WO2002018646A3 - Gene discovery using microarrays - Google Patents

Gene discovery using microarrays Download PDF

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Publication number
WO2002018646A3
WO2002018646A3 PCT/US2001/026274 US0126274W WO0218646A3 WO 2002018646 A3 WO2002018646 A3 WO 2002018646A3 US 0126274 W US0126274 W US 0126274W WO 0218646 A3 WO0218646 A3 WO 0218646A3
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WO
WIPO (PCT)
Prior art keywords
microarrays
genes
gene discovery
genome
methods
Prior art date
Application number
PCT/US2001/026274
Other languages
French (fr)
Other versions
WO2002018646A9 (en
WO2002018646A2 (en
Inventor
Daniel D Shoemaker
Stewart Scherer
Steven J Altschuler
Lani F Wu
Christopher D Armour
Original Assignee
Rosetta Inpharmatics Inc
Daniel D Shoemaker
Stewart Scherer
Steven J Altschuler
Lani F Wu
Christopher D Armour
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, Daniel D Shoemaker, Stewart Scherer, Steven J Altschuler, Lani F Wu, Christopher D Armour filed Critical Rosetta Inpharmatics Inc
Priority to EP01966103A priority Critical patent/EP1356101A2/en
Priority to CA002420657A priority patent/CA2420657A1/en
Priority to AU2001286643A priority patent/AU2001286643A1/en
Publication of WO2002018646A2 publication Critical patent/WO2002018646A2/en
Publication of WO2002018646A9 publication Critical patent/WO2002018646A9/en
Publication of WO2002018646A3 publication Critical patent/WO2002018646A3/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • 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
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/0061—The surface being organic
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00612—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports the surface being inorganic
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00605—Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00623—Immobilisation or binding
    • B01J2219/00626—Covalent
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00659—Two-dimensional arrays
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/0068—Means for controlling the apparatus of the process
    • B01J2219/00686—Automatic
    • B01J2219/00689—Automatic using computers
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/0068—Means for controlling the apparatus of the process
    • B01J2219/00695—Synthesis control routines, e.g. using computer programs
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/0068—Means for controlling the apparatus of the process
    • B01J2219/00702—Processes involving means for analysing and characterising the products
    • B01J2219/00707—Processes involving means for analysing and characterising the products separated from the reactor apparatus
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • B01J2219/00722—Nucleotides
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • B01J2219/0074—Biological products
    • B01J2219/00743—Cells
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

The invention relates to methods and systems (e.g., computer systems and computer program products) for identifying and characterizing genes using microarrays. In particular, the invention provides for improved, robust methods for detecting genes through the use of microarrays to analyze the expression state of genome. Genes which are expressed can be mapped to their respective positions in the genome, and the structure of such genes can be determined.
PCT/US2001/026274 2000-08-25 2001-08-24 Gene discovery using microarrays WO2002018646A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP01966103A EP1356101A2 (en) 2000-08-25 2001-08-24 Gene discovery using microarrays
CA002420657A CA2420657A1 (en) 2000-08-25 2001-08-24 Gene discovery using microarrays
AU2001286643A AU2001286643A1 (en) 2000-08-25 2001-08-24 Gene discovery using microarrays

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US22796600P 2000-08-25 2000-08-25
US22790200P 2000-08-25 2000-08-25
US60/227,902 2000-08-25
US60/227,966 2000-08-25
US09/781,814 2001-02-12
US09/781,814 US6713257B2 (en) 2000-08-25 2001-02-12 Gene discovery using microarrays

Publications (3)

Publication Number Publication Date
WO2002018646A2 WO2002018646A2 (en) 2002-03-07
WO2002018646A9 WO2002018646A9 (en) 2003-04-03
WO2002018646A3 true WO2002018646A3 (en) 2003-08-28

Family

ID=27397783

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/026274 WO2002018646A2 (en) 2000-08-25 2001-08-24 Gene discovery using microarrays

Country Status (5)

Country Link
US (2) US6713257B2 (en)
EP (1) EP1356101A2 (en)
AU (1) AU2001286643A1 (en)
CA (1) CA2420657A1 (en)
WO (1) WO2002018646A2 (en)

