WO2009102878A3 - Method for archiving and clonal expansion - Google Patents

Method for archiving and clonal expansion Download PDF

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Publication number
WO2009102878A3
WO2009102878A3 PCT/US2009/033936 US2009033936W WO2009102878A3 WO 2009102878 A3 WO2009102878 A3 WO 2009102878A3 US 2009033936 W US2009033936 W US 2009033936W WO 2009102878 A3 WO2009102878 A3 WO 2009102878A3
Authority
WO
WIPO (PCT)
Prior art keywords
clonal expansion
archiving
sequences
libraries
polynucleotides
Prior art date
Application number
PCT/US2009/033936
Other languages
French (fr)
Other versions
WO2009102878A2 (en
Inventor
Nurith Kurn
Original Assignee
Nugen Technologies, Inc.
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 Nugen Technologies, Inc. filed Critical Nugen Technologies, Inc.
Priority to EP09711405A priority Critical patent/EP2247727A4/en
Publication of WO2009102878A2 publication Critical patent/WO2009102878A2/en
Publication of WO2009102878A3 publication Critical patent/WO2009102878A3/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

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The present method provides methods, libraries, and kits related to the archiving and clonal expansion of sequences related to target polynucleotide sequences. The method allow for the attachment of polynucleotides with defined 3' and or 5' sequences to solid surfaces. The polynucleotides attached to the solid substrates can be stored or archived as libraries and can subsequently be retrieved for analysis, for example by clonal expansion. In some embodiments, nucleotides attached to solid surfaces can be used for sequencing of nucleotide sequences related to target RNA or target RNA. The methods are applicable to total RNA and/or total DNA analysis.
PCT/US2009/033936 2008-02-12 2009-02-12 Method for archiving and clonal expansion WO2009102878A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
EP09711405A EP2247727A4 (en) 2008-02-12 2009-02-12 Method for archiving and clonal expansion

Applications Claiming Priority (8)

Application Number Priority Date Filing Date Title
US2814608P 2008-02-12 2008-02-12
US61/028,146 2008-02-12
US3869608P 2008-03-21 2008-03-21
US61/038,696 2008-03-21
US7499108P 2008-06-23 2008-06-23
US61/074,991 2008-06-23
US8581108P 2008-08-01 2008-08-01
US61/085,811 2008-08-01

Publications (2)

Publication Number Publication Date
WO2009102878A2 WO2009102878A2 (en) 2009-08-20
WO2009102878A3 true WO2009102878A3 (en) 2010-01-21

Family

ID=40957495

Family Applications (2)

Application Number Title Priority Date Filing Date
PCT/US2009/033936 WO2009102878A2 (en) 2008-02-12 2009-02-12 Method for archiving and clonal expansion
PCT/US2009/033964 WO2009102896A2 (en) 2008-02-12 2009-02-12 Isothermal nucleic acid amplification methods and compositions

Family Applications After (1)

Application Number Title Priority Date Filing Date
PCT/US2009/033964 WO2009102896A2 (en) 2008-02-12 2009-02-12 Isothermal nucleic acid amplification methods and compositions

Country Status (2)

Country Link
EP (2) EP2250283A2 (en)
WO (2) WO2009102878A2 (en)

Families Citing this family (28)

