WO2004007755A3 - Multiplex nucleic acid reactions - Google Patents

Multiplex nucleic acid reactions Download PDF

Info

Publication number
WO2004007755A3
WO2004007755A3 PCT/US2003/022171 US0322171W WO2004007755A3 WO 2004007755 A3 WO2004007755 A3 WO 2004007755A3 US 0322171 W US0322171 W US 0322171W WO 2004007755 A3 WO2004007755 A3 WO 2004007755A3
Authority
WO
WIPO (PCT)
Prior art keywords
probe
target
sequence
downstream
primers
Prior art date
Application number
PCT/US2003/022171
Other languages
French (fr)
Other versions
WO2004007755A2 (en
WO2004007755A9 (en
Inventor
Mark Chee
Jian-Bing Fan
Kevin Gunderson
Original Assignee
Illumina Inc
Mark Chee
Jian-Bing Fan
Kevin Gunderson
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 Illumina Inc, Mark Chee, Jian-Bing Fan, Kevin Gunderson filed Critical Illumina Inc
Priority to AU2003269908A priority Critical patent/AU2003269908A1/en
Publication of WO2004007755A2 publication Critical patent/WO2004007755A2/en
Publication of WO2004007755A9 publication Critical patent/WO2004007755A9/en
Publication of WO2004007755A3 publication Critical patent/WO2004007755A3/en

Links

Classifications

    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6858—Allele-specific amplification

Abstract

The invention is directed to a variety of multiplexing methods used to amplify and/or genotype a variety of samples simultaneously. The invention provides a method of detecting a target sequence. The method consists of: (a) contacting a first and second probe with a target sequence under conditions where complementary probes form a hybridization complex with the target sequence, the first probe comprising an upstream universal priming site and a target­ specific sequence, the second probe comprising a downstream universal priming site and a target-specific sequence, wherein one of the first or second probes comprise an adapter sequence; (b) extending the first or second probe of the hybridization complex to form a modified probe; (c) amplifying the modified probe to form an amplicon, and (d) detecting the amplicon. A method of detecting the relative amounts of two or more target sequences is also provided. The method consists of (a) contacting a first and a second probe with first and second target sequences in an initial population under conditions where complementary probes form a hybridization complex with the target sequences, the first and second probes comprising a universal priming site, an adapter sequence and a target-specific sequence; (b) linearly amplifying the first and second probes forming the hybridization complex to produce first and second amplicons having distinctive adapter sequences, and (c) determining a relative amount of the first and second amplicons distinguishable by the adapter sequence, wherein the relative amount of the amplicons is indicative of the relative amounts of the first and second target sequences in the initial population. Further provided is a method of amplifying a target sequence to produce a signal within a dynamic range of a detection assay. The method consists of: (a) hybridizing a target-specific probe having an upstream universal priming site (UUP), a downstream universal priming site (DUP) and an adapter sequence with a set of differential primers, the set of differential primers comprising an upstream primer and first and second downstream primers, the second downstream primer having a lower Tm compared to the upstream primer and the first downstream primer; (b) amplifying the probe with the set of differential primers for two or more cycles of enzymatic polymerization; (c) increasing hybridization stringency to suppress hybridization of the second downstream primer, and (d) amplifying the probe from the upstream and the first downstream primers of the set for at least one cycle of enzymatic polymerization, wherein differential signals of amplicons produced from amplification of the first or the second downstream primers fall within a dynamic range of a detection assay.
PCT/US2003/022171 2002-07-15 2003-07-15 Multiplex nucleic acid reactions WO2004007755A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2003269908A AU2003269908A1 (en) 2002-07-15 2003-07-15 Multiplex nucleic acid reactions

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US39623702P 2002-07-15 2002-07-15
US60/396,237 2002-07-15

Publications (3)

Publication Number Publication Date
WO2004007755A2 WO2004007755A2 (en) 2004-01-22
WO2004007755A9 WO2004007755A9 (en) 2004-05-06
WO2004007755A3 true WO2004007755A3 (en) 2004-07-29

Family

ID=30115992

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2003/022171 WO2004007755A2 (en) 2002-07-15 2003-07-15 Multiplex nucleic acid reactions

Country Status (2)

Country Link
AU (1) AU2003269908A1 (en)
WO (1) WO2004007755A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN103361438A (en) * 2013-07-30 2013-10-23 武汉中帜生物科技有限公司 Method for detecting nucleic acid by combining template amplification and signal amplification

Families Citing this family (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8304192B2 (en) 2004-03-05 2012-11-06 University Of Toledo Methods and compositions for assessing nucleic acids and alleles
EP1745157A4 (en) 2004-04-12 2008-06-11 Ohio Med College Methods and compositions for assaying analytes
JP4777631B2 (en) * 2004-09-27 2011-09-21 株式会社日立ハイテクノロジーズ Nucleic acid amplification analysis method and apparatus
US7902345B2 (en) 2006-12-05 2011-03-08 Sequenom, Inc. Detection and quantification of biomolecules using mass spectrometry
US8133701B2 (en) * 2006-12-05 2012-03-13 Sequenom, Inc. Detection and quantification of biomolecules using mass spectrometry
ATE549419T1 (en) 2007-08-29 2012-03-15 Sequenom Inc METHODS AND COMPOSITIONS FOR UNIVERSAL SIZE-SPECIFIC POLYMERASE CHAIN REACTION
CN110438201A (en) * 2013-07-30 2019-11-12 武汉中帜生物科技股份有限公司 A kind of method of microRNA detection kit and multi-biotin Molecular Detection microRNA
CN103525942A (en) * 2013-10-31 2014-01-22 武汉中帜生物科技有限公司 Nucleic acid detection method combining RNA amplification with hybrid capture method
EP4050112A1 (en) 2016-06-21 2022-08-31 10X Genomics, Inc. Nucleic acid sequencing
US20220195502A1 (en) * 2019-04-24 2022-06-23 Genepath Diagnostics Inc. Method for detecting specific nucleic acids in samples
CN112011599A (en) * 2020-09-07 2020-12-01 苏州贝康医疗器械有限公司 PCR primer set for reducing non-specific amplification and application thereof
CN114277095A (en) * 2021-12-27 2022-04-05 上海市肺科医院 Nucleotide composition for detecting genetic variation and high-throughput sequencing library constructed by same

