WO2001005935A3 - Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays - Google Patents

Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays Download PDF

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Publication number
WO2001005935A3
WO2001005935A3 PCT/US2000/019202 US0019202W WO0105935A3 WO 2001005935 A3 WO2001005935 A3 WO 2001005935A3 US 0019202 W US0019202 W US 0019202W WO 0105935 A3 WO0105935 A3 WO 0105935A3
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WO
WIPO (PCT)
Prior art keywords
probes
polynucleotide
target polynucleotide
methods
specificity
Prior art date
Application number
PCT/US2000/019202
Other languages
French (fr)
Other versions
WO2001005935A2 (en
Inventor
Stephen H Friend
Roland Stoughton
Peter S Linsley
Julja Burchard
Original Assignee
Rosetta Inpharmatics Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Rosetta Inpharmatics Inc filed Critical Rosetta Inpharmatics Inc
Priority to EP00948665A priority Critical patent/EP1200820A4/en
Priority to JP2001511150A priority patent/JP2003505022A/en
Priority to AU62135/00A priority patent/AU6213500A/en
Priority to CA002378933A priority patent/CA2378933A1/en
Publication of WO2001005935A2 publication Critical patent/WO2001005935A2/en
Publication of WO2001005935A3 publication Critical patent/WO2001005935A3/en

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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation

Abstract

Methods and compositions are provided that are useful for detecting and reporting a plurality of different target polynucleotide sequences in a sample, such as polynucleotides corresponding to a plurality of different genes expressed by a cell or cells. In particular, the invention provides methods for screening a plurality of candidate polynucleotide probes to evaluate both the sensitivity and the specificity with which each candidate probe hybridizes to a target polynucleotide sequence. Candidate polynucleotide probes can then be ranked according to both their sensitivity and specificity, and probes that have optimal sensitivity and specificity for a target polynucleotide sequence can be selected. In one embodiment, polynucleotide probes can be selected according to the methods described herein to prepare 'screening chips' wherein a large number of target polynucleotide sequences are detected using a single microarray have a few (e.g., 1-5) probes for each target polynucleotide sequence. In a particularly preferred embodiment, the invention provides a screening chip that can detect genetic transcripts from the entire genome of an organism. In an alternative embodiment, polynucleotide probes can be selected according to the methods described herein to prepare 'signature chips' to more accurately detect certain selected 'signature genes' using several polynucleotide probes (e.g., 10-20) for each signature gene. The invention additionally provides microarrays containing polynucleotide probes for a large number of genes expressed by a cell or organism. Further, methods for detecting a plurality of polynucleotide molecules, including a large number of genes expressed by a cell or organism, are also provided.
PCT/US2000/019202 1999-07-16 2000-07-14 Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays WO2001005935A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
EP00948665A EP1200820A4 (en) 1999-07-16 2000-07-14 Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays
JP2001511150A JP2003505022A (en) 1999-07-16 2000-07-14 Iterative probe design and detailed expression profiling using flexible in-situ synthetic arrays
AU62135/00A AU6213500A (en) 1999-07-16 2000-07-14 Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays
CA002378933A CA2378933A1 (en) 1999-07-16 2000-07-14 Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US14438299P 1999-07-16 1999-07-16
US60/144,382 1999-07-16
US36475199A 1999-07-30 1999-07-30
US09/364,751 1999-07-30
US09/561,487 US7013221B1 (en) 1999-07-16 2000-04-28 Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays
US09/561,487 2000-04-28

Publications (2)

Publication Number Publication Date
WO2001005935A2 WO2001005935A2 (en) 2001-01-25
WO2001005935A3 true WO2001005935A3 (en) 2001-07-19

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/019202 WO2001005935A2 (en) 1999-07-16 2000-07-14 Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays

Country Status (6)

Country Link
US (2) US7013221B1 (en)
EP (1) EP1200820A4 (en)
JP (1) JP2003505022A (en)
AU (1) AU6213500A (en)
CA (1) CA2378933A1 (en)
WO (1) WO2001005935A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
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Also Published As

Publication number Publication date
US20060141501A1 (en) 2006-06-29
EP1200820A4 (en) 2006-08-23
EP1200820A2 (en) 2002-05-02
CA2378933A1 (en) 2001-01-25
WO2001005935A2 (en) 2001-01-25
AU6213500A (en) 2001-02-05
US7013221B1 (en) 2006-03-14
JP2003505022A (en) 2003-02-12

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