WO2009133466A3 - Asymmetric adapter library construction - Google Patents
Asymmetric adapter library construction Download PDFInfo
- Publication number
- WO2009133466A3 WO2009133466A3 PCT/IB2009/005759 IB2009005759W WO2009133466A3 WO 2009133466 A3 WO2009133466 A3 WO 2009133466A3 IB 2009005759 W IB2009005759 W IB 2009005759W WO 2009133466 A3 WO2009133466 A3 WO 2009133466A3
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- library construction
- asymmetric adapter
- adapter library
- asymmetric
- compositions
- Prior art date
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Classifications
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/1034—Isolating an individual clone by screening libraries
- C12N15/1065—Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
-
- 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
- C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
- C12Q1/6855—Ligating adaptors
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
- C12N15/66—General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
-
- 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
- C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
- C12Q2525/10—Modifications characterised by
- C12Q2525/191—Modifications characterised by incorporating an adaptor
Abstract
The present invention provides methods and compositions for asymmetrically tagging a nucleic acid fragment using asymmetric adapters.
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US4932308P | 2008-04-30 | 2008-04-30 | |
US61/049,323 | 2008-04-30 |
Publications (2)
Publication Number | Publication Date |
---|---|
WO2009133466A2 WO2009133466A2 (en) | 2009-11-05 |
WO2009133466A3 true WO2009133466A3 (en) | 2010-10-07 |
Family
ID=41255488
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/IB2009/005759 WO2009133466A2 (en) | 2008-04-30 | 2009-04-29 | Asymmetric adapter library construction |
Country Status (2)
Country | Link |
---|---|
US (4) | US8029993B2 (en) |
WO (1) | WO2009133466A2 (en) |
Cited By (1)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN106459968B (en) * | 2014-01-31 | 2020-02-21 | 斯威夫特生物科学股份有限公司 | Improved method for processing DNA substrates |
Families Citing this family (59)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US20100130369A1 (en) * | 2007-04-23 | 2010-05-27 | Advanced Liquid Logic, Inc. | Bead-Based Multiplexed Analytical Methods and Instrumentation |
US8029993B2 (en) | 2008-04-30 | 2011-10-04 | Population Genetics Technologies Ltd. | Asymmetric adapter library construction |
WO2010133972A1 (en) * | 2009-05-22 | 2010-11-25 | Population Genetics Technologies Ltd | Sorting asymmetrically tagged nucleic acids by selective primer extension |
US20120178635A1 (en) * | 2009-08-06 | 2012-07-12 | University Of Virginia Patent Foundation | Compositions and methods for identifying and detecting sites of translocation and dna fusion junctions |
WO2011100058A1 (en) | 2010-02-09 | 2011-08-18 | Sangamo Biosciences, Inc. | Targeted genomic modification with partially single-stranded donor molecules |
US20120077716A1 (en) * | 2010-09-29 | 2012-03-29 | 454 Life Sciences Corporation | System and method for producing functionally distinct nucleic acid library ends through use of deoxyinosine |
WO2013142389A1 (en) | 2012-03-20 | 2013-09-26 | University Of Washington Through Its Center For Commercialization | Methods of lowering the error rate of massively parallel dna sequencing using duplex consensus sequencing |
ES2905448T3 (en) | 2012-05-10 | 2022-04-08 | Massachusetts Gen Hospital | Methods for determining a nucleotide sequence |
WO2014153408A1 (en) | 2013-03-19 | 2014-09-25 | Directed Genomics, Llc | Enrichment of target sequences |
WO2014182574A1 (en) | 2013-05-04 | 2014-11-13 | The Board Of Trustees Of The Leland Stanford Junior University | Enrichment of dna sequencing libraries from samples containing small amounts of target dna |