Families Citing this family (80)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20040180364A1 (en) * 2003-01-08 2004-09-16 Affymetrix, Inc. Methods for analyzing global regulation of coding and non-coding RNA transcripts involving low molecular weight RNAs
US5854033A (en) * 1995-11-21 1998-12-29 Yale University Rolling circle replication reporter systems
US6881571B1 (en) * 1998-03-11 2005-04-19 Exonhit Therapeutics S.A. Qualitative differential screening
CA2255599C (en) 1996-04-25 2006-09-05 Bioarray Solutions, Llc Light-controlled electrokinetic assembly of particles near surfaces
FR2798673B1 (en) * 1999-09-16 2004-05-28 Exonhit Therapeutics Sa METHODS AND COMPOSITIONS FOR DETECTION OF PATHOLOGICAL EVENTS
WO2001031333A1 (en) * 1999-10-26 2001-05-03 Genometrix Genomics Incorporated Process for requesting biological experiments and for the delivery of experimental information
US7361488B2 (en) * 2000-02-07 2008-04-22 Illumina, Inc. Nucleic acid detection methods using universal priming
US7892854B2 (en) 2000-06-21 2011-02-22 Bioarray Solutions, Ltd. Multianalyte molecular analysis using application-specific random particle arrays
US9709559B2 (en) 2000-06-21 2017-07-18 Bioarray Solutions, Ltd. Multianalyte molecular analysis using application-specific random particle arrays
US6323009B1 (en) * 2000-06-28 2001-11-27 Molecular Staging, Inc. Multiply-primed amplification of nucleic acid sequences
US7807447B1 (en) * 2000-08-25 2010-10-05 Merck Sharp & Dohme Corp. Compositions and methods for exon profiling
US6713257B2 (en) * 2000-08-25 2004-03-30 Rosetta Inpharmatics Llc Gene discovery using microarrays
WO2002022850A2 (en) * 2000-09-13 2002-03-21 Paradigm Genetics, Inc. Genome arrays utilizing randomly selected nucleic acid fragments
US20020183936A1 (en) * 2001-01-24 2002-12-05 Affymetrix, Inc. Method, system, and computer software for providing a genomic web portal
US20020106644A1 (en) * 2001-02-05 2002-08-08 Carsten Rosenow Methods for transcription detection and analysis
AU2002307486A1 (en) * 2001-04-26 2002-11-11 Rosetta Inpharmatics, Inc. Methods and compositions for utilizing changes of hybridization signals during approach to equilibrium
US6777187B2 (en) * 2001-05-02 2004-08-17 Rubicon Genomics, Inc. Genome walking by selective amplification of nick-translate DNA library and amplification from complex mixtures of templates
US20030104426A1 (en) * 2001-06-18 2003-06-05 Linsley Peter S. Signature genes in chronic myelogenous leukemia
US7171311B2 (en) 2001-06-18 2007-01-30 Rosetta Inpharmatics Llc Methods of assigning treatment to breast cancer patients
US7514209B2 (en) 2001-06-18 2009-04-07 Rosetta Inpharmatics Llc Diagnosis and prognosis of breast cancer patients
US7262063B2 (en) 2001-06-21 2007-08-28 Bio Array Solutions, Ltd. Directed assembly of functional heterostructures
US20040091857A1 (en) * 2001-07-20 2004-05-13 Nallur Girish N. Gene expression profiling
AU2002355155A1 (en) * 2001-07-24 2003-02-17 Affinium Pharmaceuticals Inc. Methods for gene disruption and uses thereof
US7340349B2 (en) * 2001-07-25 2008-03-04 Jonathan Bingham Method and system for identifying splice variants of a gene
US7833779B2 (en) * 2001-07-25 2010-11-16 Jivan Biologies Inc. Methods and systems for polynucleotide detection
US20050032060A1 (en) * 2001-08-31 2005-02-10 Shishir Shah Arrays comprising pre-labeled biological molecules and methods for making and using these arrays
