WO2005094532A3 - Encoding and decoding reactions for determining target polynucleotides - Google Patents

Encoding and decoding reactions for determining target polynucleotides Download PDF

Info

Publication number
WO2005094532A3
WO2005094532A3 PCT/US2005/009882 US2005009882W WO2005094532A3 WO 2005094532 A3 WO2005094532 A3 WO 2005094532A3 US 2005009882 W US2005009882 W US 2005009882W WO 2005094532 A3 WO2005094532 A3 WO 2005094532A3
Authority
WO
WIPO (PCT)
Prior art keywords
encoding
present
decoding
target polynucleotides
determining target
Prior art date
Application number
PCT/US2005/009882
Other languages
French (fr)
Other versions
WO2005094532A2 (en
WO2005094532B1 (en
Inventor
Kai Qin Lao
Mark T Reed
Original Assignee
Applera Corp
Kai Qin Lao
Mark T Reed
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 Applera Corp, Kai Qin Lao, Mark T Reed filed Critical Applera Corp
Priority to EP05732398A priority Critical patent/EP1730312B1/en
Priority to JP2007505187A priority patent/JP2007530048A/en
Priority to DE602005007874T priority patent/DE602005007874D1/en
Publication of WO2005094532A2 publication Critical patent/WO2005094532A2/en
Publication of WO2005094532A3 publication Critical patent/WO2005094532A3/en
Publication of WO2005094532B1 publication Critical patent/WO2005094532B1/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
    • C12Q1/6869—Methods for sequencing
    • 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
    • C12Q1/6851—Quantitative amplification

Abstract

The present invention is directed to methods, reagents, and kits for detecting the presence or absence of (or quantifying) target polynucleotide sequences in at least one sample using encoding and decoding reactions. When a particular target polynucleotide is present in a sample, a reaction product is formed in the encoding reaction that includes addressable primer portions. At least one label and at least one address primer is employed in the decoding amplification reaction thereby providing a detectable signal value depending upon whether a sequence is present or absent. In some embodiments universal bases and reduced libraries of probes can be employed for highly multiplexed analysis of target polynucleotides.
PCT/US2005/009882 2004-03-24 2005-03-24 Encoding and decoding reactions for determining target polynucleotides WO2005094532A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP05732398A EP1730312B1 (en) 2004-03-24 2005-03-24 Encoding and decoding reactions for determining target polynucleotides
JP2007505187A JP2007530048A (en) 2004-03-24 2005-03-24 Encoding and decoding reactions to detect target polynucleotides
DE602005007874T DE602005007874D1 (en) 2004-03-24 2005-03-24 CODING AND DECODING REACTIONS FOR DETERMINING TARGET POLYNUCLEOTIDES

Applications Claiming Priority (10)

Application Number Priority Date Filing Date Title
US55616204P 2004-03-24 2004-03-24
US55616304P 2004-03-24 2004-03-24
US55622404P 2004-03-24 2004-03-24
US55615704P 2004-03-24 2004-03-24
US60/556,224 2004-03-24
US60/556,163 2004-03-24
US60/556,162 2004-03-24
US60/556,157 2004-03-24
US63068104P 2004-11-24 2004-11-24
US60/630,681 2004-11-24

Publications (3)

Publication Number Publication Date
WO2005094532A2 WO2005094532A2 (en) 2005-10-13
WO2005094532A3 true WO2005094532A3 (en) 2005-12-22
WO2005094532B1 WO2005094532B1 (en) 2006-03-02

Family

ID=35064420

Family Applications (2)

Application Number Title Priority Date Filing Date
PCT/US2005/010184 WO2005098040A2 (en) 2004-03-24 2005-03-24 Ligation and amplification reactions for determining target molecules
PCT/US2005/009882 WO2005094532A2 (en) 2004-03-24 2005-03-24 Encoding and decoding reactions for determining target polynucleotides

Family Applications Before (1)

Application Number Title Priority Date Filing Date
PCT/US2005/010184 WO2005098040A2 (en) 2004-03-24 2005-03-24 Ligation and amplification reactions for determining target molecules

Country Status (6)

Country Link
US (2) US7604937B2 (en)
EP (3) EP1730312B1 (en)
JP (2) JP2007530048A (en)
AT (2) ATE399884T1 (en)
DE (2) DE602005007874D1 (en)
WO (2) WO2005098040A2 (en)

