catccatgtg tcagggatta cgtctcccat 120 ttgtcccaac tggttgtatc tcaagcatga attcagcttt tccttaaagt cacttcattt 180 ttattttcag tgaagaactg ttctaccaga tactcattta tgattttgcc aattttggtg 240 ttctcaggtt atcggtaagt ttagatcctt ttcacttctg acatttcaac tgaccgcccc 300 gcaaacagta gctctccact aaata 325 21 341 DNA Homo sapiens 21 catttatggt ttctcacctg ccattctgat agtggattct tgggaattca ggcttcattt 60 ggatgctccg ttaaagcttg ctccttcatg ttcttgcttc ttcctaggag ccagcaccgc 120 tctttgacct tgccatgctt gccttagata gtccagagag tggctggaca gaggaagatg 180 gtcccaaaga aggacttgct gaatacattg ttgagtttct gaagaagaag gctgagatgc 240 ttgcagacta tttctctttg gaaattgatg aggtgtgaca gccattctta tacttctgtt 300 gtattctcca aataaaattt ccagccgggt gcattggctc a 341 22 260 DNA Homo sapiens 22 cagataggag gcacaaggcc tgggaaaggc actggagaaa tgggatttgt ttaaactatg 60 acagcattat ttcttgttcc cttgtccttt ttcctgcaag caggaaggga acctgattgg 120 attacccctt ctgattgaca actatgtgcc ccctttggag ggactgccta tcttcattct 180 tcgactagcc actgaggtca gtgatcaagc agatactaag catttcggta catgcatgtg 240 tgctggaggg aaagggcaaa 260 23 340 DNA Homo sapiens 23 ctatatcttc ccagcaatat tcacagtccg tttacagttt taacgcctaa agtatcacat 60 ttcgtttttt agctttaagt agtctgtgat ctccgtttag aatgagaatg tttaaattcg 120 tacctatttt gaggtattga atttctttgg accaggtgaa ttgggacgaa gaaaaggaat 180 gttttgaaag cctcagtaaa gaatgcgcta tgttctattc catccggaag cagtacatat 240 ctgaggagtc gaccctctca ggccagcagg tacagtggtg atgcacactg gcaccccagg 300 actaggacag gacctcatac atcttaggag atgaaacttg 340 24 563 DNA Homo sapiens 24 aatcctcttg tgttcaggcc tgtggatccc tgagaggcta gcccacaaga tccacttcaa 60 aagccctaga taacaccaag tctttccaga cccagtgcac atcccatcag ccaggacacc 120 agtgtatgtt gggatgcaaa cagggaggct tatgacatct aatgtgtttt ccagagtgaa 180 gtgcctggct ccattccaaa ctcctggaag tggactgtgg aacacattgt ctataaagcc 240 ttgcgctcac acattctgcc tcctaaacat ttcacagaag atggaaatat cctgcagctt 300 gctaacctgc ctgatctata caaagtcttt gagaggtgtt aaatatggtt atttatgcac 360 tgtgggatgt gttcttcttt ctctgtattc cgatacaaag tgttgtatca aagtgtgata 420 tacaaagtgt accaacataa gtgttggtag cacttaagac ttatacttgc cttctgatag 480 tattccttta tacacagtgg attgattata aataaataga tgtgtcttaa cataatttct 540 tatttaattt tattatgtat ata 563 25 137 DNA Homo sapiens 25 cttggctctt ctggcgccaa aatgtcgttc gtggcagggg ttattcggcg gctggacgag 60 acagtggtga accgcatcgc ggcgggggaa gttatccagc ggccagctaa tgctatcaaa 120 gagatgattg agaactg 137 26 91 DNA Homo sapiens 26 tttagatgca aaatccacaa gtattcaagt gattgttaaa gagggaggcc tgaagttgat 60 tcagatccaa gacaatggca ccgggatcag g 91 27 99 DNA Homo sapiens 27 aaagaagatc tggatattgt atgtgaaagg ttcactacta gtaaactgca gtcctttgag 60 gatttagcca gtatttctac ctatggcttt cgaggtgag 99 28 74 DNA Homo sapiens 28 gctttggcca gcataagcca tgtggctcat gttactatta caacgaaaac agctgatgga 60 aagtgtgcat acag 74 29 73 DNA Homo sapiens 29 agcaagttac tcagatggaa aactgaaagc ccctcctaaa ccatgtgctg gcaatcaagg 60 gacccagatc acg 73 30 92 DNA Homo sapiens 30 gtggaggacc ttttttacaa catagccacg aggagaaaag ctttaaaaaa tccaagtgaa 60 gaatatggga aaattttgga agttgttggc ag 92 31 43 DNA Homo sapiens 31 gtattcagta cacaatgcag gcattagttt ctcagttaaa aaa 43 32 89 DNA Homo sapiens 32 caaggagaga cagtagctga tgttaggaca ctacccaatg cctcaaccgt ggacaatatt 60 cgctccatct ttggaaatgc tgttagtcg 89 33 113 DNA Homo sapiens 33 agaactgata gaaattggat gtgaggataa aaccctagcc ttcaaaatga atggttacat 60 atccaatgca aactactcag tgaagaagtg catcttctta ctcttcatca acc 113 34 94 DNA Homo sapiens 34 atcgtctggt agaatcaact tccttgagaa aagccataga aacagtgtat gcagcctatt 60 tgcccaaaaa cacacaccca ttcctgtacc tcag 94 35 154 DNA Homo sapiens 35 tttagaaatc agtccccaga atgtggatgt taatgtgcac cccacaaagc atgaagttca 60 cttcctgcac gaggagagca tcctggagcg ggtgcagcag cacatcgaga gcaagctcct 120 gggctccaat tcctccagga tgtacttcac ccag 154 36 371 DNA Homo sapiens 36 actttgctac caggacttgc tggcccctct ggggagatgg ttaaatccac aacaagtctg 60 acctcgtctt ctacttctgg aagtagtgat aaggtctatg cccaccagat ggttcgtaca 120 gattcccggg aacagaagct tgatgcattt ctgcagcctc tgagcaaacc cctgtccagt 180 cagccccagg ccattgtcac agaggataag acagatattt ctagtggcag ggctaggcag 240 caagatgagg agatgcttga actcccagcc cctgctgaag tggctgccaa aaatcagagc 300 ttggaggggg atacaacaaa ggggacttca gaaatgtcag agaagagagg acctacttcc 360 agcaacccca g 371 37 149 DNA Homo sapiens 37 aaagagacat cgggaagatt ctgatgtgga aatggtggaa gatgattccc gaaaggaaat 60 gactgcagct tgtacccccc ggagaaggat cattaacctc actagtgttt tgagtctcca 120 ggaagaaatt aatgagcagg gacatgagg 149 38 109 DNA Homo sapiens 38 ttctccggga gatgttgcat aaccactcct tcgtgggctg tgtgaatcct cagtgggcct 60 tggcacagca tcaaaccaag ttataccttc tcaacaccac caagcttag 109 39 64 DNA Homo sapiens 39 tgaagaactg ttctaccaga tactcattta tgattttgcc aattttggtg ttctcaggtt 60 atcg 64 40 165 DNA Homo sapiens 40 gagccagcac cgctctttga ccttgccatg cttgccttag atagtccaga gagtggctgg 60 acagaggaag atggtcccaa agaaggactt gctgaataca ttgttgagtt tctgaagaag 120 aaggctgaga tgcttgcaga ctatttctct ttggaaattg atgag 165 41 93 DNA Homo sapiens 41 gaagggaacc tgattggatt accccttctg attgacaact atgtgccccc tttggaggga 60 ctgcctatct tcattcttcg actagccact gag 93 42 114 DNA Homo sapiens 42 gtgaattggg acgaagaaaa ggaatgtttt gaaagcctca gtaaagaatg cgctatgttc 60 tattccatcc ggaagcagta catatctgag gagtcgaccc tctcaggcca gcag 114 43 360 DNA Homo sapiens 43 agtgaagtgc ctggctccat tccaaactcc tggaagtgga ctgtggaaca cattgtctat 60 aaagccttgc gctcacacat tctgcctcct aaacatttca cagaagatgg aaatatcctg 120 cagcttgcta acctgcctga tctatacaaa gtctttgaga ggtgttaaat atggttattt 180 atgcactgtg ggatgtgttc ttctttctct gtattccgat acaaagtgtt gtatcaaagt 240 gtgatataca aagtgtacca acataagtgt tggtagcact taagacttat acttgccttc 300 tgatagtatt cctttataca cagtggattg attataaata aatagatgtg tcttaacata 360 44 19 DNA Homo sapiens 44 aggcactgag gtgattggc 19 45 19 DNA Homo sapiens 45 tcgtagccct taagtgagc 19 46 22 DNA Homo sapiens 46 aatatgtaca ttagagtagt tg 22 47 19 DNA Homo sapiens 47 cagagaaagg tcctgactc 19 48 22 DNA Homo sapiens 48 agagatttgg aaaatgagta ac 22 49 19 DNA Homo sapiens 49 acaatgtcat cacaggagg 19 50 20 DNA Homo sapiens 50 aacctttccc tttggtgagg 20 51 20 DNA Homo sapiens 51 gattactctg agacctaggc 20 52 22 DNA Homo sapiens 52 gattttctct tttccccttg gg 22 53 23 DNA Homo sapiens 53 caaacaaagc ttcaacaatt tac 23 54 26 DNA Homo sapiens 54 gggttttatt ttcaagtact tctatg 26 55 26 DNA Homo sapiens 55 gctcagcaac tgttcaatgt atgagc 26 56 18 DNA Homo sapiens 56 ctagtgtgtg tttttggc 18 57 18 DNA Homo sapiens 57 cataacctta tctccacc 18 58 23 DNA Homo sapiens 58 ctcagccatg agacaataaa tcc 23 59 21 DNA Homo sapiens 59 ggttcccaaa taatgtgatg g 21 60 18 DNA Homo sapiens 60 caaaagcttc agaatctc 18 61 23 DNA Homo sapiens 61 ctgtgggtgt ttcctgtgag tgg 23 62 24 DNA Homo sapiens 62 catgactttg tgtgaatgta cacc 24 63 24 DNA Homo sapiens 63 gaggagagcc tgatagaaca tctg 24 64 20 DNA Homo sapiens 64 gggctttttc tccccctccc 20 65 18 DNA Homo sapiens 65 aaaatctggg ctctcacg 18 66 19 DNA Homo sapiens 66 aattatacct catactagc 19 67 23 DNA Homo sapiens 67 gttttattac agaataaagg agg 23 68 19 DNA Homo sapiens 68 aagccaaagt tagaaggca 19 69 20 DNA Homo sapiens 69 tgcaacccac aaaatttggc 20 70 20 DNA Homo sapiens 70 ctttctccat ttccaaaacc 20 71 18 DNA