WO2001021838A3 - Three-dimensional microarray system for parallel genotyping of single nucleotide polymorphisms - Google Patents

Three-dimensional microarray system for parallel genotyping of single nucleotide polymorphisms Download PDF

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Publication number
WO2001021838A3
WO2001021838A3 PCT/US2000/025988 US0025988W WO0121838A3 WO 2001021838 A3 WO2001021838 A3 WO 2001021838A3 US 0025988 W US0025988 W US 0025988W WO 0121838 A3 WO0121838 A3 WO 0121838A3
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WO
WIPO (PCT)
Prior art keywords
single nucleotide
nucleotide polymorphisms
microarray system
dimensional microarray
parallel genotyping
Prior art date
Application number
PCT/US2000/025988
Other languages
French (fr)
Other versions
WO2001021838A2 (en
Inventor
Walter Klimecki
Original Assignee
Motorola Inc
Walter Klimecki
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Filing date
Publication date
Application filed by Motorola Inc, Walter Klimecki filed Critical Motorola Inc
Priority to EP00966797A priority Critical patent/EP1222310A2/en
Priority to AU77085/00A priority patent/AU7708500A/en
Priority to CA002385851A priority patent/CA2385851A1/en
Priority to JP2001525396A priority patent/JP2003510054A/en
Publication of WO2001021838A2 publication Critical patent/WO2001021838A2/en
Publication of WO2001021838A3 publication Critical patent/WO2001021838A3/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
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • B01J2219/00277—Apparatus
    • B01J2219/00279—Features relating to reactor vessels
    • B01J2219/00306—Reactor vessels in a multiple arrangement
    • B01J2219/00313—Reactor vessels in a multiple arrangement the reactor vessels being formed by arrays of wells in blocks
    • B01J2219/00315—Microtiter plates
    • B01J2219/00317—Microwell devices, i.e. having large numbers of wells
    • 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
    • B01J2219/00277—Apparatus
    • B01J2219/00497—Features relating to the solid phase 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
    • B01J2219/00585—Parallel processes
    • B01J2219/00587—High throughput 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
    • B01J2219/00596—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
    • B01J2219/00608—DNA 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
    • B01J2219/00603—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
    • B01J2219/00614—Delimitation of the attachment areas
    • B01J2219/00621—Delimitation of the attachment areas by physical means, e.g. trenches, raised areas
    • 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
    • B01J2219/00639—Making arrays on substantially continuous surfaces the compounds being trapped in or bound to a porous medium
    • B01J2219/00644—Making arrays on substantially continuous surfaces the compounds being trapped in or bound to a porous medium the porous medium being present in discrete locations, e.g. gel pads
    • 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
    • B01J2219/00583—Features relative to the processes being carried out
    • B01J2219/00603—Making arrays on substantially continuous surfaces
    • B01J2219/00664—Three-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
    • B01J2219/00718—Type of compounds synthesised
    • B01J2219/0072—Organic compounds
    • B01J2219/00722—Nucleotides
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/08—Geometry, shape and general structure
    • B01L2300/0893—Geometry, shape and general structure having a very large number of wells, microfabricated wells
    • 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
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B60/00—Apparatus specially adapted for use in combinatorial chemistry or with libraries
    • C40B60/14—Apparatus specially adapted for use in combinatorial chemistry or with libraries for creating libraries

Abstract

The present invention provides methods for detecting nucleic acid mutations and genetic polymorphisms by single base extension analysis. Specifically, the invention provides an apparatus and methods for the detection of single base extension of a particular oligonucleotide in an oligonucleotide microarray following hybridization between oligonucleotides bound to defined regions of a polymeric hydrogel-based microarray and nucleic acids in a biological sample.
PCT/US2000/025988 1999-09-22 2000-09-22 Three-dimensional microarray system for parallel genotyping of single nucleotide polymorphisms WO2001021838A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
EP00966797A EP1222310A2 (en) 1999-09-22 2000-09-22 Three-dimensional microarray system for parallel genotyping of single nucleotide polymorphisms
AU77085/00A AU7708500A (en) 1999-09-22 2000-09-22 Three-dimensional microarray system for parallel genotyping of single nucleotide polymorphisms
CA002385851A CA2385851A1 (en) 1999-09-22 2000-09-22 Three-dimensional microarray system for parallel genotyping of single nucleotide polymorphisms
JP2001525396A JP2003510054A (en) 1999-09-22 2000-09-22 A three-dimensional microarray system for parallel genotyping of single nucleotide polymorphisms

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US15543199P 1999-09-22 1999-09-22
US60/155,431 1999-09-22

Publications (2)

Publication Number Publication Date
WO2001021838A2 WO2001021838A2 (en) 2001-03-29
WO2001021838A3 true WO2001021838A3 (en) 2001-10-25

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/025988 WO2001021838A2 (en) 1999-09-22 2000-09-22 Three-dimensional microarray system for parallel genotyping of single nucleotide polymorphisms

Country Status (5)

Country Link
EP (1) EP1222310A2 (en)
JP (1) JP2003510054A (en)
AU (1) AU7708500A (en)
CA (1) CA2385851A1 (en)
WO (1) WO2001021838A2 (en)

