WO2004069849A8 - Bead emulsion nucleic acid amplification - Google Patents

Bead emulsion nucleic acid amplification

Info

Publication number
WO2004069849A8
WO2004069849A8 PCT/US2004/002484 US2004002484W WO2004069849A8 WO 2004069849 A8 WO2004069849 A8 WO 2004069849A8 US 2004002484 W US2004002484 W US 2004002484W WO 2004069849 A8 WO2004069849 A8 WO 2004069849A8
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
acid amplification
bead emulsion
emulsion nucleic
acid templates
Prior art date
Application number
PCT/US2004/002484
Other languages
French (fr)
Other versions
WO2004069849A2 (en
WO2004069849A3 (en
Inventor
Jan Berka
Yi-Ju Chen
John H Leamon
Steven Lefkowitz
Kenton Lohman
Vinod Makhijani
Gary J Sarkis
Jonathan Rothberg
Michael Weiner
Maithreyan Srinivasan
Original Assignee
454 Corp
Jan Berka
Yi-Ju Chen
John H Leamon
Steven Lefkowitz
Kenton Lohman
Vinod Makhijani
Gary J Sarkis
Jonathan Rothberg
Michael Weiner
Maithreyan Srinivasan
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
Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=32854649&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2004069849(A8) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Application filed by 454 Corp, Jan Berka, Yi-Ju Chen, John H Leamon, Steven Lefkowitz, Kenton Lohman, Vinod Makhijani, Gary J Sarkis, Jonathan Rothberg, Michael Weiner, Maithreyan Srinivasan filed Critical 454 Corp
Priority to JP2006503133A priority Critical patent/JP4768598B2/en
Priority to AT04706051T priority patent/ATE448302T1/en
Priority to CA2513535A priority patent/CA2513535C/en
Priority to AU2004209001A priority patent/AU2004209001B2/en
Priority to ES04706051.2T priority patent/ES2338654T5/en
Priority to EP04706051.2A priority patent/EP1594980B2/en
Priority to DE602004024034T priority patent/DE602004024034D1/en
Publication of WO2004069849A2 publication Critical patent/WO2004069849A2/en
Publication of WO2004069849A3 publication Critical patent/WO2004069849A3/en
Publication of WO2004069849A8 publication Critical patent/WO2004069849A8/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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • B01L3/502707—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip characterised by the manufacture of the container or its components
    • B—PERFORMING OPERATIONS; TRANSPORTING
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    • B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • B01L3/502715—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C—CHEMISTRY; METALLURGY
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    • C12N15/09—Recombinant DNA-technology
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    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1075—Isolating an individual clone by screening libraries by coupling phenotype to genotype, not provided for in other groups of this subclass
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
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    • C12Q1/6813—Hybridisation assays
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    • C12Q1/6844—Nucleic acid amplification reactions
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    • 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
    • C12Q1/6865—Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
    • 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
    • C12Q1/6867—Replicase-based amplification, e.g. using Q-beta replicase
    • 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
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    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
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    • G01N21/17—Systems in which incident light is modified in accordance with the properties of the material investigated
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    • G01R33/1269—Measuring magnetic properties of articles or specimens of solids or fluids of molecules labeled with magnetic beads
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    • B01L2300/0636—Integrated biosensor, microarrays
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    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • B—PERFORMING OPERATIONS; TRANSPORTING
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    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/508—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above
    • B01L3/5085—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above for multiple samples, e.g. microtitration plates
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L7/00—Heating or cooling apparatus; Heat insulating devices
    • B01L7/52—Heating or cooling apparatus; Heat insulating devices with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples
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    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
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    • Y—GENERAL 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
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02P—CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS
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    • Y—GENERAL 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
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Abstract

Disclosed are methods for nucleic acid amplification wherein nucleic acid templates, beads, and amplification reaction solution are emulsified and the nucleic acid templates are amplified to provide clonal copies of the nucleic acid templates attached to the beads. Also disclosed are kits and apparatuses for performing the methods of the invention.
PCT/US2004/002484 2003-01-29 2004-01-28 Bead emulsion nucleic acid amplification WO2004069849A2 (en)

Priority Applications (7)

Application Number Priority Date Filing Date Title
JP2006503133A JP4768598B2 (en) 2003-01-29 2004-01-28 Bead emulsion nucleic acid amplification
AT04706051T ATE448302T1 (en) 2003-01-29 2004-01-28 NUCLEIC ACID AMPLIFICATION BASED ON BEAD EMULSION
CA2513535A CA2513535C (en) 2003-01-29 2004-01-28 Bead emulsion nucleic acid amplification
AU2004209001A AU2004209001B2 (en) 2003-01-29 2004-01-28 Bead emulsion nucleic acid amplification
ES04706051.2T ES2338654T5 (en) 2003-01-29 2004-01-28 Pearl emulsion nucleic acid amplification
EP04706051.2A EP1594980B2 (en) 2003-01-29 2004-01-28 Bead emulsion nucleic acid amplification
DE602004024034T DE602004024034D1 (en) 2003-01-29 2004-01-28 NUCLEIC ACID AMPLIFICATION BASED ON KINGGEL EMULSION

Applications Claiming Priority (14)

Application Number Priority Date Filing Date Title
US44347103P 2003-01-29 2003-01-29
US60/443,471 2003-01-29
US46507103P 2003-04-23 2003-04-23
US60/465,071 2003-04-23
US47660203P 2003-06-06 2003-06-06
US47650403P 2003-06-06 2003-06-06
US47631303P 2003-06-06 2003-06-06
US47659203P 2003-06-06 2003-06-06
US60/476,313 2003-06-06
US60/476,504 2003-06-06
US60/476,602 2003-06-06
US60/476,592 2003-06-06
US49798503P 2003-08-25 2003-08-25
US60/497,985 2003-08-25

Publications (3)

Publication Number Publication Date
WO2004069849A2 WO2004069849A2 (en) 2004-08-19
WO2004069849A3 WO2004069849A3 (en) 2005-03-24
WO2004069849A8 true WO2004069849A8 (en) 2007-04-19

Family

ID=32854649

Family Applications (4)

Application Number Title Priority Date Filing Date
PCT/US2004/002570 WO2005003375A2 (en) 2003-01-29 2004-01-28 Methods of amplifying and sequencing nucleic acids
PCT/US2004/002484 WO2004069849A2 (en) 2003-01-29 2004-01-28 Bead emulsion nucleic acid amplification
PCT/US2004/002571 WO2004070007A2 (en) 2003-01-29 2004-01-28 Method for preparing single-stranded dna libraries
PCT/US2004/002485 WO2004070005A2 (en) 2003-01-29 2004-01-28 Double ended sequencing

Family Applications Before (1)

Application Number Title Priority Date Filing Date
PCT/US2004/002570 WO2005003375A2 (en) 2003-01-29 2004-01-28 Methods of amplifying and sequencing nucleic acids

Family Applications After (2)

Application Number Title Priority Date Filing Date
PCT/US2004/002571 WO2004070007A2 (en) 2003-01-29 2004-01-28 Method for preparing single-stranded dna libraries
PCT/US2004/002485 WO2004070005A2 (en) 2003-01-29 2004-01-28 Double ended sequencing

Country Status (10)

Country Link
US (15) US7842457B2 (en)
EP (8) EP1594950A4 (en)
JP (9) JP4768598B2 (en)
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