KR20040068122A (en) 2001-10-15 2004-07-30 바이오어레이 솔루션스 리미티드 Multiplexed analysis of polymorphic loci by concurrent interrogation and enzyme-mediated detection
EP1453973A4 (en) * 2001-12-11 2005-04-13 Affymetrix Inc Methods for determining transcriptional activity
US20030124542A1 (en) * 2001-12-28 2003-07-03 Spectral Genomics, Inc. Methods for mapping the chromosomal loci of genes expressed by a cell
US7418351B2 (en) * 2002-01-31 2008-08-26 Rosetta Inpharmatics Llc Methods for analysis of measurement errors in measured signals
US7553619B2 (en) * 2002-02-08 2009-06-30 Qiagen Gmbh Detection method using dissociated rolling circle amplification
WO2004003233A1 (en) * 2002-06-28 2004-01-08 Rosetta Inpharmatics Llc Methods to assess quality of microarrays
US7364846B2 (en) * 2002-10-11 2008-04-29 Molecular Devices Corporation Gene expression profiling from FFPE samples
US20040235008A1 (en) * 2002-11-14 2004-11-25 Affymetrix, Inc. Methods and compositions for profiling transcriptionally active sites of the genome
US7526114B2 (en) 2002-11-15 2009-04-28 Bioarray Solutions Ltd. Analysis, secure access to, and transmission of array images
US20040121338A1 (en) * 2002-12-19 2004-06-24 Alsmadi Osama A. Real-time detection of rolling circle amplification products
US9487823B2 (en) * 2002-12-20 2016-11-08 Qiagen Gmbh Nucleic acid amplification
US7996155B2 (en) 2003-01-22 2011-08-09 Microsoft Corporation ANOVA method for data analysis
DK2374900T3 (en) * 2003-03-07 2016-10-17 Rubicon Genomics Inc Polynucleotides for amplification and analysis of the total genomic and total transcription libraries generated by a DNA polymerization
US8206913B1 (en) 2003-03-07 2012-06-26 Rubicon Genomics, Inc. Amplification and analysis of whole genome and whole transcriptome libraries generated by a DNA polymerization process
US20050017981A1 (en) * 2003-03-17 2005-01-27 Jonathan Bingham Methods of representing gene product sequences and expression
US8043834B2 (en) * 2003-03-31 2011-10-25 Qiagen Gmbh Universal reagents for rolling circle amplification and methods of use
US20040248103A1 (en) * 2003-06-04 2004-12-09 Feaver William John Proximity-mediated rolling circle amplification
US8133670B2 (en) 2003-06-13 2012-03-13 Cold Spring Harbor Laboratory Method for making populations of defined nucleic acid molecules
CN100494399C (en) 2003-06-30 2009-06-03 清华大学 Genotype typing method based on DNA chip and use thereof
US20050032102A1 (en) * 2003-07-22 2005-02-10 Affymetrix, Inc. Mapping genomic rearrangements
US7964344B2 (en) * 2003-09-17 2011-06-21 Canon Kabushiki Kaisha Stable hybrid
WO2005029705A2 (en) 2003-09-18 2005-03-31 Bioarray Solutions, Ltd. Number coding for identification of subtypes of coded types of solid phase carriers
CA2539824C (en) 2003-09-22 2015-02-03 Xinwen Wang Surface immobilized polyelectrolyte with multiple functional groups capable of covalently bonding to biomolecules
US20050142589A1 (en) * 2003-10-22 2005-06-30 Broide Ron S. Oligonucleotide probe sets and uses thereof
AU2004286252A1 (en) * 2003-10-28 2005-05-12 Bioarray Solutions Ltd. Optimization of gene expression analysis using immobilized capture probes
WO2005045060A2 (en) 2003-10-29 2005-05-19 Bioarray Solutions, Ltd. Multiplexed nucleic acid analysis by fragmentation of double-stranded dna
CA2558808A1 (en) 2004-03-05 2005-09-22 Rosetta Inpharmatics Llc Classification of breast cancer patients using a combination of clinical criteria and informative genesets