ES2693217T3 (en) | 2013-12-02 | 2018-12-10 | Personal Genome Diagnostics Inc. | Method to evaluate minority variants in a sample |
AU2015205612B2 (en) * | 2014-01-07 | 2020-12-03 | Llorenc Coll Mulet | Method for generating double stranded DNA libraries and sequencing methods for the identification of methylated cytosines |
EP4219744A3 (en) | 2014-01-27 | 2023-08-30 | The General Hospital Corporation | Methods of preparing nucleic acids for sequencing |
WO2015200378A1 (en) | 2014-06-23 | 2015-12-30 | The General Hospital Corporation | Genomewide unbiased identification of dsbs evaluated by sequencing (guide-seq) |
CN107075513B (en) * | 2014-09-12 | 2020-11-03 | 深圳华大智造科技有限公司 | Isolated oligonucleotides and their use in nucleic acid sequencing |
CN107075508B (en) * | 2014-11-21 | 2021-03-16 | 深圳华大智造科技有限公司 | Methods of constructing sequencing libraries using bubbly linker elements |
WO2016093838A1 (en) | 2014-12-11 | 2016-06-16 | New England Biolabs, Inc. | Enrichment of target sequences |
US10246702B1 (en) | 2015-02-23 | 2019-04-02 | New England Biolabs, Inc. | Compositions and methods for labeling target nucleic acid molecules |
US10221448B2 (en) | 2015-03-06 | 2019-03-05 | Pillar Biosciences Inc. | Selective amplification of overlapping amplicons |
WO2016168351A1 (en) * | 2015-04-15 | 2016-10-20 | The Board Of Trustees Of The Leland Stanford Junior University | Robust quantification of single molecules in next-generation sequencing using non-random combinatorial oligonucleotide barcodes |
WO2016201142A1 (en) | 2015-06-09 | 2016-12-15 | Life Technologies Corporation | Methods, systems, compositions, kits, apparatus and computer-readable media for molecular tagging |
AU2016319110B2 (en) | 2015-09-11 | 2022-01-27 | The General Hospital Corporation | Full interrogation of nuclease DSBs and sequencing (FIND-seq) |
AU2016331185A1 (en) | 2015-09-30 | 2018-04-26 | The General Hospital Corporation | Comprehensive in vitro reporting of cleavage events by sequencing (CIRCLE-seq) |
CN108603180A (en) * | 2015-11-25 | 2018-09-28 | 豪夫迈·罗氏有限公司 | The purifying of polymerase complex |
JP6995751B2 (en) | 2015-12-07 | 2022-02-04 | アーク バイオ, エルエルシー | Methods and Compositions for Making and Using Guide Nucleic Acids |
US11332784B2 (en) * | 2015-12-08 | 2022-05-17 | Twinstrand Biosciences, Inc. | Adapters, methods, and compositions for duplex sequencing |
CN108474026A (en) * | 2016-01-29 | 2018-08-31 | 豪夫迈·罗氏有限公司 | New adapter and application method for nucleic acid sequencing |
US11384382B2 (en) | 2016-04-14 | 2022-07-12 | Guardant Health, Inc. | Methods of attaching adapters to sample nucleic acids |
WO2017181146A1 (en) | 2016-04-14 | 2017-10-19 | Guardant Health, Inc. | Methods for early detection of cancer |
EP3485033B1 (en) * | 2016-07-12 | 2022-09-28 | Qiagen Sciences, LLC | Single end duplex dna sequencing |
JP7048105B2 (en) | 2016-07-15 | 2022-04-05 | ザ リージェンツ オブ ザ ユニバーシティ オブ カリフォルニア | How to generate a nucleic acid library |
WO2018015318A1 (en) * | 2016-07-18 | 2018-01-25 | F. Hoffmann-La Roche Ag | Method for generating single-stranded circular dna libraries for single molecule sequencing |
EP3510170B1 (en) | 2016-09-12 | 2021-10-13 | Technische Hochschule Wildau | Convertible adapters |
GB201615486D0 (en) | 2016-09-13 | 2016-10-26 | Inivata Ltd | Methods for labelling nucleic acids |
EP4353830A2 (en) | 2016-09-15 | 2024-04-17 | ArcherDX, LLC | Methods of nucleic acid sample preparation for analysis of cell-free dna |
WO2018053362A1 (en) | 2016-09-15 | 2018-03-22 | ArcherDX, Inc. | Methods of nucleic acid sample preparation |
EP3559255A1 (en) | 2016-12-23 | 2019-10-30 | Grail, Inc. | Methods for high efficiency library preparation using double-stranded adapters |
US10711269B2 (en) | 2017-01-18 | 2020-07-14 | Agilent Technologies, Inc. | Method for making an asymmetrically-tagged sequencing library |
WO2018183918A1 (en) * | 2017-03-30 | 2018-10-04 | Grail, Inc. | Enhanced ligation in sequencing library preparation |