Families Citing this family (43)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2006500034A (en) * 2002-09-19 2006-01-05 アプレラ コーポレイション Methods and compositions for detecting targets
US7570443B2 (en) 2003-09-19 2009-08-04 Applied Biosystems, Llc Optical camera alignment
ATE399884T1 (en) 2004-03-24 2008-07-15 Applera Corp CODING AND DECODING REACTIONS FOR DETERMINING TARGET POLYNUCLEOTIDES
US7427479B2 (en) * 2004-04-30 2008-09-23 Applera Corporation Methods and kits for identifying target nucleotides in mixed populations
WO2005108618A2 (en) * 2004-04-30 2005-11-17 Applera Corporation Methods and kits for methylation detection
US7575863B2 (en) * 2004-05-28 2009-08-18 Applied Biosystems, Llc Methods, compositions, and kits comprising linker probes for quantifying polynucleotides
WO2006005055A2 (en) * 2004-06-30 2006-01-12 Applera Corporation Methods reaction mixtures and kits for ligating polynucleotides
US7642055B2 (en) * 2004-09-21 2010-01-05 Applied Biosystems, Llc Two-color real-time/end-point quantitation of microRNAs (miRNAs)
EP1910549B1 (en) * 2005-07-15 2010-11-24 Life Technologies Corporation Analyzing messenger rna and micro rna in the same reaction mixture
WO2007011867A2 (en) * 2005-07-15 2007-01-25 Applera Corporation Fluid processing device and method
WO2007024778A2 (en) * 2005-08-22 2007-03-01 Applera Corporation Device, system and method for depositing processed immiscible-fluid-discrete-volumes
WO2007025281A2 (en) 2005-08-24 2007-03-01 Applera Corporation A method to quantify sirnas, mirnas and polymorphic mirnas
JP2009536525A (en) * 2006-05-10 2009-10-15 ディクステリティー ダイアグノーティクス Detection of nucleic acid targets using chemically reactive oligonucleotide probes
US8597938B2 (en) * 2007-10-12 2013-12-03 Qiagen Sciences Llc System for providing control reactions for real time RT-PCR
WO2009100449A1 (en) * 2008-02-08 2009-08-13 Fluidigm Corporation Dynamic array assay methods
EP2326732A4 (en) * 2008-08-26 2012-11-14 Fluidigm Corp Assay methods for increased throughput of samples and/or targets
JP5608998B2 (en) * 2009-03-31 2014-10-22 東洋紡株式会社 Nucleic acid amplification detection reagent kit with excellent storage stability
EP2765205B1 (en) * 2009-04-01 2016-05-18 DxTerity Diagnostics Incorporated Chemical ligation dependent probe amplification (CLPA)
CN102439177B (en) 2009-04-02 2014-10-01 弗卢伊蒂格姆公司 Multi-primer amplification method for barcoding of target nucleic acids
US8574864B2 (en) 2009-11-05 2013-11-05 Epicentre Technologies Corporation Methods and kits for 3'-end-tagging of RNA
EP2510126B1 (en) * 2009-12-07 2017-08-09 Illumina, Inc. Multi-sample indexing for multiplex genotyping
EP2534263B1 (en) * 2010-02-09 2020-08-05 Unitaq Bio Methods and compositions for universal detection of nucleic acids
AU2011305445B2 (en) 2010-09-24 2017-03-16 The Board Of Trustees Of The Leland Stanford Junior University Direct capture, amplification and sequencing of target DNA using immobilized primers
US9353406B2 (en) * 2010-10-22 2016-05-31 Fluidigm Corporation Universal probe assay methods
WO2012106668A2 (en) * 2011-02-03 2012-08-09 Fluidigm Corporation Multifunctional probe-primers
WO2012142003A2 (en) 2011-04-15 2012-10-18 Life Technologies Corporation Chemical ligation
CN108342453A (en) 2011-05-09 2018-07-31 富鲁达公司 Detection of nucleic acids based on probe
DK2710145T3 (en) 2011-05-17 2016-02-22 Dxterity Diagnostics Inc METHOD AND COMPOSITIONS FOR THE DETECTION OF TARGET NUCLEIC ACIDS
SG10201605049QA (en) 2011-05-20 2016-07-28 Fluidigm Corp Nucleic acid encoding reactions
EP2764100A4 (en) * 2011-10-03 2015-09-16 Univ Florida Rapid and reliable detection of infectious agents
AU2012362466A1 (en) 2011-12-30 2014-07-03 University Of Washington, Through Its Center For Commercialization Chromophoric polymer dots with narrow-band emission
US10648030B2 (en) 2012-01-13 2020-05-12 Affymetrix, Inc. Methods of determining the presence or absence of a plurality of target polynucleotides in a sample
US8838394B2 (en) * 2012-02-03 2014-09-16 California Institute Of Technology Signal encoding and decoding in multiplexed biochemical assays
AU2013221480B2 (en) 2012-02-14 2018-08-23 Cornell University Method for relative quantification of nucleic acid sequence, expression, or copy changes, using combined nuclease, ligation, and polymerase reactions
SG11201407901PA (en) 2012-05-21 2015-01-29 Fluidigm Corp Single-particle analysis of particle populations
ES2746237T3 (en) 2013-03-14 2020-03-05 Univ Cornell Method for the relative quantification of changes in DNA methylation, using combined nuclease, ligation, and polymerase reactions
ES2807222T3 (en) 2014-04-01 2021-02-22 Univ Cornell Detection of DNA methylation using combined ligation and nuclease reactions
CA2951561C (en) 2014-06-10 2023-04-18 Dxterity Diagnostics Incorporated Devices and methods for collecting and stabilizing biological samples
CN107002145B (en) 2014-10-08 2021-07-30 康奈尔大学 Method for identifying one or more nucleic acid molecules containing a target nucleotide sequence in a sample
US11118216B2 (en) 2015-09-08 2021-09-14 Affymetrix, Inc. Nucleic acid analysis by joining barcoded polynucleotide probes
EP3390658B1 (en) 2015-12-16 2022-08-03 Standard BioTools Inc. High-level multiplex amplification
EP3347497A4 (en) * 2016-01-31 2019-01-23 Affymetrix, Inc. Nucleic acid analysis by joining barcoded polynucleotide probes
US10066263B2 (en) 2016-06-17 2018-09-04 California Institute Of Technology Nucleic acid reactions and related methods and compositions