US7881872B2 (en) * 2004-03-12 2011-02-01 Microsoft Corporation Methods of analyzing multi-channel profiles
US7848889B2 (en) 2004-08-02 2010-12-07 Bioarray Solutions, Ltd. Automated analysis of multiplexed probe-target interaction patterns: pattern matching and allele identification
DE102005011349A1 (en) * 2005-03-11 2006-09-21 Eppendorf Ag Microarray with temperature-specific controls
EP1863908B1 (en) * 2005-04-01 2010-11-17 Qiagen GmbH Reverse transcription and amplification of rna with simultaneous degradation of dna
US8486629B2 (en) 2005-06-01 2013-07-16 Bioarray Solutions, Ltd. Creation of functionalized microparticle libraries by oligonucleotide ligation or elongation
US20070048764A1 (en) * 2005-08-23 2007-03-01 Jonathan Bingham Indicator polynucleotide controls
EP1762627A1 (en) 2005-09-09 2007-03-14 Qiagen GmbH Method for the activation of a nucleic acid for performing a polymerase reaction
CN101374964B (en) * 2005-12-09 2013-07-17 贝勒研究院 Module-level analysis of peripheral blood leukocyte transcriptional profiles
US20070255054A1 (en) * 2005-12-30 2007-11-01 Affymetrix, Inc. Oligonucleotide synthesis with intermittent and post synthetic oxidation
DE102006020885A1 (en) * 2006-05-05 2007-11-08 Qiagen Gmbh Inserting a tag sequence into a nucleic acid comprises using an anchor oligonucleotide comprising a hybridizing anchor sequence and a nonhybridizing tag-template sequence
US20070292842A1 (en) * 2006-06-14 2007-12-20 Fulmer-Smentek Stephanie B Detection of viral or viral vector integration sites in genomic DNA
US7437249B2 (en) * 2006-06-30 2008-10-14 Agilent Technologies, Inc. Methods and systems for detrending signal intensity data from chemical arrays
EP2084296B1 (en) * 2006-09-29 2015-08-05 Agendia N.V. High-throughput diagnostic testing using arrays
US8105777B1 (en) 2008-02-13 2012-01-31 Nederlands Kanker Instituut Methods for diagnosis and/or prognosis of colon cancer
US20090270270A1 (en) * 2008-04-28 2009-10-29 Centre Rene Huguenin Method for detecting intragenic large rearrangements
US20110129817A1 (en) * 2009-11-30 2011-06-02 Baylor Research Institute Blood transcriptional signature of active versus latent mycobacterium tuberculosis infection
JP2011526152A (en) * 2008-06-25 2011-10-06 ベイラー リサーチ インスティテュート Blood transcription signature of Mycobacterium tuberculosis infection
US8580514B2 (en) * 2009-11-06 2013-11-12 National Taiwan University Microchip for identifying Phellinus species and the method thereof
US20190300945A1 (en) 2010-04-05 2019-10-03 Prognosys Biosciences, Inc. Spatially Encoded Biological Assays
DK2556171T3 (en) 2010-04-05 2015-12-14 Prognosys Biosciences Inc Spatially CODED BIOLOGICAL ASSAYS
US10787701B2 (en) 2010-04-05 2020-09-29 Prognosys Biosciences, Inc. Spatially encoded biological assays
US9268903B2 (en) 2010-07-06 2016-02-23 Life Technologies Corporation Systems and methods for sequence data alignment quality assessment
GB201106254D0 (en) 2011-04-13 2011-05-25 Frisen Jonas Method and product
CN111662960B (en) 2013-06-25 2024-04-12 普罗格诺西斯生物科学公司 Spatially encoded bioanalytical analysis using microfluidic devices
US20170247751A1 (en) * 2014-07-25 2017-08-31 Microscale Devices Llc Apparatus and methods for detecting multiple labelled biopolymers
DK3901281T3 (en) 2015-04-10 2023-01-23 Spatial Transcriptomics Ab SPATIALLY SEPARATE, MULTIPLEX NUCLEIC ACID ANALYSIS OF BIOLOGICAL SAMPLES
CN105297145B (en) * 2015-11-06 2019-03-08 艾吉泰康生物科技(北京)有限公司 A kind of method preparing gene DNA Probe Library and kit