Homo sapiens 71 tggtgtctct agttctgg 18 72 20 DNA Homo sapiens 72 cattgttgta gtagctctgc 20 73 18 DNA Homo sapiens 73 cccatttgtc ccaactgg 18 74 19 DNA Homo sapiens 74 cggtcagttg aaatgtcag 19 75 22 DNA Homo sapiens 75 catttggatg ctccgttaaa gc 22 76 23 DNA Homo sapiens 76 cacccggctg gaaattttat ttg 23 77 22 DNA Homo sapiens 77 ggaaaggcac tggagaaatg gg 22 78 25 DNA Homo sapiens 78 ccctccagca cacatgcatg taccg 25 79 20 DNA Homo sapiens 79 taagtagtct gtgatctccg 20 80 18 DNA Homo sapiens 80 atgtatgagg tcctgtcc 18 81 18 DNA Homo sapiens 81 gacaccagtg tatgttgg 18 82 20 DNA Homo sapiens 82 gagaaagaag aacacatccc 20 83 38 DNA Homo sapiens 83 tgtaaaacga cggccagtca ctgaggtgat tggctgaa 38 84 19 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 84 tagcccttaa gtgagcccg 19 85 38 DNA Homo sapiens 85 tgtaaaacga cggccagtta cattagagta gttgcaga 38 86 19 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 86 aggtcctgac tcttccatg 19 87 40 DNA Homo sapiens 87 tgtaaaacga cggccagttt ggaaaatgag taacatgatt 40 88 19 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 88 tgtcatcaca ggaggatat 19 89 38 DNA Homo sapiens 89 tgtaaaacga cggccagtct ttccctttgg tgaggtga 38 90 20 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 90 tactctgaga cctaggccca 20 91 40 DNA Homo sapiens 91 tgtaaaacga cggccagttc tcttttcccc ttgggattag 40 92 23 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 92 acaaagcttc aacaatttac tct 23 93 46 DNA Homo sapiens 93 tgtaaaacga cggccagtgt tttattttca agtacttcta tgaatt 46 94 26 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 94 cagcaactgt tcaatgtatg agcact 26 95 36 DNA Homo sapiens 95 tgtaaaacga cggccagtgt gtgtgttttt ggcaac 36 96 18 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 96 aaccttatct ccaccagc 18 97 41 DNA Homo sapiens 97 tgtaaaacga cggccagtag ccatgagaca ataaatcctt g 41 98 22 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 98 tcccaaataa tgtgatggaa tg 22 99 37 DNA Homo sapiens 99 tgtaaaacga cggccagtaa gcttcagaat ctctttt 37 100 23 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 100 tgggtgtttc ctgtgagtgg att 23 101 42 DNA Homo sapiens 101 tgtaaaacga cggccagtac tttgtgtgaa tgtacacctg tg 42 102 24 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 102 gagagcctga tagaacatct gttg 24 103 39 DNA Homo sapiens 103 tgtaaaacga cggccagtct ttttctcccc ctcccacta 39 104 17 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 104 tctgggctct cacgtct 17 105 18 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 105 cttattctga gtctctcc 18 106 35 DNA Homo sapiens 106 tgtaaaacga cggccagtgt ttgctcagag gctgc 35 107 21 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 107 gatggttcgt acagattccc g 21 108 41 DNA Homo sapiens 108 tgtaaaacga cggccagttt attacagaat aaaggaggta g 41 109 39 DNA Homo sapiens 109 tgtaaaacga cggccagtaa cccacaaaat ttggctaag 39 110 20 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 110 tctccatttc caaaaccttg 20 111 18 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 111 tgtctctagt tctggtgc 18 112 38 DNA Homo sapiens 112 tgtaaaacga cggccagttg ttgtagtagc tctgcttg 38 113 20 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 113 atttgtccca actggttgta 20 114 39 DNA Homo sapiens 114 tgtaaaacga cggccagttc agttgaaatg tcagaagtg 39 115 18 DNA Homo sapiens 115 tgtaaaacga cggccagt 18 116 23 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 116 ccggctggaa attttatttg gag 23 117 41 DNA Homo sapiens 117 tgtaaaacga cggccagtag gcactggaga aatgggattt g 41 118 26 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 118 tccagcacac atgcatgtac cgaaat 26 119 20 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 119 gtagtctgtg atctccgttt 20 120 36 DNA Homo sapiens 120 tgtaaaacga cggccagtta tgaggtcctg tcctag 36 121 19 DNA Homo sapiens misc_feature (1)..(1) The residue is biotinylated 121 accagtgtat gttgggatg 19 122 39 DNA Homo sapiens 122 tgtaaaacga cggccagtga aagaagaaca catcccaca 39 123 770 PRT Saccharomyces cerevisiae 123 Met Ser Leu Arg Ile Lys Ala Leu Asp Ala Ser Val Val Asn Lys Ile 1 5 10 15 Ala Ala Gly Glu Ile Ile Ile Ser Pro Val Asn Ala Leu Lys Glu Met 20 25 30 Met Glu Asn Ser Ile Asp Ala Asn Ala Thr Met Ile Asp Ile Leu Val 35 40 45 Lys Glu Gly Gly Ile Lys Val Leu Gln Ile Thr Asp Asn Gly Ser Gly 50 55 60 Ile Asn Lys Ala Asp Leu Pro Ile Leu Cys Glu Arg Phe Thr Thr Ser 65 70 75 80 Lys Leu Gln Lys Phe Glu Asp Leu Ser Gln Ile Gln Thr Tyr Gly Phe 85 90 95 Arg Gly Glu Ala Leu Ala Ser Ile Ser His Val Ala Arg Val Thr Val 100 105 110 Thr Thr Lys Val Lys Glu Asp Arg Cys Ala Trp Arg Val Ser Tyr Ala 115 120 125 Glu Gly Lys Met Leu Glu Ser Pro Lys Pro Val Ala Gly Lys Asp Gly 130 135 140 Thr Thr Ile Leu Val Glu Asp Leu Phe Phe Asn Ile Pro Ser Arg Leu 145 150 155 160 Arg Ala Leu Arg Ser His Asn Asp Glu Tyr Ser Lys Ile Leu Asp Val 165 170 175 Val Gly Arg Tyr Ala Ile His Ser Lys Asp Ile Gly Phe Ser Cys Lys 180 185 190 Lys Phe Gly Asp Ser Asn Tyr Ser Leu Ser Val Lys Pro Ser Tyr Thr 195 200 205 Val Gln Asp Arg Ile Arg Thr Val Phe Asn Lys Ser Val Ala Ser Asn 210 215 220 Leu Ile Thr Phe His Ile Ser Lys Val Glu Asp Leu Asn Leu Glu Ser 225 230 235 240 Val Asp Gly Lys Val Cys Asn Leu Asn Phe Ile Ser Lys Lys Ser Ile 245 250 255 Ser Leu Ile Phe Phe Ile Asn Asn Arg Leu Val Thr Cys Asp Leu Leu 260 265 270 Arg Arg Ala Leu Asn Ser Val Tyr Ser Asn Tyr Leu Pro Lys Gly Phe 275 280 285 Arg Pro Phe Ile Tyr Leu Gly Ile Val Ile Asp Pro Ala Ala Val Asp 290 295 300 Val Asn Val His Pro Thr Lys Arg Glu Val Arg Phe Leu Ser Gln Asp 305 310 315 320 Glu Ile Ile Glu Lys Ile Ala Asn Gln Leu His Ala Glu Leu Ser Ala 325 330 335 Ile Asp Thr Ser Arg Thr Phe Lys Ala Ser Ser Ile Ser Thr Asn Lys 340 345 350 Pro Glu Ser Leu Ile Pro Phe Asn Asp Thr Ile Glu Ser Asp Arg Asn 355 360 365 Arg Lys Ser Leu Arg Gln Ala Gln Val Val Glu Asn Ser Tyr Thr Thr 370 375 380 Ala Asn Ser Gln Leu Arg Lys Ala Lys Arg Gln Glu Asn Lys Leu Val 385 390 395 400 Arg Ile Asp Ala Ser Gln Ala Lys Ile Thr Ser Phe Leu Ser Ser Ser 405 410 415 Gln Gln Phe Asn Phe Glu Gly Ser Ser Thr Lys Arg Gln Leu Ser Glu 420 425 430 Pro Lys Val Thr Asn Val Ser His Ser Gln Glu Ala Glu Lys Leu Thr 435 440 445 Leu Asn Glu Ser Glu Gln Pro Arg Asp Ala Asn Thr Ile Asn Asp Asn 450 455 460 Asp Leu Lys Asp Gln Pro Lys Lys Lys Gln Lys Gln Leu Gly Asp Tyr 465 470 475 480 Lys Val Pro Ser Ile Ala Asp Asp Glu Lys Asn Ala Leu Pro Ile Ser 485 490 495 Lys Asp Gly Tyr Ile Arg Val Pro Lys Glu Arg Val Asn Val Asn Leu 500 505 510 Thr Ser Ile Lys Lys Leu Arg Glu Lys Val Asp Asp Ser Ile His Arg 515 520 525 Glu Leu Thr Asp Ile Phe Ala Asn Leu Asn Tyr Val Gly Val Val Asp 530 535 540 Glu Glu Arg Arg Leu Ala Ala Ile Gln His Asp Leu Lys Leu Phe Leu 545 550 555 560 Ile Asp Tyr Gly Ser Val Cys Tyr Glu Leu Phe Tyr Gln Ile Gly Leu 565 570 575 Thr Asp Phe Ala Asn Phe Gly Lys Ile Asn Leu Gln Ser Thr Asn Val 580 585 590 Ser Asp Asp Ile Val Leu Tyr Asn Leu Leu Ser Glu Phe Asp Glu Leu 595 600 605 Asn Asp Asp Ala Ser Lys Glu Lys Ile Ile Ser Lys Ile Trp Asp Met 610 615 620 Ser Ser Met Leu Asn Glu Tyr Tyr Ser Ile Glu Leu Val Asn Asp Gly 625 630 635 640 Leu Asp Asn Asp