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001055454A1 (en) * 2000-01-28 2001-08-02 Althea Technologies, Inc. Methods for analysis of gene expression
WO2002070749A2 (en) * 2001-02-20 2002-09-12 Applied Gene Technologies, Inc. Methods and compositions for analyzing nucleic acids

Family Cites Families (21)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4988617A (en) 1988-03-25 1991-01-29 California Institute Of Technology Method of detecting a nucleotide change in nucleic acids
US5494810A (en) 1990-05-03 1996-02-27 Cornell Research Foundation, Inc. Thermostable ligase-mediated DNA amplifications system for the detection of genetic disease
DK51092D0 (en) 1991-05-24 1992-04-15 Ole Buchardt OLIGONUCLEOTIDE ANALOGUE DESCRIBED BY PEN, MONOMERIC SYNTHONES AND PROCEDURES FOR PREPARING THEREOF, AND APPLICATIONS THEREOF
ATE173767T1 (en) 1992-04-03 1998-12-15 Perkin Elmer Corp SAMPLES COMPOSITION AND METHODS
WO1996015271A1 (en) 1994-11-16 1996-05-23 Abbott Laboratories Multiplex ligations-dependent amplification
GB9609441D0 (en) 1996-05-04 1996-07-10 Zeneca Ltd Process
EP0912761A4 (en) 1996-05-29 2004-06-09 Cornell Res Foundation Inc Detection of nucleic acid sequence differences using coupled ligase detection and polymerase chain reactions
US7014994B1 (en) * 1999-03-19 2006-03-21 Cornell Research Foundation,Inc. Coupled polymerase chain reaction-restriction-endonuclease digestion-ligase detection reaction process
US6331393B1 (en) 1999-05-14 2001-12-18 University Of Southern California Process for high-throughput DNA methylation analysis
AU2001265121A1 (en) * 2000-05-30 2001-12-11 Applera Corporation Methods for detecting target nucleic acids using coupled ligation and amplification
US20030119004A1 (en) * 2001-12-05 2003-06-26 Wenz H. Michael Methods for quantitating nucleic acids using coupled ligation and amplification
EP1319718A1 (en) 2001-12-14 2003-06-18 Keygene N.V. High throughput analysis and detection of multiple target sequences
WO2003060163A2 (en) * 2001-12-28 2003-07-24 Keygene N.V. Discrimination and detection of target nucleotide sequences using mass spectrometry
US6960436B2 (en) * 2002-02-06 2005-11-01 Epigenomics Ag Quantitative methylation detection in DNA samples
US7176002B2 (en) * 2002-05-16 2007-02-13 Applera Corporation Universal-tagged oligonucleotide primers and methods of use
US20040214196A1 (en) 2002-09-19 2004-10-28 Applera Corporation Methods and compositions for detecting targets
JP2006500034A (en) 2002-09-19 2006-01-05 アプレラ コーポレイション Methods and compositions for detecting targets
US20040235005A1 (en) 2002-10-23 2004-11-25 Ernest Friedlander Methods and composition for detecting targets
US20040110134A1 (en) 2002-12-05 2004-06-10 Wenz H. Michael Methods for quantitating nucleic acids using coupled ligation and amplification
WO2005026389A2 (en) 2003-08-29 2005-03-24 MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. Ligation-based method of analysis of single nucleotide polymorphisms on genomic dna
ATE399884T1 (en) 2004-03-24 2008-07-15 Applera Corp CODING AND DECODING REACTIONS FOR DETERMINING TARGET POLYNUCLEOTIDES