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999023256A1 (en) * 1997-10-30 1999-05-14 Cold Spring Harbor Laboratory Probe arrays and methods of using probe arrays for distinguishing dna
WO2000053811A1 (en) * 1999-03-11 2000-09-14 Orion Genomics, Llc Genome chips and optical transcript mapping

Family Cites Families (77)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4946778A (en) * 1987-09-21 1990-08-07 Genex Corporation Single polypeptide chain binding molecules
US5525464A (en) 1987-04-01 1996-06-11 Hyseq, Inc. Method of sequencing by hybridization of oligonucleotide probes
US5744101A (en) 1989-06-07 1998-04-28 Affymax Technologies N.V. Photolabile nucleoside protecting groups
US6040138A (en) 1995-09-15 2000-03-21 Affymetrix, Inc. Expression monitoring by hybridization to high density oligonucleotide arrays
US5143854A (en) 1989-06-07 1992-09-01 Affymax Technologies N.V. Large scale photolithographic solid phase synthesis of polypeptides and receptor binding screening thereof
US5545522A (en) 1989-09-22 1996-08-13 Van Gelder; Russell N. Process for amplifying a target polynucleotide sequence using a single primer-promoter complex
US5217889A (en) * 1990-10-19 1993-06-08 Roninson Igor B Methods and applications for efficient genetic suppressor elements
RU1794088C (en) 1991-03-18 1993-02-07 Институт Молекулярной Биологии Ан@ Ссср Method of dna nucleotide sequence determination and a device for its realization
US5973910A (en) * 1991-12-31 1999-10-26 Intel Corporation Decoupling capacitor in an integrated circuit
US5262311A (en) * 1992-03-11 1993-11-16 Dana-Farber Cancer Institute, Inc. Methods to clone polyA mRNA
US5981176A (en) 1992-06-17 1999-11-09 City Of Hope Method of detecting and discriminating between nucleic acid sequences
US5503980A (en) 1992-11-06 1996-04-02 Trustees Of Boston University Positional sequencing by hybridization
US5556749A (en) 1992-11-12 1996-09-17 Hitachi Chemical Research Center, Inc. Oligoprobe designstation: a computerized method for designing optimal DNA probes
US5837832A (en) 1993-06-25 1998-11-17 Affymetrix, Inc. Arrays of nucleic acid probes on biological chips
US6027880A (en) 1995-08-02 2000-02-22 Affymetrix, Inc. Arrays of nucleic acid probes and methods of using the same for detecting cystic fibrosis
US6007987A (en) 1993-08-23 1999-12-28 The Trustees Of Boston University Positional sequencing by hybridization
US6045996A (en) 1993-10-26 2000-04-04 Affymetrix, Inc. Hybridization assays on oligonucleotide arrays
JP3488465B2 (en) 1993-10-28 2004-01-19 ヒューストン・アドバンスド・リサーチ・センター Microfabricated flow-through porosity device for separately detecting binding reactions
US5578832A (en) 1994-09-02 1996-11-26 Affymetrix, Inc. Method and apparatus for imaging a sample on a device
US5539083A (en) 1994-02-23 1996-07-23 Isis Pharmaceuticals, Inc. Peptide nucleic acid combinatorial libraries and improved methods of synthesis
US5571639A (en) * 1994-05-24 1996-11-05 Affymax Technologies N.V. Computer-aided engineering system for design of sequence arrays and lithographic masks
US6013436A (en) * 1994-07-08 2000-01-11 Visible Genetics, Inc. Compositions and methods for diagnosis of mutation in the von Hippel-Lindau tumor suppressor gene
US5856103A (en) 1994-10-07 1999-01-05 Board Of Regents The University Of Texas Method for selectively ranking sequences for antisense targeting
US5556752A (en) 1994-10-24 1996-09-17 Affymetrix, Inc. Surface-bound, unimolecular, double-stranded DNA
US5690894A (en) * 1995-05-23 1997-11-25 The Regents Of The University Of California High density array fabrication and readout method for a fiber optic biosensor
US5569588A (en) 1995-08-09 1996-10-29 The Regents Of The University Of California Methods for drug screening
US5723320A (en) 1995-08-29 1998-03-03 Dehlinger; Peter J. Position-addressable polynucleotide arrays
US6156502A (en) 1995-12-21 2000-12-05 Beattie; Kenneth Loren Arbitrary sequence oligonucleotide fingerprinting
US5817461A (en) * 1996-01-03 1998-10-06 Hamilton Civic Hospitals Research Development Inc. Methods and compositions for diagnosis of hyperhomocysteinemia
US6027890A (en) * 1996-01-23 2000-02-22 Rapigene, Inc. Methods and compositions for enhancing sensitivity in the analysis of biological-based assays
US20030165931A1 (en) * 1998-03-11 2003-09-04 Bruno Tocque Qualitative differential screening
FR2775984B1 (en) * 1998-03-11 2006-09-15 Bioscreen Therapeutics Sa QUALITATIVE DIFFERENTIAL SCREENING
US6881571B1 (en) * 1998-03-11 2005-04-19 Exonhit Therapeutics S.A. Qualitative differential screening
WO1998012354A1 (en) 1996-09-19 1998-03-26 Affymetrix, Inc. Identification of molecular sequence signatures and methods involving the same
US5935793A (en) 1996-09-27 1999-08-10 The Chinese University Of Hong Kong Parallel polynucleotide sequencing method using tagged primers
DE69737724T2 (en) 1996-11-13 2008-06-12 Qbi Enterprises Ltd. Genidentifikationsverfahren