Leu Lys Ser Val Lys Leu Lys Ser Leu Pro Leu Leu 645 650 655 Leu Lys Gly Tyr Ile Pro Ser Leu Val Lys Leu Pro Phe Phe Ile Tyr 660 665 670 Arg Leu Gly Lys Glu Val Asp Trp Glu Asp Glu Gln Glu Cys Leu Asp 675 680 685 Gly Ile Leu Arg Glu Ile Ala Leu Leu Tyr Ile Pro Asp Met Val Pro 690 695 700 Lys Val Asp Thr Leu Asp Ala Ser Leu Ser Glu Asp Glu Lys Ala Gln 705 710 715 720 Phe Ile Asn Arg Lys Glu His Ile Ser Ser Leu Leu Glu His Val Leu 725 730 735 Phe Pro Cys Ile Lys Arg Arg Phe Leu Ala Pro Arg His Ile Leu Lys 740 745 750 Asp Val Val Glu Ile Ala Asn Leu Pro Asp Leu Tyr Lys Val Phe Glu 755 760 765 Arg Cys 770 124 64 PRT Homo sapiens 124 Val Asn Arg Ile Ala Ala Gly Glu Val Ile Gln Arg Pro Ala Asn Ala 1 5 10 15 Ile Lys Glu Met Ile Glu Asn Cys Leu Asp Ala Lys Phe Thr Ser Ile 20 25 30 Gln Val Ile Val Lys Glu Gly Gly Leu Lys Leu Ile Gln Ile Gln Asp 35 40 45 Asn Gly Thr Gly Ile Arg Lys Glu Asp Leu Asp Ile Val Cys Glu Arg 50 55 60 125 64 PRT Homo sapiens 125 Val Asn Arg Ile Ala Ala Gly Glu Val Ile Gln Arg Pro Ala Asn Ala 1 5 10 15 Ile Lys Glu Met Ile Glu Asn Cys Leu Asp Ala Lys Ser Thr Ser Ile 20 25 30 Gln Val Ile Val Lys Glu Gly Gly Leu Lys Leu Ile Gln Ile Gln Asp 35 40 45 Asn Gly Thr Gly Ile Arg Lys Glu Asp Leu Asp Ile Val Cys Glu Arg 50 55 60 126 52 PRT Mus musculus 126 Pro Ala Asn Ala Ile Lys Glu Met Ile Glu Asn Cys Leu Asp Ala Lys 1 5 10 15 Ser Thr Asn Ile Gln Val Val Val Lys Glu Gly Gly Leu Lys Leu Ile 20 25 30 Gln Ile Gln Asp Asn Gly Thr Gly Ile Arg Lys Glu Asp Leu Asp Ile 35 40 45 Val Cys Glu Arg 50 127 64 PRT Saccharomyces cerevisiae 127 Val Asn Lys Ile Ala Ala Gly Glu Ile Ile Ile Ser Pro Val Asn Ala 1 5 10 15 Leu Lys Glu Met Met Glu Asn Ser Ile Asp Ala Asn Ala Thr Met Ile 20 25 30 Asp Ile Leu Val Lys Glu Gly Gly Ile Lys Val Leu Gln Ile Thr Asp 35 40 45 Asn Gly Ser Gly Ile Asn Lys Ala Asp Leu Pro Ile Leu Cys Glu Arg 50 55 60 128 64 PRT Saccharomyces cerevisiae 128 Val His Arg Ile Thr Ser Gly Gln Val Ile Thr Asp Leu Thr Thr Ala 1 5 10 15 Val Lys Glu Leu Val Asp Asn Ser Ile Asp Ala Asn Ala Asn Gln Ile 20 25 30 Glu Ile Ile Phe Lys Asp Tyr Gly Leu Glu Ser Ile Glu Cys Ser Asp 35 40 45 Asn Gly Asp Gly Ile Asp Pro Ser Asn Tyr Glu Phe Leu Ala Leu Lys 50 55 60 129 64 PRT Escherichia coli 129 Ala Asn Gln Ile Ala Ala Gly Glu Val Val Glu Arg Pro Ala Ser Val 1 5 10 15 Val Lys Glu Leu Val Glu Asn Ser Leu Asp Ala Gly Ala Thr Arg Ile 20 25 30 Asp Ile Asp Ile Glu Arg Gly Gly Ala Lys Leu Ile Arg Ile Arg Asp 35 40 45 Asn Gly Cys Gly Ile Lys Lys Asp Glu Leu Ala Leu Ala Leu Ala Arg 50 55 60 130 64 PRT Salmonella typhimurium 130 Ala Asn Gln Ile Ala Ala Gly Glu Val Val Glu Arg Pro Ala Ser Val 1 5 10 15 Val Lys Glu Leu Val Glu Asn Ser Leu Asp Ala Gly Ala Thr Arg Val 20 25 30 Asp Ile Asp Ile Glu Arg Gly Gly Ala Lys Leu Ile Arg Ile Arg Asp 35 40 45 Asn Gly Cys Gly Ile Lys Lys Glu Glu Leu Ala Leu Ala Leu Ala Arg 50 55 60 131 64 PRT Streptococcus pneumoniae 131 Ala Asn Gln Ile Ala Ala Gly Glu Val Ile Glu Arg Pro Ala Ser Val 1 5 10 15 Cys Lys Glu Leu Val Glu Asn Ala Ile Asp Ala Gly Ser Ser Gln Ile 20 25 30 Ile Ile Glu Ile Glu Glu Ala Gly Leu Lys Lys Val Gln Ile Thr Asp 35 40 45 Asn Gly His Gly Ile Ala His Asp Glu Val Glu Leu Ala Leu Arg Arg 50 55 60 132 2687 DNA Homo sapiens 132 ccatggagcg agctgagagc tcgagtacag aacctgctaa ggccatcaaa cctattgatc 60 ggaagtcagt ccatcagatt tgctctgggc aggtggtact gagtctaagc actgcggtaa 120 aggagttagt agaaaacagt ctggatgctg gtgccactaa tattgatcta aagcttaagg 180 actatggagt ggatcttatt gaagtttcag acaatggatg tggggtagaa gaagaaaact 240 tcgaaggctt aactctgaaa catcacacat ctaagattca agagtttgcc gacctaactc 300 aggttgaaac ttttggcttt cggggggaag ctctgagctc actttgtgca ctgagcgatg 360 tcaccatttc tacctgccac gcatcggcga aggttggaac tcgactgatg tttgatcaca 420 atgggaaaat tatccagaaa accccctacc cccgccccag agggaccaca gtcagcgtgc 480 agcagttatt ttccacacta cctgtgcgcc ataaggaatt tcaaaggaat attaagaagg 540 agtatgccaa aatggtccag gtcttacatg catactgtat catttcagca ggcatccgtg 600 taagttgcac caatcagctt ggacaaggaa aacgacagcc tgtggtatgc acaggtggaa 660 gccccagcat aaaggaaaat atcggctctg tgtttgggca gaagcagttg caaagcctca 720 ttccttttgt tcagctgccc cctagtgact ccgtgtgtga agagtacggt ttgagctgtt 780 cggatgctct gcataatctt ttttacatct caggtttcat ttcacaatgc acgcatggag 840 ttggaaggag ttcaacagac agacagtttt tctttatcaa ccggcggcct tgtgacccag 900 caaaggtctg cagactcgtg aatgaggtct accacatgta taatcgacac cagtatccat 960 ttgttgttct taacatttct gttgattcag aatgcgttga tatcaatgtt actccagata 1020 aaaggcaaat tttgctacaa gaggaaaagc ttttgttggc agttttaaag acctctttga 1080 taggaatgtt tgatagtgat gtcaacaagc taaatgtcag tcagcagcca ctgctggatg 1140 ttgaaggtaa cttaataaaa atgcatgcag cggatttgga aaagcccatg gtagaaaagc 1200 aggatcaatc cccttcatta aggactggag aagaaaaaaa agacgtgtcc atttccagac 1260 tgcgagaggc cttttctctt cgtcacacaa cagagaacaa gcctcacagc ccaaagactc 1320 cagaaccaag aaggagccct ctaggacaga aaaggggtat gctgtcttct agcacttcag 1380 gtgccatctc tgacaaaggc gtcctgagat ctcagaaaga ggcagtgagt tccagtcacg 1440 gacccagtga ccctacggac agagcggagg tggagaagga ctcggggcac ggcagcactt 1500 ccgtggattc tgaggggttc agcatcccag acacgggcag tcactgcagc agcgagtatg 1560 cggccagctc cccaggggac aggggctcgc aggaacatgt ggactctcag gagaaagcgc 1620 ctgaaactga cgactctttt tcagatgtgg actgccattc aaaccaggaa gataccggat 1680 gtaaatttcg agttttgcct cagccaacta atctcgcaac cccaaacaca aagcgtttta 1740 aaaaagaaga aattctttcc agttctgaca tttgtcaaaa gttagtaaat actcaggaca 1800 tgtcagcctc tcaggttgat tgagctgtga aaattaataa gaaagttgtg cccctggact 1860 tttctatgag ttctttagct aaacgaataa agcagttaca tcatgaagca cagcaaagtg 1920 aaggggaaca gaattacagg aagtttaggg caaagatttg tcctggagaa aatcaagcag 1980 ccgaagatga actaagaaaa gagataagta aaacgatgtt tgcagaaatg gaaatcattg 2040 gtcagtttaa cctgggattt ataataacca aactgaatga ggatatcttc atagtggacc 2100 agcatgccac ggacgagaag tataacttcg agatgctgca gcagcacacc gtgctccagg 2160 ggcagaggct catagcacct cagactctca acttaactgc tgttaatgaa gctgttctga 2220 tagaaaatct ggaaatattt agaaagaatg gctttgattt tgttatcgat gaaaatgctc 2280 cagtcactga aagggctaaa ctgatttcct tgccaactag taaaaactgg accttcggac 2340 cccaggacgt cgatgaactg atcttcatgc tgagcgacag ccctggggtc atgtgccgcc 2400 cttcccgagt caagcagatg tttgcctcca gagcctgccg gaagtcggtg atgattggga 2460 ctgctctcaa cacaagcgaa tgaagaaact gatcacccac atgggggaga tgggccaccc 2520 ctggaactgt ccccatggaa ggccaccatg agacacatcg ccaacctggg tgtcatttct 2580 cagaactgac cgtagtcact gtatggaata attggtttta tcgcagattt ttatgttttg 2640 aaagacagag tcttcactaa ccttttttgt tttaaaatga aacctgc 2687 133 862 PRT Homo sapiens 133 Met Glu Arg Ala Glu Ser Ser Ser Thr Glu Pro Ala Lys Ala Ile Lys 1 5 10 15 Pro Ile Asp Arg Lys Ser Val His Gln Ile Cys Ser Gly Gln Val Val 20 25 30 Leu Ser Leu Ser Thr Ala Val Lys Glu Leu Val Glu Asn Ser Leu Asp 35 40 45 Ala Gly Ala Thr Asn Ile Asp Leu Lys Leu Lys Asp Tyr Gly Val Asp 50 55 60 Leu Ile Glu Val Ser Asp Asn Gly Cys Gly Val Glu Glu Glu Asn Phe 65 70 75 80 Glu Gly Leu Thr Leu Lys His His Thr Ser Lys Ile Gln Glu Phe Ala 85 90 95 Asp Leu Thr Gln Val Glu Thr Phe Gly Phe Arg Gly Glu Ala Leu Ser 100 105 110 Ser Leu Cys Ala Leu Ser Asp Val Thr Ile Ser Thr Cys His Ala Ser 115 120 125 