WO2018183897A1 (en) | 2017-03-31 | 2018-10-04 | Grail, Inc. | Higher target capture efficiency using probe extension |
CA3065384A1 (en) * | 2017-06-07 | 2018-12-13 | Arc Bio, Llc | Creation and use of guide nucleic acids |
US10155939B1 (en) | 2017-06-15 | 2018-12-18 | New England Biolabs, Inc. | Method for performing multiple enzyme reactions in a single tube |
US11542540B2 (en) | 2017-06-16 | 2023-01-03 | Life Technologies Corporation | Control nucleic acids, and compositions, kits, and uses thereof |
US10920268B2 (en) * | 2017-07-18 | 2021-02-16 | Pacific Biosciences Of California, Inc. | Methods and compositions for isolating asymmetric nucleic acid complexes |
EP3672612A4 (en) | 2017-08-23 | 2021-09-29 | The General Hospital Corporation | Engineered crispr-cas9 nucleases with altered pam specificity |
WO2019075197A1 (en) | 2017-10-11 | 2019-04-18 | The General Hospital Corporation | Methods for detecting site-specific and spurious genomic deamination induced by base editing technologies |
US11739367B2 (en) | 2017-11-08 | 2023-08-29 | Twinstrand Biosciences, Inc. | Reagents and adapters for nucleic acid sequencing and methods for making such reagents and adapters |
CA3087001A1 (en) | 2018-01-12 | 2019-07-18 | Claret Bioscience, Llc | Methods and compositions for analyzing nucleic acid |
CN112313241A (en) | 2018-04-17 | 2021-02-02 | 总医院公司 | Sensitive in vitro assay of substrate preference and site for nucleic acid binding, modification, and cleavage reagents |
EP3802864A1 (en) | 2018-06-06 | 2021-04-14 | The Regents Of The University Of California | Methods of producing nucleic acid libraries and compositions and kits for practicing same |
KR20210059694A (en) | 2018-07-12 | 2021-05-25 | 트윈스트랜드 바이오사이언시스, 인코포레이티드 | Methods and reagents for identifying genome editing, clonal expansion, and related fields |
EP3899031A2 (en) | 2018-12-19 | 2021-10-27 | New England Biolabs, Inc. | Methods for nucleic acid target enrichment |
KR102159008B1 (en) * | 2019-10-18 | 2020-09-23 | 고려대학교 산학협력단 | Self-priming and replicating hairpin adaptor for NGS library preparation and method for making NGS library using the same |
KR102279846B1 (en) | 2019-12-26 | 2021-07-21 | 이원다이애그노믹스(주) | Double-strands nucleic acid molecules and method for removing free adapters in DNA library using the same |
WO2021178893A2 (en) | 2020-03-06 | 2021-09-10 | Singular Genomics Systems, Inc. | Linked paired strand sequencing |
WO2022053610A1 (en) * | 2020-09-11 | 2022-03-17 | Illumina Cambridge Limited | Methods of enriching a target sequence from a sequencing library using hairpin adaptors |
EP4294941A1 (en) * | 2021-02-18 | 2023-12-27 | F. Hoffmann-La Roche AG | Structure to prevent threading of nucleic acid templates through a nanopore during sequencing |
WO2023081485A1 (en) | 2021-11-08 | 2023-05-11 | Pacific Biosciences Of California, Inc. | Stepwise sequencing of a polynucleotide with a homogenous reaction mixture |
WO2023172934A1 (en) | 2022-03-09 | 2023-09-14 | New England Biolabs, Inc. | Target enrichment |
Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US20070065834A1 (en) * | 2005-09-19 | 2007-03-22 | Hillis William D | Method and sequences for determinate nucleic acid hybridization |
US20070172839A1 (en) * | 2006-01-24 | 2007-07-26 | Smith Douglas R | Asymmetrical adapters and methods of use thereof |
WO2007087262A2 (en) * | 2006-01-23 | 2007-08-02 | Population Genetics Technologies Ltd. | Selective genome amplification |
Family Cites Families (17)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5712126A (en) * | 1995-08-01 | 1998-01-27 | Yale University | Analysis of gene expression by display of 3-end restriction fragments of CDNA |
US6287825B1 (en) * | 1998-09-18 | 2001-09-11 | Molecular Staging Inc. | Methods for reducing the complexity of DNA sequences |
JP2003527087A (en) | 1999-08-13 | 2003-09-16 | イェール・ユニバーシティ | Binary coded array tags |