US6110676A (en) 1996-12-04 2000-08-29 Boston Probes, Inc. Methods for suppressing the binding of detectable probes to non-target sequences in hybridization assays
US5981190A (en) 1997-01-08 1999-11-09 Ontogeny, Inc. Analysis of gene expression, methods and reagents therefor
US6165709A (en) * 1997-02-28 2000-12-26 Fred Hutchinson Cancer Research Center Methods for drug target screening
US6028189A (en) 1997-03-20 2000-02-22 University Of Washington Solvent for oligonucleotide synthesis and methods of use
EP0994946A1 (en) 1997-08-15 2000-04-26 Oncormed Inc. Coding sequence haplotypes of the human brca2 gene
US6051379A (en) 1997-09-23 2000-04-18 Oncormed, Inc. Cancer susceptibility mutations of BRCA2
WO1999019357A2 (en) 1997-10-15 1999-04-22 President And Fellows Of Harvard College Cell regulatory genes, encoded products, and uses related thereto
EP1038009A1 (en) * 1997-12-12 2000-09-27 The Regents of the University of California Methods for defining cell types
WO1999033963A1 (en) 1997-12-31 1999-07-08 Chiron Corporation Metastatic cancer regulated gene
CA2224475A1 (en) 1998-02-25 1999-08-25 University Of British Columbia Protein interaction and transcription factor trap
US6020135A (en) * 1998-03-27 2000-02-01 Affymetrix, Inc. P53-regulated genes
EP1084271A2 (en) 1998-05-07 2001-03-21 Axys Pharmaceuticals, Inc. Genotyping the human udp-glucuronosyltransferase 1 (ugt1) gene
GB9809764D0 (en) 1998-05-07 1998-07-08 Isis Innovation MMP-9 Gene polymorphisms
US6324479B1 (en) 1998-05-08 2001-11-27 Rosetta Impharmatics, Inc. Methods of determining protein activity levels using gene expression profiles
US5965352A (en) 1998-05-08 1999-10-12 Rosetta Inpharmatics, Inc. Methods for identifying pathways of drug action
US6132969A (en) 1998-06-19 2000-10-17 Rosetta Inpharmatics, Inc. Methods for testing biological network models
US6218122B1 (en) 1998-06-19 2001-04-17 Rosetta Inpharmatics, Inc. Methods of monitoring disease states and therapies using gene expression profiles
JP2002526745A (en) 1998-07-21 2002-08-20 ラットガーズ，ザ・ステート・ユニバーシティ Linking gene sequence to gene function by determining three-dimensional (3D) structure of protein
US6146830A (en) 1998-09-23 2000-11-14 Rosetta Inpharmatics, Inc. Method for determining the presence of a number of primary targets of a drug
US6950752B1 (en) 1998-10-27 2005-09-27 Rosetta Inpharmatics Llc Methods for removing artifact from biological profiles
US6203987B1 (en) 1998-10-27 2001-03-20 Rosetta Inpharmatics, Inc. Methods for using co-regulated genesets to enhance detection and classification of gene expression patterns
US6245518B1 (en) 1998-12-11 2001-06-12 Hyseq, Inc. Polynucleotide arrays and methods of making and using the same
US6801859B1 (en) 1998-12-23 2004-10-05 Rosetta Inpharmatics Llc Methods of characterizing drug activities using consensus profiles
US6351712B1 (en) 1998-12-28 2002-02-26 Rosetta Inpharmatics, Inc. Statistical combining of cell expression profiles
US6222093B1 (en) 1998-12-28 2001-04-24 Rosetta Inpharmatics, Inc. Methods for determining therapeutic index from gene expression profiles
CA2361373A1 (en) 1999-01-25 2000-07-27 Combimatrix Corporation A method for selecting oligonucleotides having low cross hybridization
GB9902971D0 (en) 1999-02-11 1999-03-31 Zeneca Ltd Assay
GB9902970D0 (en) 1999-02-11 1999-03-31 Zeneca Ltd Novel matrix
CA2369533A1 (en) 1999-03-19 2000-09-28 Francis Barany Coupled polymerase chain reaction-restriction endonuclease digestion-ligase detection reaction process
US6355431B1 (en) * 1999-04-20 2002-03-12 Illumina, Inc. Detection of nucleic acid amplification reactions using bead arrays
WO2000065088A2 (en) 1999-04-26 2000-11-02 Amersham Pharmacia Biotech Ab Primers for identifying typing or classifying nucleic acids
US6132997A (en) * 1999-05-28 2000-10-17 Agilent Technologies Method for linear mRNA amplification
US20010053849A1 (en) 1999-06-16 2001-12-20 Mary Jeanne Kreek Plural biological sample arrays, and preparation and uses thereof
WO2000079006A1 (en) 1999-06-17 2000-12-28 Fred Hutchinson Cancer Research Center Oligonucleotide arrays for high resolution hla typing
US7013221B1 (en) 1999-07-16 2006-03-14 Rosetta Inpharmatics Llc Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays
US7371516B1 (en) * 1999-07-16 2008-05-13 Rosetta Inpharmatics Llc Methods for determining the specificity and sensitivity of oligonucleo tides for hybridization
US6271002B1 (en) 1999-10-04 2001-08-07 Rosetta Inpharmatics, Inc. RNA amplification method
US20020048763A1 (en) 2000-02-04 2002-04-25 Penn Sharron Gaynor Human genome-derived single exon nucleic acid probes useful for gene expression analysis
AU3087801A (en) 2000-02-04 2001-08-14 Molecular Dynamics Inc Human genome-derived single exon nucleic acid probes useful for analysis of geneexpression in human breast and hbl 100 cells
WO2001081632A1 (en) 2000-04-25 2001-11-01 Affymetrix, Inc. Methods for monitoring the expression of alternatively spliced genes
US6713257B2 (en) * 2000-08-25 2004-03-30 Rosetta Inpharmatics Llc Gene discovery using microarrays