Ala Lys Val Gly Thr Arg Leu Met Phe Asp His Asn Gly Lys Ile Ile 130 135 140 Gln Lys Thr Pro Tyr Pro Arg Pro Arg Gly Thr Thr Val Ser Val Gln 145 150 155 160 Gln Leu Phe Ser Thr Leu Pro Val Arg His Lys Glu Phe Gln Arg Asn 165 170 175 Ile Lys Lys Glu Tyr Ala Lys Met Val Gln Val Leu His Ala Tyr Cys 180 185 190 Ile Ile Ser Ala Gly Ile Arg Val Ser Cys Thr Asn Gln Leu Gly Gln 195 200 205 Gly Lys Arg Gln Pro Val Val Cys Ile Gly Gly Ser Pro Ser Ile Lys 210 215 220 Glu Asn Ile Gly Ser Val Phe Gly Gln Lys Gln Leu Gln Ser Leu Ile 225 230 235 240 Pro Phe Val Gln Leu Pro Pro Ser Asp Ser Val Cys Glu Glu Tyr Gly 245 250 255 Leu Ser Cys Ser Asp Ala Leu His Asn Leu Phe Tyr Ile Ser Gly Phe 260 265 270 Ile Ser Gln Cys Thr His Gly Val Gly Arg Ser Ser Thr Asp Arg Gln 275 280 285 Phe Phe Phe Ile Asn Arg Arg Pro Cys Asp Pro Ala Lys Val Cys Arg 290 295 300 Leu Val Asn Glu Val Tyr His Met Tyr Asn Arg His Gln Tyr Pro Phe 305 310 315 320 Val Val Leu Asn Ile Ser Val Asp Ser Glu Cys Val Asp Ile Asn Val 325 330 335 Thr Pro Asp Lys Arg Gln Ile Leu Leu Gln Glu Glu Lys Leu Leu Leu 340 345 350 Ala Val Leu Lys Thr Ser Leu Ile Gly Met Phe Asp Ser Asp Val Asn 355 360 365 Lys Leu Asn Val Ser Gln Gln Pro Leu Leu Asp Val Glu Gly Asn Leu 370 375 380 Ile Lys Met His Ala Ala Asp Leu Glu Lys Pro Met Val Glu His Gln 385 390 395 400 Asp Gln Ser Pro Ser Leu Arg Ile Gly Glu Glu Lys Lys Asp Val Ser 405 410 415 Ile Ser Arg Leu Arg Glu Ala Phe Ser Leu Arg His Thr Thr Glu Asn 420 425 430 Lys Pro His Ser Pro Lys Thr Pro Glu Pro Arg Arg Ser Pro Leu Gly 435 440 445 Gln Lys Arg Gly Met Leu Ser Ser Ser Thr Ser Gly Ala Ile Ser Asp 450 455 460 Lys Gly Val Leu Arg Ser Gln Lys Glu Ala Val Ser Ser Ser His Gly 465 470 475 480 Pro Ser Asp Pro Thr Asp Arg Ala Glu Val Glu Lys Asp Ser Gly His 485 490 495 Gly Ser Thr Ser Val Asp Ser Glu Gly Phe Ser Ile Pro Asp Thr Gly 500 505 510 Ser His Cys Ser Ser Glu Tyr Ala Ala Ser Ser Pro Gly Asp Arg Gly 515 520 525 Ser Gln Glu His Val Asp Ser Gln Glu Lys Ala Pro Glu Thr Asp Asp 530 535 540 Ser Phe Ser Asp Val Asp Cys His Ser Asn Gln Glu Asp Thr Gly Cys 545 550 555 560 Lys Phe Arg Val Leu Pro Gln Pro Ile Asn Leu Ala Thr Pro Asn Thr 565 570 575 Lys Arg Phe Lys Lys Glu Glu Ile Leu Ser Ser Ser Asp Ile Cys Gln 580 585 590 Lys Leu Val Asn Thr Gln Asp Met Ser Ala Ser Gln Val Asp Val Ala 595 600 605 Val Lys Ile Asn Lys Lys Val Val Pro Leu Asp Phe Ser Met Ser Ser 610 615 620 Leu Ala Lys Arg Ile Lys Gln Leu His His Glu Ala Gln Gln Ser Glu 625 630 635 640 Gly Glu Gln Asn Tyr Arg Lys Phe Arg Ala Lys Ile Cys Pro Gly Glu 645 650 655 Asn Gln Ala Ala Glu Asp Glu Leu Arg Lys Glu Ile Ser Lys Thr Met 660 665 670 Phe Ala Glu Met Glu Ile Ile Gly Gln Phe Asn Leu Gly Phe Ile Ile 675 680 685 Thr Lys Leu Asn Glu Asp Ile Phe Ile Val Asp Gln His Ala Thr Asp 690 695 700 Glu Lys Tyr Asn Phe Glu Met Leu Gln Gln His Thr Val Leu Gln Gly 705 710 715 720 Gln Arg Leu Ile Ala Pro Gln Thr Leu Asn Leu Thr Ala Val Asn Glu 725 730 735 Ala Val Leu Ile Glu Asn Leu Glu Ile Phe Arg Lys Asn Gly Phe Asp 740 745 750 Phe Val Ile Asp Glu Asn Ala Pro Val Thr Glu Arg Ala Lys Leu Ile 755 760 765 Ser Leu Pro Thr Ser Lys Asn Trp Thr Phe Gly Pro Gln Asp Val Asp 770 775 780 Glu Leu Ile Phe Met Leu Ser Asp Ser Pro Gly Val Met Cys Arg Pro 785 790 795 800 Ser Arg Val Lys Gln Met Phe Ala Ser Arg Ala Cys Arg Lys Ser Val 805 810 815 Met Ile Gly Thr Ala Leu Asn Thr Ser Glu Met Lys Lys Leu Ile Thr 820 825 830 His Met Gly Glu Met Gly His Pro Trp Asn Cys Pro His Gly Arg Pro 835 840 845 Thr Met Arg His Ile Ala Asn Leu Gly Val Ile Ser Gln Asn 850 855 860 134 903 PRT Saccharomyces cerevisiae 134 Met Phe His His Ile Glu Asn Leu Leu Ile Glu Thr Glu Lys Arg Cys 1 5 10 15 Lys Gln Lys Glu Gln Arg Tyr Ile Pro Val Lys Tyr Leu Phe Ser Met 20 25 30 Thr Gln Ile His Gln Ile Asn Asp Ile Asp Val His Arg Ile Thr Ser 35 40 45 Gly Gln Val Ile Thr Asp Leu Thr Thr Ala Val Lys Glu Leu Val Asp 50 55 60 Asn Ser Ile Asp Ala Asn Ala Asn Gln Ile Glu Ile Ile Phe Lys Asp 65 70 75 80 Tyr Gly Leu Glu Ser Ile Glu Cys Ser Asp Asn Gly Asp Gly Ile Asp 85 90 95 Pro Ser Asn Tyr Glu Phe Leu Ala Leu Lys His Tyr Thr Ser Lys Ile 100 105 110 Ala Lys Phe Gln Asp Val Ala Lys Val Gln Thr Leu Gly Phe Arg Gly 115 120 125 Glu Ala Leu Ser Ser Leu Cys Gly Ile Ala Lys Leu Ser Val Ile Thr 130 135 140 Thr Thr Ser Pro Pro Lys Ala Asp Lys Leu Glu Tyr Asp Met Val Gly 145 150 155 160 His Ile Thr Ser Lys Thr Thr Ser Arg Asn Lys Gly Thr Thr Val Leu 165 170 175 Val Ser Gln Leu Phe His Asn Leu Pro Val Arg Gln Lys Glu Phe Ser 180 185 190 Lys Thr Phe Lys Arg Gln Phe Thr Lys Cys Leu Thr Val Ile Gln Gly 195 200 205 Tyr Ala Ile Ile Asn Ala Ala Ile Lys Phe Ser Val Trp Asn Ile Thr 210 215 220 Pro Lys Gly Lys Lys Asn Leu Ile Leu Ser Thr Met Arg Asn Ser Ser 225 230 235 240 Met Arg Lys Asn Ile Ser Ser Val Phe Gly Ala Gly Gly Met Phe Gly 245 250 255 Leu Glu Glu Val Asp Leu Val Leu Asp Leu Asn Pro Phe Lys Asn Arg 260 265 270 Met Leu Gly Lys Tyr Thr Asp Asp Pro Asp Phe Leu Asp Leu Asp Tyr 275 280 285 Lys Ile Arg Val Lys Gly Tyr Ile Ser Gln Asn Ser Phe Gly Cys Gly 290 295 300 Arg Asn Ser Lys Asp Arg Gln Phe Ile Tyr Val Asn Lys Arg Pro Val 305 310 315 320 Glu Tyr Ser Thr Leu Leu Lys Cys Cys Asn Glu Val Tyr Lys Thr Phe 325 330 335 Asn Asn Val Gln Phe Pro Ala Val Phe Leu Asn Leu Glu Leu Pro Met 340 345 350 Ser Leu Ile Asp Val Asn Val Thr Pro Asp Lys Arg Val Ile Leu Leu 355 360 365 His Asn Glu Arg Ala Val Ile Asp Ile Phe Lys Thr Thr Leu Ser Asp 370 375 380 Tyr Tyr Asn Arg Gln Glu Leu Ala Leu Pro Lys Arg Met Cys Ser Gln 385 390 395 400 Ser Glu Gln Gln Ala Gln Lys Arg Leu Lys Thr Glu Val Phe Asp Asp 405 410 415 Arg Ser Thr Thr His Glu Ser Asp Asn Glu Asn Tyr His Thr Ala Arg 420 425 430 Ser Glu Ser Asn Gln Ser Asn His Ala His Phe Asn Ser Thr Thr Gly 435 440 445 Val Ile Asp Lys Ser Asn Gly Thr Glu Leu Thr Ser Val Met Asp Gly 450 455 460 Asn Tyr Thr Asn Val Thr Asp Val Ile Gly Ser Glu Cys Glu Val Ser 465 470 475 480 Val Asp Ser Ser Val Val Leu Asp Glu Gly Asn Ser Ser Thr Pro Thr 485 490 495 Lys Lys Leu Pro Ser Ile Lys Thr Asp Ser Gln Asn Leu Ser Asp Leu 500 505 510 Asn Leu Asn Asn Phe Ser Asn Pro Glu Phe Gln Asn Ile Thr Ser Pro 515 520 525 Asp Lys Ala Arg Ser Leu Glu Lys Val Val Glu Glu Pro Val Tyr Phe 530 535 540 Asp Ile Asp Gly Glu Lys Phe Gln Glu Lys Ala Val Leu Ser Gln Ala 545 550 555 560 Asp Gly Leu Val Phe Val Asp Asn Glu Cys His Glu His Thr Asn Asp 565 570 575 Cys Cys His Gln Glu Arg Arg Gly Ser Thr Asp Ile Glu Gln Asp Asp 580 585 590 Glu Ala Asp Ser Ile Tyr Ala Glu Ile Glu Pro Val Glu Ile Asn Val 595 600 605 Arg Thr Pro Leu Lys Asn Ser Arg Lys Ser Ile Ser Lys Asp Asn Tyr 610 615 620 Arg Ser Leu Ser Asp Gly Leu Thr His Arg Lys Phe Glu Asp Glu Ile 625 630 635 640 Leu Glu Tyr Asn Leu Ser Thr Lys Asn Phe Lys Glu Ile Ser Lys Asn 645 650 655 Gly Lys Gln Met Ser Ser Ile Ile Ser Lys Arg Lys Ser Glu Ala Gln 660 665 670 Glu Asn Ile Ile Lys Asn Lys Asp Glu Leu Glu Asp Phe Glu Gln Gly 675 680 685 Glu Lys Tyr Leu Thr Leu Thr Val Ser Lys Asn Asp Phe Lys Lys Met 690 695 700 Glu Val Val Gly Gln Phe Asn Leu Gly Phe Ile Ile Val Thr Arg Lys 