Families Citing this family (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2002353997A1 (en) * 2001-11-01 2003-05-12 Rensselaer Polytechnic Institute In vitro metabolic engineering on microscale devices
US11001881B2 (en) 2006-08-24 2021-05-11 California Institute Of Technology Methods for detecting analytes
US11525156B2 (en) 2006-07-28 2022-12-13 California Institute Of Technology Multiplex Q-PCR arrays
WO2008014485A2 (en) 2006-07-28 2008-01-31 California Institute Of Technology Multiplex q-pcr arrays
US11560588B2 (en) 2006-08-24 2023-01-24 California Institute Of Technology Multiplex Q-PCR arrays
US20120141986A1 (en) * 2007-03-27 2012-06-07 Kenneth Kuhn Multivalent substrate elements for detection of nucleic acid sequences
AU2011241208B2 (en) * 2010-04-15 2017-02-02 Digital Sensing Limited Microarrays
US9708647B2 (en) 2015-03-23 2017-07-18 Insilixa, Inc. Multiplexed analysis of nucleic acid hybridization thermodynamics using integrated arrays
US9499861B1 (en) 2015-09-10 2016-11-22 Insilixa, Inc. Methods and systems for multiplex quantitative nucleic acid amplification
WO2017155858A1 (en) 2016-03-07 2017-09-14 Insilixa, Inc. Nucleic acid sequence identification using solid-phase cyclic single base extension
CN110678557A (en) 2017-03-31 2020-01-10 玛赛拉·基亚里 Genotyping of mutations by in-tube hybridization in combination with universal tag-microarray
CN113924041A (en) 2019-03-14 2022-01-11 因斯利克萨公司 Method and system for fluorescence detection based on time gating
CN113943324B (en) * 2021-10-25 2023-07-28 中元汇吉生物技术股份有限公司 Modified nucleotide, composition and reagent

Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1990009455A1 (en) * 1989-02-13 1990-08-23 Geneco Pty Ltd Detection of a nucleic acid sequence or a change therein
EP0535242A1 (en) * 1991-03-18 1993-04-07 Institut Molekulyarnoi Biologii Imeni V.A. Engelgardta Akademii Nauk Sssr Method and device for determining nucleotide sequence of dna
WO1993025563A1 (en) * 1992-06-17 1993-12-23 City Of Hope A method of detecting and discriminating between nucleic acid sequences
US5770721A (en) * 1993-08-11 1998-06-23 University Of Chicago Method of manufacturing a matrix for the detection of mismatches
WO1998028438A1 (en) * 1996-12-20 1998-07-02 Diatech Pty. Ltd. Process for detecting point mutations in which the primer is bound to a solid support and extension does not occur if the terminal nucleotide(s) mis-match
WO1998044152A1 (en) * 1997-04-01 1998-10-08 Glaxo Group Limited Method of nucleic acid sequencing
WO1999018242A1 (en) * 1997-10-07 1999-04-15 Motorola Inc. Sensors for electrically sensing binding events for supported molecular receptors
WO2000031148A2 (en) * 1998-11-25 2000-06-02 Motorola, Inc. Polyacrylamide hydrogels and hydrogel arrays made from polyacrylamide reactive prepolymers

Patent Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1990009455A1 (en) * 1989-02-13 1990-08-23 Geneco Pty Ltd Detection of a nucleic acid sequence or a change therein
EP0535242A1 (en) * 1991-03-18 1993-04-07 Institut Molekulyarnoi Biologii Imeni V.A. Engelgardta Akademii Nauk Sssr Method and device for determining nucleotide sequence of dna
WO1993025563A1 (en) * 1992-06-17 1993-12-23 City Of Hope A method of detecting and discriminating between nucleic acid sequences
US5770721A (en) * 1993-08-11 1998-06-23 University Of Chicago Method of manufacturing a matrix for the detection of mismatches
WO1998028438A1 (en) * 1996-12-20 1998-07-02 Diatech Pty. Ltd. Process for detecting point mutations in which the primer is bound to a solid support and extension does not occur if the terminal nucleotide(s) mis-match
WO1998044152A1 (en) * 1997-04-01 1998-10-08 Glaxo Group Limited Method of nucleic acid sequencing
WO1999018242A1 (en) * 1997-10-07 1999-04-15 Motorola Inc. Sensors for electrically sensing binding events for supported molecular receptors
WO2000031148A2 (en) * 1998-11-25 2000-06-02 Motorola, Inc. Polyacrylamide hydrogels and hydrogel arrays made from polyacrylamide reactive prepolymers

Non-Patent Citations (4)

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Title
DUBILEY ET AL.: "POLYMORPHISM ANALYSIS AND GENE DETECTION BY MINISEQUENCING ON AN ARRAY OF GEL-IMMOBILIZED PRIMERS", NUCLEIC ACIDS RESEARCH/ONLINE, vol. 27, no. 18, August 1999 (1999-08-01), pages e19, XP002153648 *
MCKENZIE STEVEN E ET AL: "Parallel molecular genetic analysis.", EUROPEAN JOURNAL OF HUMAN GENETICS, vol. 6, no. 5, 1998, pages 417 - 429, XP000953351, ISSN: 1018-4813 *
SYVANEN ANN-CHRISTINE: "From gels to chips: "minisequencing" primer extension for analysis of point mutations and single nucleotide polymorphisms.", HUMAN MUTATION, vol. 13, no. 1, 6 April 1999 (1999-04-06), pages 1 - 10, XP000953256, ISSN: 1059-7794 *
YERSHOV G ET AL: "DNA ANALYSIS AND DIAGNOSTICS ON OLIGONUCLEOTIDE MICROCHIPS", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA,US,NATIONAL ACADEMY OF SCIENCE. WASHINGTON, vol. 93, 1 May 1996 (1996-05-01), pages 4913 - 4918, XP002064987, ISSN: 0027-8424 *

Also Published As

Publication number Publication date
EP1222310A2 (en) 2002-07-17
AU7708500A (en) 2001-04-24
JP2003510054A (en) 2003-03-18
CA2385851A1 (en) 2001-03-29
WO2001021838A2 (en) 2001-03-29

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