* Cited by examiner, † Cited by third party
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SG10201402770YA (en) 2009-04-02 2014-08-28 Fluidigm Corp Multi-primer amplification method for barcoding of target nucleic acids
US9309566B2 (en) 2010-12-17 2016-04-12 Life Technologies Corporation Methods, compositions, systems, apparatuses and kits for nucleic acid amplification
US20120156728A1 (en) 2010-12-17 2012-06-21 Life Technologies Corporation Clonal amplification of nucleic acid on solid surface with template walking
US9334531B2 (en) 2010-12-17 2016-05-10 Life Technologies Corporation Nucleic acid amplification
US9309557B2 (en) 2010-12-17 2016-04-12 Life Technologies Corporation Nucleic acid amplification
EP2369325A1 (en) 2010-03-12 2011-09-28 Eppendorf Ag Array analysis for online detection
KR101726238B1 (en) * 2010-10-15 2017-04-12 (주) 하임바이오텍 Method for non-specifically extending base sequences of target polynucleotide, primer composition for performing the method and kit for improving sensitivity of detecting target polynucleotide
TWI435935B (en) * 2010-12-06 2014-05-01 Univ Nat Cheng Kung Kit and method for rapidly detecting a target nucleic acid fragment
CN103890245B (en) 2011-05-20 2020-11-17 富鲁达公司 Nucleic acid encoding reactions
SG11201404243WA (en) 2012-01-26 2014-08-28 Nugen Technologies Inc Compositions and methods for targeted nucleic acid sequence enrichment and high efficiency library generation
US9487828B2 (en) 2012-05-10 2016-11-08 The General Hospital Corporation Methods for determining a nucleotide sequence contiguous to a known target nucleotide sequence
WO2013191775A2 (en) 2012-06-18 2013-12-27 Nugen Technologies, Inc. Compositions and methods for negative selection of non-desired nucleic acid sequences
US20150011396A1 (en) 2012-07-09 2015-01-08 Benjamin G. Schroeder Methods for creating directional bisulfite-converted nucleic acid libraries for next generation sequencing
EP2971130A4 (en) 2013-03-15 2016-10-05 Nugen Technologies Inc Sequential sequencing
CN105849264B (en) 2013-11-13 2019-09-27 纽亘技术公司 For identifying the composition and method that repeat sequencing reading
EP4219744A3 (en) 2014-01-27 2023-08-30 The General Hospital Corporation Methods of preparing nucleic acids for sequencing
WO2015131107A1 (en) 2014-02-28 2015-09-03 Nugen Technologies, Inc. Reduced representation bisulfite sequencing with diversity adaptors
GB201410646D0 (en) * 2014-06-14 2014-07-30 Illumina Cambridge Ltd Methods of increasing sequencing accuracy
CA2957633A1 (en) 2014-08-06 2016-02-11 Nugen Technologies, Inc. Digital measurements from targeted sequencing
EP3274470B1 (en) * 2015-03-25 2023-06-21 Angle Europe Limited Solid phase nucleic acid target capture and replication using strand displacing polymerases
WO2017106777A1 (en) 2015-12-16 2017-06-22 Fluidigm Corporation High-level multiplex amplification
CN105624302B (en) * 2016-02-04 2019-10-18 浙江大学 Composite label and its application for arthropod bio-diversity high-flux sequence
US10704082B2 (en) 2016-09-15 2020-07-07 ArcherDX, Inc. Methods of nucleic acid sample preparation
US10683531B2 (en) 2016-09-15 2020-06-16 ArcherDX, Inc. Methods of nucleic acid sample preparation for analysis of cell-free DNA
US11099202B2 (en) 2017-10-20 2021-08-24 Tecan Genomics, Inc. Reagent delivery system
WO2020172199A1 (en) * 2019-02-19 2020-08-27 Pioneer Biolabs, Llc Guide strand library construction and methods of use thereof
CN111662962B (en) * 2020-06-09 2023-06-23 珠海市坤元科技有限公司 Nucleic acid isothermal amplification method adopting bidirectional strand replacement loop circulation
GB202215624D0 (en) * 2022-10-21 2022-12-07 Dnae Diagnostics Ltd Clonal amplification

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20040096853A1 (en) * 2000-12-08 2004-05-20 Pascal Mayer Isothermal amplification of nucleic acids on a solid support
US20040203025A1 (en) * 1999-09-13 2004-10-14 Nurith Kurn Methods and compositions for linear isothermal amplification of polynucleotide sequences using a RNA DNA composite primer
US20050079510A1 (en) * 2003-01-29 2005-04-14 Jan Berka Bead emulsion nucleic acid amplification
US20050123950A1 (en) * 1999-03-19 2005-06-09 Takara Bio Nic. Method for amplifying nucleic acid sequence
US20070054301A1 (en) * 2005-09-06 2007-03-08 Gen-Probe Incorporated Methods, compositions and kits for isothermal amplification of nucleic acids

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
IL153504A0 (en) * 2001-03-09 2003-07-06 Nugen Technologies Inc Methods and compositions for amplification of rna sequences
EP1929046B1 (en) * 2005-09-07 2012-07-11 Nugen Technologies, Inc. Improved nucleic acid amplification procedure

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20050123950A1 (en) * 1999-03-19 2005-06-09 Takara Bio Nic. Method for amplifying nucleic acid sequence
US20040203025A1 (en) * 1999-09-13 2004-10-14 Nurith Kurn Methods and compositions for linear isothermal amplification of polynucleotide sequences using a RNA DNA composite primer
US20040096853A1 (en) * 2000-12-08 2004-05-20 Pascal Mayer Isothermal amplification of nucleic acids on a solid support
US20050079510A1 (en) * 2003-01-29 2005-04-14 Jan Berka Bead emulsion nucleic acid amplification
US20070054301A1 (en) * 2005-09-06 2007-03-08 Gen-Probe Incorporated Methods, compositions and kits for isothermal amplification of nucleic acids

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
CELINE ADESSI ET AL.: "Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms.", NUCLEIC ACIDS RESEARCH, vol. 28, no. 20, 2000, pages E87 *
NURITH KURN ET AL.: "Novel isothermal, linear nucleic acid amplification systems for highly multiplexed applications.", CLINICAL CHEMISTRY, vol. 51, no. 10, 2005, pages 1973 - 1981 *
See also references of EP2247727A4 *

Also Published As

Publication number Publication date
EP2247727A2 (en) 2010-11-10
EP2247727A4 (en) 2011-08-03
WO2009102896A3 (en) 2009-11-19
EP2250283A2 (en) 2010-11-17
WO2009102878A2 (en) 2009-08-20
WO2009102896A2 (en) 2009-08-20

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