705 710 715 720 Val Asp Asn Lys Ser Lys Leu Phe Ile Val Asp Gln His Ala Ser Asp 725 730 735 Glu Lys Tyr Asn Phe Glu Thr Leu Gln Ala Val Thr Val Phe Lys Ser 740 745 750 Gln Lys Leu Ile Ile Pro Gln Pro Val Glu Leu Ser Val Ile Asp Glu 755 760 765 Leu Val Val Leu Asp Asn Leu Pro Val Phe Glu Lys Asn Gly Phe Lys 770 775 780 Leu Lys Ile Asp Glu Glu Glu Glu Phe Gly Ser Arg Val Lys Leu Leu 785 790 795 800 Ser Leu Pro Thr Ser Lys Gln Thr Leu Phe Asp Leu Gly Asp Phe Asn 805 810 815 Glu Leu Ile His Leu Ile Lys Glu Asp Gly Gly Leu Arg Arg Asp Asn 820 825 830 Ile Arg Cys Ser Lys Ile Arg Ser Met Phe Ala Met Arg Ala Cys Arg 835 840 845 Ser Ser Ile Met Ile Gly Lys Pro Leu Asn Lys Lys Thr Met Thr Arg 850 855 860 Val Val His Asn Leu Ser Glu Leu Asp Lys Pro Trp Asn Cys Pro His 865 870 875 880 Gly Arg Pro Thr Met Arg His Leu Met Glu Ile Arg Asp Trp Ser Ser 885 890 895 Phe Ser Lys Asp Tyr Glu Ile 900 135 2577 DNA Mus musculus 135 ttccggccaa tgctatcaaa gagatgatag aaaactgttt agatgcaaaa tctacaaata 60 ttcaagtggt tgttaaggaa ggtggcctga agctaattca gatccaagac aatggcactg 120 gaatcaggaa ggaagatctg gatattgtgt gtgagaggtt cactacgagt aaactgcaga 180 cttttgagga tttagccagt atttctacct atggctttcg tggtgagcat ttggcaagca 240 taagtcatgt ggcccatgtc actattacaa ccaaaacagc tgatgggaaa tgtgcgtaca 300 gagcaagtta ctcagatgga aagctgcaag cccctcctaa accctgtgca ggcaaccagg 360 gcaccctgat cacggtggaa gacctttttt acaacataat cacaaggagg aaagctttaa 420 aaaatccaag tgaagagtac ggaaaaattt tggaagttgt tggcaggtat tcaatacaca 480 attcaggcat tagtatctca gttaaaaaac aaggtgagac agtatctgat gtcagaacac 540 tgcccaatgc cacaaccgtg gacaacattc gctccatctt tggaaatgcg gttagtcgag 600 aactgataga agttgggtgt gaggataaaa ccctagcttt caaaatgaat ggctatatat 660 cgaatgcaaa gtattcagtg aagaagtgca ttttcctact cttcatcaac caccgtctgg 720 tagaatcagc tgccttgaga aaagccattg aaactgtata tgcagcatac ttgccaaaaa 780 cacacaccca ttcctgtacc tcagtttgaa atcagccctc agaacgtgac gtcaatgtac 840 accccaccaa gacagaagtt cattttctgc acgaggagag cattctgcag cgtgtgcagc 900 agcacattga gagcaagctg ctgggctcca attcctccag gatgtatttc acccagacct 960 tgcttccagg acttgctggg cctctgggga ggcagctaga cccacgacag gggtggcttc 1020 ctcatccact agtggaagtg gcgacaaggt ctacgcttac cagatgtcgc gtacggactc 1080 ccgggatcag aagcttgacg cctttctgca gcctgtaacc agccttgtgc ccagccagcc 1140 ccaggaccct cgccctgtcc gaggggccag gacagagggc tctcctgaaa gggccacgcg 1200 ggaggatgag gagatgcttg ctctcccagc ccccgctgaa gcagctgctg agagtgagaa 1260 cttggagagg gaatcactaa tggagacttc agacgcagcc cagaaagcgg cacccacttc 1320 cagtccagga agctccagaa agagtcatcg ggaggactct gatgtggaaa tggtggaaaa 1380 tgcttccggg aaggaaatga cagctgcttg ctaccccagg aggaggatca ttaacctcac 1440 cagcgtcttg agtctccagg aagagattag tgagcggtgc catgagactc tccgggagat 1500 actccgtaac cattcctttg tgggctgtgt gaatcctcag tgggccttgg cacagcacca 1560 gaccaagcta tacctcctca acactaccaa gctcagtgaa gagctgttct accagatact 1620 catttatgat tttgccaact ttggtgttct gaggttatcg gaaccagcgc cactcttcga 1680 cctggccatg ctggcttaga cagtcctgaa agtggctgga cagaggacga cggcccgaag 1740 aagggcttgc agagtacatt gtcgagtttc tgaagagaag cgagatgctt gcagactatt 1800 ctctgtgaga tcgatgagaa gggaacctga ttgattactc ttctgatgac agctatgtgc 1860 cacctttgga gggactgcct atcttcattc ttcgactggc cactgaggtg aattgggtga 1920 agaaaaggag tgttttgaaa gtctcagtaa agaatgtgct atgttttact ccattcggaa 1980 gcagtatata ctggaggagt cgaccctctc aggccagcag agtgacatgc ctggctccac 2040 gtcaaagccc tggaagtgga ctgtggagca cattatctat aaagccttcc gctcacacct 2100 cctacctccg aagcatttca cagaagatgg caatgtcctg cagcttgcca acctgccaga 2160 tctatacaaa gtctttgagc ggtgttaaat acaatcatag ccaccgtaga gactgcatga 2220 ccatccaagg cgaagtgtat ggtactaatc tggaagccac agaataggac acttggtttc 2280 agctccaggg ttttcagtgc tcactattct tgttctgtat cccagtattg gtgctgcaac 2340 ttaatgtact tcacctgtgg attggctgca aataaactca cgtgtattgg aaaaaaggaa 2400 ttcctgcagc ccgggggatc cactagttct agagcggccg ccaccggtgg agctccagct 2460 tttgttccct ttagtgaggg ttaatttcga gcttggcgta atcatggtca tagctgtttc 2520 ctgtgtgaaa ttgttatccg ctcacaattc cacacaacat acgagccgga agcataa 2577 136 728 PRT Mus musculus 136 Pro Ala Asn Ala Ile Lys Glu Met Ile Glu Asn Cys Leu Asp Ala Lys 1 5 10 15 Ser Thr Asn Ile Gln Val Val Val Lys Glu Gly Gly Leu Lys Leu Ile 20 25 30 Gln Ile Gln Asp Asn Gly Thr Gly Ile Arg Lys Glu Asp Leu Asp Ile 35 40 45 Val Cys Glu Arg Phe Thr Thr Ser Lys Leu Gln Thr Phe Glu Asp Leu 50 55 60 Ala Ser Ile Ser Thr Tyr Gly Phe Arg Gly Glu His Leu Ala Ser Ile 65 70 75 80 Ser His Val Ala His Val Thr Ile Thr Thr Lys Thr Ala Asp Gly Lys 85 90 95 Cys Ala Tyr Arg Ala Ser Tyr Ser Asp Gly Lys Leu Gln Ala Pro Pro 100 105 110 Lys Pro Cys Ala Gly Asn Gln Gly Thr Leu Ile Thr Val Glu Asp Leu 115 120 125 Phe Tyr Asn Ile Ile Thr Arg Arg Lys Ala Leu Lys Asn Pro Ser Glu 130 135 140 Glu Tyr Gly Lys Ile Leu Glu Val Val Gly Arg Tyr Ser Ile His Asn 145 150 155 160 Ser Gly Ile Ser Ile Ser Val Lys Lys Gln Gly Glu Thr Val Ser Asp 165 170 175 Val Arg Thr Leu Pro Asn Ala Thr Thr Val Asp Asn Ile Arg Ser Ile 180 185 190 Phe Gly Asn Ala Val Ser Arg Glu Leu Ile Glu Val Gly Cys Glu Asp 195 200 205 Lys Thr Leu Ala Phe Lys Met Asn Gly Tyr Ile Ser Asn Ala Lys Tyr 210 215 220 Ser Val Lys Lys Cys Ile Phe Leu Leu Phe Ile Asn His Arg Leu Val 225 230 235 240 Glu Ser Ala Ala Leu Arg Lys Ala Ile Glu Thr Val Tyr Ala Ala Tyr 245 250 255 Leu Pro Lys Thr His Thr His Ser Cys Thr Ser Val Glx Asn Gln Pro 260 265 270 Ser Glu Arg Asp Val Asn Val His Pro Thr Lys Thr Glu Val His Phe 275 280 285 Leu His Glu Glu Ser Ile Leu Gln Arg Val Gln Gln His Ile Glu Ser 290 295 300 Lys Leu Leu Gly Ser Asn Ser Ser Arg Met Val Phe His Pro Asp Leu 305 310 315 320 Ala Ser Arg Thr Cys Trp Ala Ser Gly Glu Ala Ala Arg Pro Thr Thr 325 330 335 Gly Val Ala Ser Ser Ser Thr Ser Gly Ser Gly Asp Lys Val Tyr Ala 340 345 350 Tyr Gln Met Ser Arg Thr Asp Ser Arg Asp Gln Lys Leu Asp Ala Phe 355 360 365 Leu Gln Pro Val Ser Ser Leu Val Pro Ser Gln Pro Gln Asp Pro Arg 370 375 380 Pro Val Arg Gly Ala Arg Thr Glu Gly Ser Pro Glu Arg Ala Thr Arg 385 390 395 400 Glu Asp Glu Glu Met Leu Ala Leu Pro Ala Pro Ala Glu Ala Ala Ala 405 410 415 Glu Ser Glu Asn Leu Glu Arg Glu Ser Leu Met Glu Thr Ser Asp Ala 420 425 430 Ala Gln Lys Ala Ala Pro Thr Ser Ser Pro Gly Ser Ser Arg Lys Ser 435 440 445 His Arg Glu Asp Ser Asp Val Glu Met Val Glu Asn Ala Ser Gly Lys 450 455 460 Glu Met Thr Ala Ala Cys Tyr Pro Arg Arg Arg Ile Ile Asn Leu Thr 465 470 475 480 Ser Val Leu Ser Leu Gln Glu Glu Ile Ser Glu Arg Cys His Glu Thr 485 490 495 Leu Arg Glu Ile Leu Arg Asn His Ser Phe Val Gly Cys Val Asn Pro 500 505 510 Gln Trp Ala Leu Ala Gln His Gln Thr Lys Leu Tyr Leu Leu Asn Thr 515 520 525 Thr Lys Leu Ser Glu Glu Leu Phe Tyr Gln Ile Leu Ile Tyr Asp Phe 530 535 540 Ala Asn Phe Gly Val Leu Arg Leu Ser Glu Pro Ala Pro Leu Phe Asp 545 550 555 560 Leu Ala Met Leu Ala Glx Thr Val Leu Lys Val Ala Gly Gln Arg Thr 565 570 575 Thr Ala Arg Arg Arg Ala Cys Arg Val His Cys Arg Val Ser Glu Glu 580 585 590 Lys Arg Asp Ala Cys Arg Leu Phe Ser Val Arg Ser Met Arg Arg Glu 595 600 605 Pro Asp Glx Leu Leu Phe Glx Glx Gln Leu Cys Ala Thr Phe Gly Gly 610 615 620 Thr Ala Tyr Leu His Ser Ser