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999023256A1 (en) * 1997-10-30 1999-05-14 Cold Spring Harbor Laboratory Probe arrays and methods of using probe arrays for distinguishing dna
WO2000053811A1 (en) * 1999-03-11 2000-09-14 Orion Genomics, Llc Genome chips and optical transcript mapping

Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
CLAVERIE JEAN-MICHEL: "Computational methods for the identification of genes in vertebrate genomes sequences.", HUMAN MOLECULAR GENETICS, vol. 6, no. 10, 1997, pages 1735 - 1744, XP002225597, ISSN: 0964-6906 *
DENNIS C: "Tiled arrays for gene hunting.", NATURE REVIEWS. GENETICS. ENGLAND MAR 2001, vol. 2, no. 3, March 2001 (2001-03-01), pages 161, XP002225598, ISSN: 1471-0056 *
JAIN K K: "Biotechnological applications of lab-chips and microarrays", TRENDS IN BIOTECHNOLOGY, ELSEVIER, AMSTERDAM, NL, vol. 18, no. 7, 1 July 2000 (2000-07-01), pages 278 - 280, XP004213275, ISSN: 0167-7799 *
SHOEMAKER D D ET AL: "Experimental annotation of the human genome using microarray technology.", NATURE (LONDON), vol. 409, no. 6822, 2001, pages 922 - 927, XP002225599, ISSN: 0028-0836 *
STEPHAN DIETRICH A ET AL: "Positional cloning utilizing genomic DNA microarrays: The Niemann-Pick Type C gene as a model system.", MOLECULAR GENETICS AND METABOLISM, vol. 70, no. 1, May 2000 (2000-05-01), pages 10 - 18, XP002225596, ISSN: 1096-7192 *

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