WO2004104172A3 - Hybridization-mediated analysis of polymorphisms - Google Patents

Hybridization-mediated analysis of polymorphisms Download PDF

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Publication number
WO2004104172A3
WO2004104172A3 PCT/US2004/015224 US2004015224W WO2004104172A3 WO 2004104172 A3 WO2004104172 A3 WO 2004104172A3 US 2004015224 W US2004015224 W US 2004015224W WO 2004104172 A3 WO2004104172 A3 WO 2004104172A3
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WO
WIPO (PCT)
Prior art keywords
methods
probes
polymorphisms
hybridization
amplicons
Prior art date
Application number
PCT/US2004/015224
Other languages
French (fr)
Other versions
WO2004104172A2 (en
Inventor
Ghazala Hashmi
Michael Seul
Original Assignee
Bioarray Solutions Ltd
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 Bioarray Solutions Ltd filed Critical Bioarray Solutions Ltd
Priority to TW093117905A priority Critical patent/TW200538552A/en
Publication of WO2004104172A2 publication Critical patent/WO2004104172A2/en
Publication of WO2004104172A3 publication Critical patent/WO2004104172A3/en

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809Methods for determination or identification of nucleic acids involving differential detection
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813Hybridisation assays
    • C12Q1/6827Hybridisation assays for detection of mutation or polymorphism
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813Hybridisation assays
    • C12Q1/6834Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/156Polymorphic or mutational markers
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/16Primer sets for multiplex assays
    • YGENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10STECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S436/00Chemistry: analytical and immunological testing
    • Y10S436/80Fluorescent dyes, e.g. rhodamine
    • YGENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10STECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S436/00Chemistry: analytical and immunological testing
    • Y10S436/805Optical property
    • YGENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10TTECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00Chemistry: analytical and immunological testing
    • Y10T436/14Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333Saccharide [e.g., DNA, etc.]

Abstract

Described are methods of assay design and assay image correction, useful for multiplexed genetic screening for mutations and polymorphisms, including CF-related mutants and polymorphs, using an array of probe pairs (in one aspect, where one member is complementary to a particular mutant or polymorphic allele and the other member is complementary to a corresponding wild type allele, with probes bound to encoded particles (e.g., beads wherein the encoding allows identification of the attached probe. The methods relate to avoiding cross-hybridization by selection of probes and amplicons, as well as separation of reactions of certain probes and amplicons where a homology threshold is exceeded. Methods of correcting a fluorescent image using a background map, where the particles also contain an optical encoding system, are also disclosed.
PCT/US2004/015224 2003-05-15 2004-05-17 Hybridization-mediated analysis of polymorphisms WO2004104172A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
TW093117905A TW200538552A (en) 2004-05-17 2004-06-21 Hybridization-mediated analysis of polymorphisms

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US47080603P 2003-05-15 2003-05-15
US60/470,806 2003-05-15

Publications (2)

Publication Number Publication Date
WO2004104172A2 WO2004104172A2 (en) 2004-12-02
WO2004104172A3 true WO2004104172A3 (en) 2005-05-12

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2004/015224 WO2004104172A2 (en) 2003-05-15 2004-05-17 Hybridization-mediated analysis of polymorphisms

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US (7) US20040229269A1 (en)
WO (1) WO2004104172A2 (en)

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ATE319087T1 (en) 2000-06-21 2006-03-15 Bioarray Solutions Ltd MULTI-ANALYTICAL MOLECULAR ANALYSIS BY 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
US7262063B2 (en) * 2001-06-21 2007-08-28 Bio Array Solutions, Ltd. Directed assembly of functional heterostructures
WO2003034029A2 (en) 2001-10-15 2003-04-24 Bioarray Solutions, Ltd. Multiplexed analysis of polymorphic loci by concurrent interrogation and enzyme-mediated detection
US7526114B2 (en) 2002-11-15 2009-04-28 Bioarray Solutions Ltd. Analysis, secure access to, and transmission of array images
US7927796B2 (en) * 2003-09-18 2011-04-19 Bioarray Solutions, Ltd. Number coding for identification of subtypes of coded types of solid phase carriers
TW200521436A (en) 2003-09-22 2005-07-01 Bioarray Solutions Ltd Surface immobilized polyelectrolyte with multiple functional groups capable of covalently bonding to biomolecules
WO2005042763A2 (en) 2003-10-28 2005-05-12 Bioarray Solutions Ltd. Optimization of gene expression analysis using immobilized capture probes
JP2007509629A (en) 2003-10-29 2007-04-19 バイオアレイ ソリューションズ リミテッド Complex nucleic acid analysis by cleavage of double-stranded DNA
US7848889B2 (en) 2004-08-02 2010-12-07 Bioarray Solutions, Ltd. Automated analysis of multiplexed probe-target interaction patterns: pattern matching and allele identification
US8486629B2 (en) 2005-06-01 2013-07-16 Bioarray Solutions, Ltd. Creation of functionalized microparticle libraries by oligonucleotide ligation or elongation
US20070116376A1 (en) 2005-11-18 2007-05-24 Kolterman James C Image based correction for unwanted light signals in a specific region of interest
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US8140270B2 (en) * 2007-03-22 2012-03-20 National Center For Genome Resources Methods and systems for medical sequencing analysis
AU2009231582B2 (en) * 2008-04-03 2015-02-26 iRepertoire, Inc. Amplicon rescue multiplex polymerase chain reaction for amplificaton of multiple targets
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WO2011050341A1 (en) * 2009-10-22 2011-04-28 National Center For Genome Resources Methods and systems for medical sequencing analysis
US20110136104A1 (en) * 2009-12-04 2011-06-09 Massachusetts Institute Of Technology Multiplexed quantitative pcr end point analysis of nucleic acid targets
WO2011068518A1 (en) * 2009-12-04 2011-06-09 Massachusetts Institute Of Technology Multiplexed quantitative pcr end point analysis of nucleic acid targets
EP2576839B1 (en) 2010-06-07 2017-05-10 Firefly Bioworks, Inc. Nucleic acid detection and quantification by post-hybridization labeling and universal encoding
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Also Published As

Publication number Publication date
US7771939B2 (en) 2010-08-10
US20110262911A1 (en) 2011-10-27
US20060228744A1 (en) 2006-10-12
US20070128617A1 (en) 2007-06-07
US20060228742A1 (en) 2006-10-12
US20060228743A1 (en) 2006-10-12
US20130210642A1 (en) 2013-08-15
US7501266B2 (en) 2009-03-10
US20040229269A1 (en) 2004-11-18
WO2004104172A2 (en) 2004-12-02

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