Thr Gly His Glx Gly Glu Leu Gly Glu 625 630 635 640 Glu Lys Glu Cys Phe Glu Ser Leu Ser Lys Glu Cys Ala Met Phe Tyr 645 650 655 Ser Ile Arg Lys Gln Tyr Ile Leu Glu Glu Ser Thr Leu Ser Gly Gln 660 665 670 Gln Ser Asp Met Pro Gly Ser Thr Ser Lys Pro Trp Lys Trp Thr Val 675 680 685 Glu His Ile Ile Tyr Lys Ala Phe Arg Ser His Leu Leu Pro Pro Lys 690 695 700 His Phe Thr Glu Asp Gly Asn Val Leu Gln Leu Ala Asn Leu Pro Asp 705 710 715 720 Leu Tyr Lys Val Phe Glu Arg Cys 725 137 3065 DNA Mus musculus 137 cggtgaaggt cctgaagaat ttccagattc ctgagtatca ttggaggaga cagataacct 60 gtcgtcaggt aacgatggtg tatatgcaac agaaatgggt gttcctggag acgcgtcttt 120 tcccgagagc ggcaccgcaa ctctcccgcg gtgactgtga ctggaggagt cctgcatcca 180 tggagcaaac cgaaggcgtg agtacagaat gtgctaaggc catcaagcct attgatggga 240 agtcagtcca tcaaatttgt tctgggcagg tgatactcag tttaagcacc gctgtgaagg 300 agttgataga aaatagtgta gatgctggtg ctactactat tgatctaagg cttaaagact 360 atggggtgga cctcattgaa gtttcagaca atggatgtgg ggtagaagaa gaaaactttg 420 aaggtctagc tctgaaacat cacacatcta agattcaaga gtttgccgac ctcacgcagg 480 ttgaaacttt cggctttcgg ggggaagctc tgagctctct gtgtgcacta agtgatgtca 540 ctatatctac ctgccacggg tctgcaagcg ttgggactcg actggtgttt gaccataatg 600 ggaaaatcac ccagaaaact ccctaccccc gacctaaagg aaccacagtc agtgtgcagc 660 acttatttta tacactaccc gtgcgttaca aagagtttca gaggaacatt aaaaaggagt 720 attccaaaat ggtgcaggtc ttacaggcgt actgtatcat ctcagcaggc gtccgtgtaa 780 gctgcactaa tcagctcgga caggggaagc ggcacgctgt ggtgtgcaca agcggcacgt 840 ctggcatgaa ggaaaatatc gggtctgtgt ttggccagaa gcagttgcaa agcctcattc 900 cttttgttca gctgccccct agtgacgctg tgtgtgaaga gtacggcctg agcacttcag 960 gacgccacaa aaccttttct acgttttcgg gcttcatttc acagtgcacg cacggcgccg 1020 ggaggagtgc aacagacagg cagtttttct tcatcaatca gaggccctgt gacccagcaa 1080 aggtctctaa gcttgtcaat gaggtttatc acatgtataa ccggcatcag tacccatttg 1140 tcgtccttaa cgtttccgtt gactcagaat gtgtggatat taatgtaact ccagataaaa 1200 ggcaaattct actacaagaa gagaagctat tgctggccgt tttaaagacc tccttgatag 1260 gaatgtttga cagtgatgca aacaagctta atgtcaacca gcagccactg ctagatgttg 1320 aaggtaactt agtaaagtcg catactgcag aactagaaaa gcctgtgcca ggaaagcaag 1380 ataactctcc ttcactgaag agcacagcag acgagaaaag ggtagcatcc atctccaggc 1440 tgagagaggc cttttctctt catcctacta aagagatcaa gtctaggggt ccagagactg 1500 ctgaactgac acggagtttt ccaagtgaga aaaggggcgt gttatcctct tatccttcag 1560 acgtcatctc ttacagaggc ctccgtggct cgcaggacaa attggtgagt cccacggaca 1620 gccctggtga ctgtatggac agagagaaaa tagaaaaaga ctcagggctc agcagcacct 1680 cagctggctc tgaggaagag ttcagcaccc cagaagtggc cagtagcttt agcagtgact 1740 ataacgtgag ctccctagaa gacagacctt ctcaggaaac cataaactgt ggtgacctgc 1800 tgccgtcctc caggtacagg acagtccttg aagccagaag accatggata tcaatgcaaa 1860 gctctacctc tagctcgtct gtcacccaca aatgccaagc gcttcaagac agaggaagac 1920 cctcaaatgt caacatatct caaagattgc ctggtcctca gagcacctca gcagctgagg 1980 tcgatgtagc cataaaaatg aataagagat cgtgctcctc gagttctcta gctaagcgaa 2040 tgaagcagtt acagcaccta aaggcgcaga acaaacatga actgagttac agaaaattta 2100 gggccaagat ttgccctgga gaaaaccaag cagcagaaga tgaactcaga aaagagatta 2160 gtaaatcgat gtttgcagag atggagatct tgggtcagtt taacctggga tttatagtaa 2220 ccaaactgaa agaggacctc ttcctggtgg accagcatgc tgcggatgag aagtacaact 2280 ttgagatgct gcagcagcac acggtgctcc aggcgcagag gctcatcacg tgggtgcaca 2340 caggcttcag agttcccaga ccccagactc tgaacttaac tgctgtcaat gaagctgtac 2400 tgatagaaaa tctggaaata ttcagaaaga atggctttga ctttgtcatt gatgaggatg 2460 ctccagtcac tgaaagggct aaattgattt ccttaccaac tagtaaaaac tggacctttg 2520 gaccccaaga tatagatgaa ctgatcttta tgttaagtga cagccctggg gtcatgtgcc 2580 ggccctcacg agtcagacag atgtttgctt ccagagcctg tcggaagtca gtgatgattg 2640 gaacggcgct caatgcgagc gagatgaaga agctcatcac ccacatgggt gagatggacc 2700 acccctggaa ctgcccccac ggcaggccaa ccatgaggca cgttgccaat ctggatgtca 2760 tctctcagaa ctgacacacc ccttgtagca tagagtttat tacagattgt tcggttcgca 2820 aagagaaggt tttaagtaat ctgattatcg ttgtacaaaa attagcatgc tgctttaatg 2880 tactggatcc atttaaaagc agtgttaagg caggcatgat ggagtgttcc tctagctcag 2940 ctacttgggt gatccggtgg gagctcatgt gagcccagga ctttgagacc actccgagcc 3000 acattcatga gactcaattc aaggacaaaa aaaaaaagat atttttgaag ccttttaaaa 3060 aaaaa 3065 138 864 PRT Mus musculus 138 Met Glu Gln Thr Glu Gly Val Ser Thr Glu Cys Ala Lys Ala Ile Lys 1 5 10 15 Pro Ile Asp Gly Lys Ser Val His Gln Ile Cys Ser Gly Gln Val Ile 20 25 30 Leu Ser Leu Ser Thr Ala Val Lys Glu Leu Ile Glu Asn Ser Val Asp 35 40 45 Ala Gly Ala Thr Thr Ile Asp Leu Arg Leu Lys Asp Tyr Gly Val Asp 50 55 60 Leu Ile Glu Val Ser Asp Asn Gly Cys Gly Val Glu Glu Glu Asn Phe 65 70 75 80 Glu Gly Leu Ala Leu Lys His His Thr Ser Lys Ile Gln Glu Phe Ala 85 90 95 Asp Leu Thr Gln Val Glu Thr Phe Gly Phe Arg Gly Glu Ala Leu Ser 100 105 110 Ser Leu Cys Ala Leu Ser Asp Val Thr Ile Ser Thr Cys His Gly Ser 115 120 125 Ala Ser Val Gly Thr Arg Leu Val Phe Asp His Asn Gly Lys Ile Thr 130 135 140 Gln Lys Thr Pro Tyr Pro Arg Pro Lys Gly Thr Thr Val Ser Val Gln 145 150 155 160 His Leu Phe Tyr Thr Leu Pro Val Arg Tyr Lys Glu Phe Gln Arg Asn 165 170 175 Ile Lys Lys Glu Tyr Ser Lys Met Val Gln Val Leu Gln Ala Tyr Cys 180 185 190 Ile Ile Ser Ala Gly Val Arg Val Ser Cys Thr Asn Gln Leu Gly Gln 195 200 205 Gly Lys Arg His Ala Val Val Cys Thr Ser Gly Thr Ser Gly Met Lys 210 215 220 Glu Asn Ile Gly Ser Val Phe Gly Gln Lys Gln Leu Gln Ser Leu Ile 225 230 235 240 Pro Phe Val Gln Leu Pro Pro Ser Asp Ala Val Cys Glu Glu Tyr Gly 245 250 255 Leu Ser Thr Ser Gly Arg His Lys Thr Phe Ser Thr Phe Ser Gly Phe 260 265 270 Ile Ser Gln Cys Thr His Gly Ala Gly Arg Ser Ala Thr Asp Arg Gln 275 280 285 Phe Phe Phe Ile Asn Gln Arg Pro Cys Asp Pro Ala Lys Val Ser Lys 290 295 300 Leu Val Asn Glu Val Tyr His Met Tyr Asn Arg His Gln Tyr Pro Phe 305 310 315 320 Val Val Leu Asn Val Ser Val Asp Ser Glu Cys Val Asp Ile Asn Val 325 330 335 Thr Pro Asp Lys Arg Gln Ile Leu Leu Gln Glu Glu Lys Leu Leu Leu 340 345 350 Ala Val Leu Lys Thr Ser Leu Ile Gly Met Phe Asp Ser Asp Ala Asn 355 360 365 Lys Leu Asn Val Asn Gln Gln Pro Leu Leu Asp Val Glu Gly Asn Leu 370 375 380 Val Lys Ser His Thr Ala Glu Leu Glu Lys Pro Val Pro Gly Lys Gln 385 390 395 400 Asp Asn Ser Pro Ser Leu Lys Ser Thr Ala Asp Glu Lys Arg Val Ala 405 410 415 Ser Ile Ser Arg Leu Arg Glu Ala Phe Ser Leu His Pro Thr Lys Glu 420 425 430 Ile Lys Ser Arg Gly Pro Glu Thr Ala Glu Leu Thr Arg Ser Phe Pro 435 440 445 Ser Glu Lys Arg Gly Val Leu Ser Ser Tyr Pro Ser Asp Val Ile Ser 450 455 460 Tyr Arg Gly Leu Arg Gly Ser Gln Asp Lys Leu Val Ser Pro Thr Asp 465 470 475 480 Ser Pro Gly Asp Cys Met Asp Arg Glu Lys Ile Glu Lys Asp Ser Gly 485 490 495 Leu Ser Ser Thr Ser Ala Gly Ser Glu Glu Glu Phe Ser Thr Pro Glu 500 505 510 Val Ala Ser Ser Phe Ser Ser Asp Tyr Asn Val Ser Ser Leu Glu Asp 515 520 525 Arg Pro Ser Gln Glu Thr Ile Asn Cys Gly Asp Leu Leu Pro Ser Ser 530 535 540 Arg Tyr Arg Thr Val Leu Glu Ala Arg Arg Pro Trp Ile Ser Met Gln 545 550 555 560 Ser Ser Thr Ser Ser Ser Ser Val Thr His Lys Cys Gln Ala Leu Gln 565 570 575 Asp Arg Gly Arg Pro Ser Asn Val Asn Ile Ser Gln Arg Leu Pro Gly 580 585 590 Pro Gln Ser Thr Ser