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001055454A1 (en) * 2000-01-28 2001-08-02 Althea Technologies, Inc. Methods for analysis of gene expression
WO2002070749A2 (en) * 2001-02-20 2002-09-12 Applied Gene Technologies, Inc. Methods and compositions for analyzing nucleic acids

Also Published As

Publication number Publication date
US20050260640A1 (en) 2005-11-24
US7601821B2 (en) 2009-10-13
DE602005007874D1 (en) 2008-08-14
EP1727913A2 (en) 2006-12-06
ATE431433T1 (en) 2009-05-15
EP1727913B8 (en) 2009-08-19
JP2007530048A (en) 2007-11-01
WO2005098040A2 (en) 2005-10-20
DE602005014453D1 (en) 2009-06-25
US20050272071A1 (en) 2005-12-08
ATE399884T1 (en) 2008-07-15
WO2005098040A8 (en) 2005-12-01
EP2161346B1 (en) 2013-06-19
EP1730312A2 (en) 2006-12-13
EP2161346A1 (en) 2010-03-10
WO2005094532A2 (en) 2005-10-13
EP1730312B1 (en) 2008-07-02
EP1727913B1 (en) 2009-05-13
US7604937B2 (en) 2009-10-20
JP2007530051A (en) 2007-11-01
WO2005098040A3 (en) 2006-03-23

Similar Documents

Publication Publication Date Title
WO2005094532A3 (en) Encoding and decoding reactions for determining target polynucleotides
WO2005094532B1 (en) Encoding and decoding reactions for determining target polynucleotides
AU2001282920A1 (en) Methods for detecting and assaying nucleic acid sequences
WO2005047543A3 (en) Ligation assay
Lee et al. Single-molecule visualization of ROS-induced DNA damage in large DNA molecules
WO2001083823A8 (en) Methods and compositions for polynucleotide analysis using generic capture sequences
WO2005010494A3 (en) Multiplexed analyte detection
DE69528706T2 (en) COUPLED AMPFLICATION AND LIGATION PROCEDURE
WO2004027082A3 (en) Methods and compositions for detecting targets
WO2002066952A3 (en) Mass defect labeling for the determination of oligomer sequences
WO2008119081A8 (en) System and method for high resolution analysis of nucleic acids to detect sequence variations
WO2004099434A3 (en) Homogeneous multiplex screening assays and kits
WO2001036681A3 (en) Immunological detection of rna:dna hybrids on microarrays
WO2002083839A3 (en) P450 single nucleotide polymorphism biochip analysis
TW200613564A (en) Bacteria detection instrument, bacteria detection method and bacteria detection kit
WO2005090610A3 (en) Methods, kits and compositions pertaining to nucleic acid probes using fluorescence quenching
WO2005003386A3 (en) Oligonucleotide ligation assay by detecting released pyrophosphate
WO2004027081A3 (en) Methods and composition for detecting targets
WO1998014611A3 (en) Detection and identification of non-polio enteroviruses
HK1068377A1 (en) Analytical method and kit
DE59913055D1 (en) DNA detection via a strand-annealing complex
WO2004046344A3 (en) Polynucleotide sequence detection assays
SG153624A1 (en) Isometric primer extension method and kit for detection and quantification of specific nucleic acid
WO2004020603A3 (en) Analyte detection
WO2008140620A3 (en) Ultra sensitive biomolecule detection using double stranded dna co-loaded gold nanoparticles and co-immobilized capture molecules

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 BW BY BZ CA CH CN CO CR CU CZ DE DK DM DZ EC EE EG 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 NA NI NO NZ OM PG PH PL PT RO RU SC SD SE SG SK SL SM 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): BW GH GM KE LS MW MZ NA 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 IS IT LT LU MC NL PL PT RO SE SI SK TR BF BJ CF CG CI CM GA GN GQ GW ML MR NE SN TD TG

B Later publication of amended claims

Effective date: 20060117

DPEN Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed from 20040101)
WWE Wipo information: entry into national phase

Ref document number: 2005732398

Country of ref document: EP

WWE Wipo information: entry into national phase

Ref document number: 2007505187

Country of ref document: JP

NENP Non-entry into the national phase

Ref country code: DE

WWW Wipo information: withdrawn in national office

Country of ref document: DE

WWP Wipo information: published in national office

Ref document number: 2005732398

Country of ref document: EP

DPE1 Request for preliminary examination filed after expiration of 19th month from priority date (pct application filed from 20040101)