AU2001278934A1 (en) | 2000-07-18 | 2002-01-30 | Pioneer Hi-Bred International, Inc. | Methods of transforming plants and identifying parental origin of a chromosome in those plants |
US6777180B1 (en) | 2000-11-28 | 2004-08-17 | Trustees Of Columbia University In The City Of New York | Method for full-length cDNA cloning using degenerate stem-loop annealing primers |
US20040209299A1 (en) | 2003-03-07 | 2004-10-21 | Rubicon Genomics, Inc. | In vitro DNA immortalization and whole genome amplification using libraries generated from randomly fragmented DNA |
EP2202322A1 (en) | 2003-10-31 | 2010-06-30 | AB Advanced Genetic Analysis Corporation | Methods for producing a paired tag from a nucleic acid sequence and methods of use thereof |
GB0400584D0 (en) | 2004-01-12 | 2004-02-11 | Solexa Ltd | Nucleic acid chacterisation |
CA2555377A1 (en) * | 2004-02-12 | 2005-09-01 | Compass Genetics, Llc | Genetic analysis by sequence-specific sorting |
ATE510930T1 (en) | 2005-08-02 | 2011-06-15 | Rubicon Genomics Inc | COMPOSITIONS AND METHODS FOR EDITING AND AMPLIFICATION OF DNA USING MULTIPLE ENZYMES IN A SINGLE REACTION |
GB0522310D0 (en) | 2005-11-01 | 2005-12-07 | Solexa Ltd | Methods of preparing libraries of template polynucleotides |
WO2007111937A1 (en) | 2006-03-23 | 2007-10-04 | Applera Corporation | Directed enrichment of genomic dna for high-throughput sequencing |
US20090093378A1 (en) | 2007-08-29 | 2009-04-09 | Helen Bignell | Method for sequencing a polynucleotide template |
US8029993B2 (en) * | 2008-04-30 | 2011-10-04 | Population Genetics Technologies Ltd. | Asymmetric adapter library construction |
WO2010133972A1 (en) | 2009-05-22 | 2010-11-25 | Population Genetics Technologies Ltd | Sorting asymmetrically tagged nucleic acids by selective primer extension |
US20110105364A1 (en) | 2009-11-02 | 2011-05-05 | Nugen Technologies, Inc. | Compositions and methods for targeted nucleic acid sequence selection and amplification |
US20120196279A1 (en) | 2011-02-02 | 2012-08-02 | Pacific Biosciences Of California, Inc. | Methods and compositions for nucleic acid sample preparation |
-
2009
- 2009-04-29 US US12/432,080 patent/US8029993B2/en active Active
- 2009-04-29 WO PCT/IB2009/005759 patent/WO2009133466A2/en active Application Filing
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2011
- 2011-09-01 US US13/224,134 patent/US8288097B2/en active Active
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2012
- 2012-09-11 US US13/610,410 patent/US8420319B2/en active Active
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2013
- 2013-03-11 US US13/794,170 patent/US8883990B2/en active Active
Patent Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US20070065834A1 (en) * | 2005-09-19 | 2007-03-22 | Hillis William D | Method and sequences for determinate nucleic acid hybridization |
WO2007087262A2 (en) * | 2006-01-23 | 2007-08-02 | Population Genetics Technologies Ltd. | Selective genome amplification |
US20070172839A1 (en) * | 2006-01-24 | 2007-07-26 | Smith Douglas R | Asymmetrical adapters and methods of use thereof |
Non-Patent Citations (1)
Title |
---|
SIPA KATARZYNA ET AL: "Effect of base modifications on structure, thermodynamic stability, and gene silencing activity of short interfering RNA", August 2007, RNA (COLD SPRING HARBOR), VOL. 13, NR. 8, PAGE(S) 1301-1316, ISSN: 1355-8382, XP002595128 * |
Cited By (1)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN106459968B (en) * | 2014-01-31 | 2020-02-21 | 斯威夫特生物科学股份有限公司 | Improved method for processing DNA substrates |
Also Published As
Publication number | Publication date |
---|---|
US8883990B2 (en) | 2014-11-11 |
WO2009133466A2 (en) | 2009-11-05 |
US8029993B2 (en) | 2011-10-04 |
US20140030704A1 (en) | 2014-01-30 |
US20090275087A1 (en) | 2009-11-05 |
US20130029380A1 (en) | 2013-01-31 |
US20120083017A1 (en) | 2012-04-05 |
US8420319B2 (en) | 2013-04-16 |
US8288097B2 (en) | 2012-10-16 |
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