Ala Ala Glu Val Asp Val Ala Ile Lys Met Asn 595 600 605 Lys Arg Ser Cys Ser Ser Ser Ser Leu Ala Lys Arg Met Lys Gln Leu 610 615 620 Gln His Leu Lys Ala Gln Asn Lys His Glu Leu Ser Tyr Arg Lys Phe 625 630 635 640 Arg Ala Lys Ile Cys Pro Gly Glu Asn Gln Ala Ala Glu Asp Glu Leu 645 650 655 Arg Lys Glu Ile Ser Lys Ser Met Phe Ala Glu Met Glu Ile Leu Gly 660 665 670 Gln Phe Asn Leu Gly Phe Ile Val Thr Lys Leu Lys Glu Asp Leu Phe 675 680 685 Leu Val Asp Gln His Ala Ala Asp Glu Lys Tyr Asn Phe Glu Met Leu 690 695 700 Gln Gln His Thr Val Leu Gln Ala Gln Arg Leu Ile Thr Trp Val His 705 710 715 720 Thr Gly Phe Arg Val Pro Arg Pro Gln Thr Leu Asn Leu Thr Ala Val 725 730 735 Asn Glu Ala Val Leu Ile Glu Asn Leu Glu Ile Phe Arg Lys Asn Gly 740 745 750 Phe Asp Phe Val Ile Asp Glu Asp Ala Pro Val Thr Glu Arg Ala Lys 755 760 765 Leu Ile Ser Leu Pro Thr Ser Lys Asn Trp Thr Phe Gly Pro Gln Asp 770 775 780 Ile Asp Glu Leu Ile Phe Met Leu Ser Asp Ser Pro Gly Val Met Cys 785 790 795 800 Arg Pro Ser Arg Val Arg Gln Met Phe Ala Ser Arg Ala Cys Arg Lys 805 810 815 Ser Val Met Ile Gly Thr Ala Leu Asn Ala Ser Glu Met Lys Lys Leu 820 825 830 Ile Thr His Met Gly Glu Met Asp His Pro Trp Asn Cys Pro His Gly 835 840 845 Arg Pro Thr Met Arg His Val Ala Asn Leu Asp Val Ile Ser Gln Asn 850 855 860 139 29 DNA Artificial Artificial sequence is synthesized 139 cttgattcta gagcytcncc nckraancc 29 140 29 DNA Artificial Artificial sequence is synthesized 140 aggtcggagc tcaargaryt ngtnganaa 29 141 15 DNA Homo sapiens 141 acttgtggat tttgc 15 142 15 DNA Homo sapiens 142 acttgtgaat tttgc 15 143 22 DNA Mus musculus 143 ttcggtgaca gatttgtaaa tg 22 144 16 DNA Mus musculus 144 tttacggagc cctggc 16 145 22 DNA Mus musculus 145 tcaccataaa aatagtttcc cg 22 146 22 DNA Mus musculus 146 tcctggatca tattttctga gc 22 147 22 DNA Mus musculus 147 tttcaggtat gtcctgttac cc 22 148 22 DNA Mus musculus 148 tgaggcagct tttaagaaac tc 22 149 2385 DNA Homo sapiens 149 gcacgagctc gtgccgttta gatgcaaaat ccacaagtat tcaagtgatt gttaaagagg 60 gaggcctgaa gttgattcag atccaagaca atggcaccgg gatcaggaaa gaagatctgg 120 atattgtatg tgaaaggttc actactagta aactgcagtc ctttgaggat ttagccagta 180 tttctaccta tggctttcga ggtgaggctt tggccagcat aagccatgtg gctcatgtta 240 ctattacaac gaaaacagct gatggaaagt gtgcatacag agcaagttac tcagatggaa 300 aactgaaagc ccctcctaaa ccatgtgctg gcaatcaagg gacccagatc acggtggagg 360 acctttttta caacatagcc acgaggagaa aagctttaaa aaatccaagt gaagaatatg 420 ggaaaatttt ggaagttgtt ggcaggtatt cagtacacaa tgcaggcatt agtttctcag 480 ttaaaaaaca aggagagaca gtagctgatg ttaggacact acccaatgcc tcaaccgtgg 540 acaatattcg ctccatcttt ggaaatgctg ttagtcgaga actgatagaa attggatgtg 600 aggataaaac cctagccttc aaaatgaatg gttacatatc caatgcaaac tactcagtga 660 agaagtgcat cttcttactc ttcatcaacc atcgtctggt agaatcaact tccttgagaa 720 aagccataga aacagtgtat gcagcctatt tgcccaaaaa cacacaccca ttcctgtacc 780 tcagtttaga aatcagtccc cagaatgtgg atgttaatgt gcaccccaca aagcatgaag 840 ttcacttcct gcacgaggag agcatcctgg agcgggtgca gcagcacatc gagagcaagc 900 tcctgggctc caattcctcc aggatgtact tcacccagac tttgctacca ggacttgctg 960 gcccctctgg ggagatggtt aaatccacaa caagtctgac ctcgtcttct acttctggaa 1020 gtagtgataa ggtctatgcc caccagatgg ttcgtacaga ttcccgggaa cagaagcttg 1080 atgcatttct gcagcctctg agcaaacccc tgtccagtca gccccaggcc attgtcacag 1140 aggataagac agatatttct agtggcaggg ctaggcagca agatgaggag atgcttgaac 1200 tcccagcccc tgctgaagtg gctgccaaaa atcagagctt ggcgggggat acaacaaagg 1260 ggacttcaga aatgtcagag aagagaggac ctacttccag caaccccaga aagagacatc 1320 gggaagattc ttgtggaaat ggtggaagat gatcccgaaa ggaaatgact gcagctgtcc 1380 ccccggagaa ggatcattaa cctcactagt gttttgagtc tccaggaaga aattaatgag 1440 cagggacatg aggttctccg ggagatgttg cataaccact ccttcgtggg ctgtgtgaat 1500 cctcagtggg ccttggcaca gcatcaaacc aagttatacc ttctcaacac caccaagctt 1560 agtgaagaac tgttctacca gatactcatt tatgattttg ccaattttgg tgttctcagg 1620 ttatcggagc cagcaccgct ctttgacctt gccatgcttg ccttagatag tccagagagt 1680 ggctggacag aggaagatgg tcccaaagaa ggacttgctg aatacattgt tgagtttctg 1740 aagaagaagg ctgagatgct tgcagactat ttctctttgg aaattgatga ggaagggaac 1800 ctgattggat taccccttct gattgacaac tatgtgcccc ctttggaggg actgcctatc 1860 ttcattcttc gactagccac tgaggtgaat tgggacgaag aaaaggaatg ttttgaaagc 1920 ctcagtaaag aatgcgctat gttctattcc atccggaagc agtacatatc tgaggagtcg 1980 accctctcag gccagcagag tgaagtgcct ggctccattc caaactcctg gaagtggact 2040 gtggaacaca ttgtctataa agccttgcgc tcacacattc tgcctcctaa catttcacag 2100 aagatggaaa tatcctgcag cttgctaacc tgcctgatct atacaaagtc tttgagaggt 2160 gtaaatatgg ttatttatgc actgtgggat gtgttcttct ttctctgtat tccgagacaa 2220 agtgttgtat caaagtgtga tatacaaagt gtgccaacat aagtgttggt agcacttaag 2280 acttatactt gccttctgat agtattcctt tatacacagt ggattgatta taaataaata 2340 gatgtgtctt aacataaaaa aaaaaaaaaa agggggggcc cggta 2385 150 821 DNA Homo sapiens 150 cccccctcga ggtcgacggt atcgataagc ttgatatcga attcctcgag gccacgaagg 60 ccccatggag cgagctgaga gctcgagtac agaacctgct aaggccatca aacctattga 120 tcggaagtca gtccatcaga tttgctctgg gccggtggta ccgagtctaa gcactgcggt 180 gaaggagtta gtagaaaaca gtctggatgc tggtgccact aatattgatc taaagcttaa 240 ggactatgga gtggatctca ttgaagtttc aggcaatgga tgtggggtag aagaagaaaa 300 cttcgaaggc ttaactctga aacatcacac atctaagatt caagagtttg ccgacctacc 360 tcaggttgaa acttttggct ttcgggggga agctctgagc tcactttgtg cactgagtga 420 tgtcaccatt tctacctgcc atgtatcggc gaaggttggg actcgactgg tgtttgatca 480 ctatgggaaa atcatccaga aaacccccta cccccacccc agagggatga cagtcagtgt 540 gaagcagtta ttttctacgc tacctgtgca ccataaagaa tttcaaagga atattaagaa 600 gaaacgtgcc tgcttccctt cgccttctgc cgtgattgtc agtttcctga ggcctcccca 660 gccatgcttc ctgtacagcc tgcagaacta tggattcttg ctctgtcacc caggctggag 720 tgcaatgcct cgatgtctgc tgactgcaac ctccgccctc ccaggtcaag tagttctcct 780 gcctcggcct cctgagtagc tgggattaca ggcatgagca c 821 151 651 DNA Homo sapiens 151 aaccgaggca aaaaaaaaat caattgaagg agttgccggg aaaaaaccca atgtgggaaa 60 ttaaaaggcc aaattcccgg caaagaaaac ctcaatttta aacacccctc cccggggagg 120 ggaaaaccct aaactcccaa gacctcttta ttgaacttgt cttgaaagaa gcctggaaaa 180 ttaagaaaga tggccttgat ttgttatcgt gaaatgctca attcactgaa aggctaaact 240 gattgccttg ccaactagtc aaaactgaac cttcgggacc ccaggacgtc gatgaactga 300 tcttcatgct gagcgacagc cctggggtca tgtgccgacc ttcccgagtc aagcagatgt 360 ttgcctccag agcctgccgg aagtcggtga tgattgggac tgctctcaac acaagcgaat 420 gaagaaactg atcacccaca tgggggagat gggccacccc tggaactgtc cccatggaag 480 gccaccatga gacacatcgc caacctgggt gtcatttctc agaactgacc gtagtcactg 540 tatggaataa ttggttttat cgcagatttt tatgttttga aagacagagt cttcactaac 600 cttttttgtt ttaaaatgaa acctgcggcc ctcgtggcct cgaggaattc c 651 152 177 DNA Homo sapiens 152 ctgtttagat gcaaaatcca caagtattca agtgattgtt aagagggagg cctgaagttg 60 attcagatcc aagacaatgg caccgggatc aggaaagaag atctggatat tgtatgtgaa 120 aggttcacta ctagtaaact gcagtccttt gaggatttag ccagtatttc tacctat 177 153 178 DNA Homo sapiens 153 cagtctggat gctggtgcca ctaatattga tctaaagctt aaggactatg gagtggatct 60 tattgaagtt tcagacaatg gatgtggggt agaagaagaa aacttcgaag gcttaactct 120 gaaacatcac acatctaaga ttcaagagtt tgccgaccta actcaggttg aaactttt 178