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5601978A (en) * 1993-09-03 1997-02-11 Abbott Laboratories Oligonucleotides and methods for the detection of chlamydia trachomatis
US6060245A (en) * 1996-12-13 2000-05-09 Stratagene Methods and adaptors for generating specific nucleic acid populations
US20020006617A1 (en) * 2000-02-07 2002-01-17 Jian-Bing Fan Nucleic acid detection methods using universal priming
US6355431B1 (en) * 1999-04-20 2002-03-12 Illumina, Inc. Detection of nucleic acid amplification reactions using bead arrays
US6511810B2 (en) * 2000-07-03 2003-01-28 Applera Corporation Polynucleotide sequence assay

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5601978A (en) * 1993-09-03 1997-02-11 Abbott Laboratories Oligonucleotides and methods for the detection of chlamydia trachomatis
US6060245A (en) * 1996-12-13 2000-05-09 Stratagene Methods and adaptors for generating specific nucleic acid populations
US6355431B1 (en) * 1999-04-20 2002-03-12 Illumina, Inc. Detection of nucleic acid amplification reactions using bead arrays
US20020006617A1 (en) * 2000-02-07 2002-01-17 Jian-Bing Fan Nucleic acid detection methods using universal priming
US6511810B2 (en) * 2000-07-03 2003-01-28 Applera Corporation Polynucleotide sequence assay

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN103361438A (en) * 2013-07-30 2013-10-23 武汉中帜生物科技有限公司 Method for detecting nucleic acid by combining template amplification and signal amplification
CN103361438B (en) * 2013-07-30 2016-09-28 武汉中帜生物科技股份有限公司 A kind of template amplification and signal amplify the method combining detection nucleic acid

Also Published As

Publication number Publication date
WO2004007755A2 (en) 2004-01-22
AU2003269908A1 (en) 2004-02-02
AU2003269908A8 (en) 2004-02-02
WO2004007755A9 (en) 2004-05-06

Similar Documents

Publication Publication Date Title
WO2004007755A3 (en) Multiplex nucleic acid reactions
CN102154489B (en) Singly labeled oligonucleotide fluorescent probe and method for detecting nuclease
AU2709995A (en) Method of amplification for increasing the sensitivity of detecting nucleic acid-probe target hybrids
WO2001049883A3 (en) Amplification based polymorphism detection
EP1087020A3 (en) Universal probes and methods for detection of nucleic acids
ATE245198T1 (en) PCR PRIMER DESIGNS FOR AN INTEGRATED SIGNAL SYSTEM
HUP0301031A2 (en) Degradable nucleic acid probes and nucleic acid detection methods
WO1999040226A3 (en) Determination of a genotype of an amplification product at multiple allelic sites
WO2002061133A3 (en) Nucleic acid detection using structured probes
EP2180064A3 (en) Multiplex quantification of nucleic acids in diseased cells
WO2002083839A3 (en) P450 single nucleotide polymorphism biochip analysis
DK1427852T3 (en) Single nucleotide implication and detection by polymerase
KR910014510A (en) Amplification of Target Nucleic Acids Applicable to Both Polymerase and Ligase Chain Reactions
HUP0101385A2 (en) Method for detection of target nucleic acids using for
WO2005030929A3 (en) Polymeric nucleic acid hybridization probes
CA2378408A1 (en) Polynucleotide amplification method
CA2399733A1 (en) Nucleic acid detection methods using universal priming
WO2003087297A3 (en) Infectious disease microarray
WO2005089508A3 (en) Dna sequence detection by limited primer extension
WO2004013357A3 (en) Nucleotide sequences specific to francisella tularensis and methods for the detection of francisella tularensis
JP2013543385A (en) Enhancement of ionic signal
JP2006515760A5 (en)
EP0803578A3 (en) Kit for amplification and detection of nucleic acid of cytomegalovirus (cmv) utilizing a nucleic acid sequence (ss2.7)
WO2005047468A3 (en) Improved methods for detecting and measuring specific nucleic acid sequences
EP3736346B1 (en) Methods and compositions for diagnosing bacterial vaginosis

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CO CR CU CZ DE DK DM DZ EC EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NI NO NZ OM PG PH PL PT RO RU SC SD SE SG SK SL SY TJ TM TN TR TT TZ UA UG US UZ VC VN YU ZA ZM ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZM ZW AM AZ BY KG KZ MD RU TJ TM AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HU IE IT LU MC NL PT RO SE SI SK TR BF BJ CF CG CI CM GA GN GQ GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
COP Corrected version of pamphlet

Free format text: PAGES 1/28-28/28, DRAWINGS, REPLACED BY NEW PAGES 1/28-28/28; DUE TO LATE TRANSMITTAL BY THE RECEIVING OFFICE

122 Ep: pct application non-entry in european phase
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
NENP Non-entry into the national phase

Ref country code: JP

WWW Wipo information: withdrawn in national office

Country of ref document: JP