WO2000060126A3 - Quantitative assay for expression of genes in microarray - Google Patents

Quantitative assay for expression of genes in microarray Download PDF

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Publication number
WO2000060126A3
WO2000060126A3 PCT/US2000/009526 US0009526W WO0060126A3 WO 2000060126 A3 WO2000060126 A3 WO 2000060126A3 US 0009526 W US0009526 W US 0009526W WO 0060126 A3 WO0060126 A3 WO 0060126A3
Authority
WO
WIPO (PCT)
Prior art keywords
expression
spots
energy
developed
detection
Prior art date
Application number
PCT/US2000/009526
Other languages
French (fr)
Other versions
WO2000060126A2 (en
Inventor
Eugenia Wang
Original Assignee
Sir Mortimer B Davis Jewish Ge
Eugenia Wang
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
Priority claimed from CA002268695A external-priority patent/CA2268695A1/en
Priority claimed from US09/299,193 external-priority patent/US6511849B1/en
Application filed by Sir Mortimer B Davis Jewish Ge, Eugenia Wang filed Critical Sir Mortimer B Davis Jewish Ge
Priority to AU42244/00A priority Critical patent/AU4224400A/en
Priority to EP00921995A priority patent/EP1230383A2/en
Priority to IL14582600A priority patent/IL145826A0/en
Priority to JP2000609615A priority patent/JP2004502129A/en
Priority to CA002367413A priority patent/CA2367413A1/en
Publication of WO2000060126A2 publication Critical patent/WO2000060126A2/en
Publication of WO2000060126A3 publication Critical patent/WO2000060126A3/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
    • C12Q1/6813—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
    • 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
    • B01J2219/00596—Solid-phase processes
    • 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
    • B01J2219/00659—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
    • B01J2219/00702—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
    • 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

Landscapes

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

Abstract

A method has been developed for detection of gene expression or hybridization in microarrays, for example, in combinatorial libraries where quantities are very small and spots located very closely, resulting in uncomfortable situations where intense reaction can spill over into the adjacent spots, and therefore obscure the accuracy of the reaction of the neighboring sites. The assay uses a digoxigenin enzyme assay for detection. A method for enhancing the reliability of analysis of expression of DNA in microarray formats has also been developed, using software analysis that normalizes the spots. This process uses deformable template techniques to quantify large-scale array data automatically, despite possible spatial distortion of the arrays. Each node in the deformable template represents a gene spot, and iterates according to the gradient descent rule, which minimizes an energy function combining data mismatch energy and template deformation energy.
PCT/US2000/009526 1999-04-08 2000-04-10 Quantitative assay for expression of genes in microarray WO2000060126A2 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
AU42244/00A AU4224400A (en) 1999-04-08 2000-04-10 Quantitative assay for expression of genes in microarray
EP00921995A EP1230383A2 (en) 1999-04-08 2000-04-10 Quantitative assay for expression of genes in microarray
IL14582600A IL145826A0 (en) 1999-04-08 2000-04-10 Quantitative assay for expression of genes in microarray
JP2000609615A JP2004502129A (en) 1999-04-08 2000-04-10 Quantitative assays for gene expression on microarrays
CA002367413A CA2367413A1 (en) 1999-04-08 2000-04-10 Quantitative assay for expression of genes in microarray

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
CA2,268,695 1999-04-08
CA002268695A CA2268695A1 (en) 1999-04-08 1999-04-08 Apparatus and method for analyzing information in arrays of information sites
US12923399P 1999-04-14 1999-04-14
US60/129,233 1999-04-14
US09/299,193 1999-04-23
US09/299,193 US6511849B1 (en) 1999-04-23 1999-04-23 Microarrays of biological materials

Publications (2)

Publication Number Publication Date
WO2000060126A2 WO2000060126A2 (en) 2000-10-12
WO2000060126A3 true WO2000060126A3 (en) 2002-06-20

Family

ID=27170957

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/009526 WO2000060126A2 (en) 1999-04-08 2000-04-10 Quantitative assay for expression of genes in microarray

Country Status (5)

Country Link
EP (1) EP1230383A2 (en)
JP (1) JP2004502129A (en)
AU (1) AU4224400A (en)
IL (1) IL145826A0 (en)
WO (1) WO2000060126A2 (en)

Families Citing this family (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7157227B2 (en) * 2000-03-31 2007-01-02 University Of Louisville Research Foundation Microarrays to screen regulatory genes
US7219016B2 (en) * 2001-04-20 2007-05-15 Yale University Systems and methods for automated analysis of cells and tissues
CN1424405A (en) * 2001-12-14 2003-06-18 宋克 Gene chip molecular probe and related technology
DE10212958A1 (en) * 2002-03-22 2003-10-09 Friz Biochem Gmbh Detecting nucleic acid-oligonucleotide hybridization, useful e.g. for diagnostic tests, comprises using solid support that includes one or more built-in reference regions to indicate complete (optionally also zero or partial) hybridization
CN102138160B (en) * 2008-07-15 2014-06-04 韩国巴斯德研究所 Method and apparatus for imaging of features on a substrate
CA2768391C (en) 2009-07-21 2016-09-06 Gen-Probe Incorporated Methods and compositions for quantitative detection of nucleic acid sequences over an extended dynamic range
US20110224088A1 (en) * 2010-03-11 2011-09-15 Heidi Lyng Biomarkers for subtypes of cervical cancer
JP5543310B2 (en) * 2010-09-29 2014-07-09 富士フイルム株式会社 Immunochromatographic inspection method and apparatus
JP5543888B2 (en) * 2010-09-29 2014-07-09 富士フイルム株式会社 Immunochromatographic inspection method and apparatus

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0324474A1 (en) * 1988-01-12 1989-07-19 Roche Diagnostics GmbH Method for the detection of nucleic acids
WO1998021321A1 (en) * 1996-11-12 1998-05-22 Qbi Enterprises Ltd. Method for identifying translationally regulated genes
WO1998029736A1 (en) * 1996-12-31 1998-07-09 Genometrix Incorporated Multiplexed molecular analysis apparatus and method
WO1998052961A1 (en) * 1997-05-19 1998-11-26 Mirus Corporation Method for single-step attachment of a label to target molecules

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0324474A1 (en) * 1988-01-12 1989-07-19 Roche Diagnostics GmbH Method for the detection of nucleic acids
WO1998021321A1 (en) * 1996-11-12 1998-05-22 Qbi Enterprises Ltd. Method for identifying translationally regulated genes
WO1998029736A1 (en) * 1996-12-31 1998-07-09 Genometrix Incorporated Multiplexed molecular analysis apparatus and method
WO1998052961A1 (en) * 1997-05-19 1998-11-26 Mirus Corporation Method for single-step attachment of a label to target molecules

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
CHEN JEREMY J W ET AL: "Profiling expression patterns and isolating differentially expressed genes by cDNA microarray system with colorimetry detection", GENOMICS, ACADEMIC PRESS, SAN DIEGO, US, vol. 51, no. 3, 1 August 1998 (1998-08-01), pages 313 - 324, XP002159705, ISSN: 0888-7543 *

Also Published As

Publication number Publication date
AU4224400A (en) 2000-10-23
WO2000060126A2 (en) 2000-10-12
IL145826A0 (en) 2002-07-25
JP2004502129A (en) 2004-01-22
EP1230383A2 (en) 2002-08-14

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