Claims

We claim:

1. A method of determining whether a person is susceptible to cancer comprising:

collecting a sample from the person,

contacting the sample with antibodies that bind specifically to a mutL homolog protein, and

detecting binding or lack of binding antibodies to mutL homolog protein.

2. The method of claim 1 comprising specific binding of antibodies to hMLH1 protein as shown in SEQ ID NO: 5.

3. The method of claim 1, wherein the antibodies are polyclonal.

4. The method of claim 1, wherein the antibodies are monoclonal.

5. The method of claim 1, wherein the antibodies are conjugated to a fluorescent compound.

6. A method of determining whether tumor tissue has a deficient amount of a mutL homolog protein comprising

obtaining a cross-section of a tumor specimen,

contacting the cross-section with a purified antibody that binds specifically to a mutL homolog protein, and

determining the presence or absence of antibody bound to a mutL homolog protein in the cross-section.

7. The method of claim 6, wherein the antibody is a monoclonal antibody.

8. The method of claim 6, wherein the antibody is a polyclonal antibody.

9. The method of claim 6, wherein the antibody is conjugated to a fluorescent compound.

10. The method of claim 6 further comprising

prescribing a therapy regimen based at least partially on results of the determining step.

11. The method of claim 6 further comprising

eluting unbound antibody from the cross-section.

12. The method of claim 6, wherein the antibody binds specifically to hMLH1 protein.

13. A method of manufacturing antibodies that bind specifically to a mutL homolog protein comprising

synthesizing or isolating at least a portion of a mutL homolog protein,

overexpressing the protein in bacteria,

purifying the protein,

injecting the protein into a mouse,

generating a hybridoma by fusing a lymphocyte from the mouse with a myeloma cell, and

isolating monoclonal antibodies produced by the hybridoma, wherein the antibodies bind specifically to a mutL homolog protein.

14. The method of claim 13, wherein the monoclonal antibodies bind specifically to hMLH1 protein as shown in SEQ ID NO: 5.