JP2024511760A - エラー補正のための固有分子識別子を有するトランスポゾンベースの技術を使用した指向性タグメンテーション配列決定ライブラリーの調製方法 - Google Patents

エラー補正のための固有分子識別子を有するトランスポゾンベースの技術を使用した指向性タグメンテーション配列決定ライブラリーの調製方法 Download PDF

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JP2024511760A
JP2024511760A JP2023557365A JP2023557365A JP2024511760A JP 2024511760 A JP2024511760 A JP 2024511760A JP 2023557365 A JP2023557365 A JP 2023557365A JP 2023557365 A JP2023557365 A JP 2023557365A JP 2024511760 A JP2024511760 A JP 2024511760A
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sequence
umi
nucleic acid
double
transposon
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スーザン シー． ベリティ，
ロバート スコット キュルステン，
ナイル アンソニー ゴームリー，
アンドリュー ビー． ケネディ，
サラ イー． シュルツァバーガー，
アンドリュー スラッター，
エマ ベル，
セバスチャン ジョルジ ガブリエル リクー，
グレース デサンティス，
フィオナ ケイパー，
ハン－ユー チュアン，
オリバー ジョン ミラー，
ジェイソン リチャード ベトリー，
スティーブン グロス，
マッツ エクストランド，
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イルミナ インコーポレイテッド
イルミナ ケンブリッジ リミテッド
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
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    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
    • C12N15/1068—Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
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    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/50—Other enzymatic activities
    • C12Q2521/507—Recombinase
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/191—Modifications characterised by incorporating an adaptor
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    • 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
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/179—Nucleic acid detection characterized by the use of physical, structural and functional properties the label being a nucleic acid

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  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
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  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
JP2023557365A 2021-03-31 2022-03-29 エラー補正のための固有分子識別子を有するトランスポゾンベースの技術を使用した指向性タグメンテーション配列決定ライブラリーの調製方法 Pending JP2024511760A (ja)

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US202163168802P 2021-03-31 2021-03-31
US63/168,802 2021-03-31
PCT/US2022/022379 WO2022212402A1 (en) 2021-03-31 2022-03-29 Methods of preparing directional tagmentation sequencing libraries using transposon-based technology with unique molecular identifiers for error correction

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JP2024511760A5 JP2024511760A5 (https=) 2025-04-08

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US (1) US20240026348A1 (https=)
EP (1) EP4314283A1 (https=)
JP (1) JP2024511760A (https=)
KR (1) KR20230164668A (https=)
CN (1) CN117015603A (https=)
AU (1) AU2022249289A1 (https=)
BR (1) BR112023019945A2 (https=)
CA (1) CA3211172A1 (https=)
IL (1) IL307164A (https=)
MX (1) MX2023011218A (https=)
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JP2026506068A (ja) * 2023-02-17 2026-02-20 ツイスト バイオサイエンス コーポレーション 正規化のための試薬および方法

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2017514487A (ja) * 2014-04-29 2017-06-08 イルミナ インコーポレイテッド 鋳型切換え及びタグメンテーションを用いる単一細胞の遺伝子発現の多重分析
JP2018526026A (ja) * 2015-08-28 2018-09-13 イルミナ インコーポレイテッド 単一細胞の核酸配列分析
WO2020144373A1 (en) * 2019-01-11 2020-07-16 Illumina Cambridge Limited Complex surface-bound transposome complexes
JP2020533272A (ja) * 2018-05-17 2020-11-19 イルミナ インコーポレイテッド 低減した増幅バイアスによるハイスループット単一細胞シークエンシング
CN112251422A (zh) * 2020-10-21 2021-01-22 华中农业大学 含独特分子标签序列的转座酶复合体及其应用

Family Cites Families (65)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA1323293C (en) 1987-12-11 1993-10-19 Keith C. Backman Assay using template-dependent nucleic acid probe reorganization
CA1341584C (en) 1988-04-06 2008-11-18 Bruce Wallace Method of amplifying and detecting nucleic acid sequences
AU3539089A (en) 1988-04-08 1989-11-03 Salk Institute For Biological Studies, The Ligase-based amplification method
JP2837868B2 (ja) * 1988-05-24 1998-12-16 アンリツ株式会社 分光装置
ATE144556T1 (de) 1988-06-24 1996-11-15 Amgen Inc Verfahren und mittel zum nachweis von nukleinsäuresequenzen
US5130238A (en) 1988-06-24 1992-07-14 Cangene Corporation Enhanced nucleic acid amplification process
ATE138106T1 (de) 1988-07-20 1996-06-15 David Segev Verfahren zur amplifizierung und zum nachweis von nukleinsäuresequenzen
US5185243A (en) 1988-08-25 1993-02-09 Syntex (U.S.A.) Inc. Method for detection of specific nucleic acid sequences
WO1991006678A1 (en) 1989-10-26 1991-05-16 Sri International Dna sequencing
US5573907A (en) 1990-01-26 1996-11-12 Abbott Laboratories Detecting and amplifying target nucleic acids using exonucleolytic activity
CA2035010C (en) 1990-01-26 1996-12-10 Keith C. Backman Method of amplifying target nucleic acids applicable to both polymerase and ligase chain reactions
US5455166A (en) 1991-01-31 1995-10-03 Becton, Dickinson And Company Strand displacement amplification
WO1995021271A1 (en) 1994-02-07 1995-08-10 Molecular Tool, Inc. Ligase/polymerase-mediated genetic bit analysistm of single nucleotide polymorphisms and its use in genetic analysis
US5677170A (en) 1994-03-02 1997-10-14 The Johns Hopkins University In vitro transposition of artificial transposons
WO1995025180A1 (en) 1994-03-16 1995-09-21 Gen-Probe Incorporated Isothermal strand displacement nucleic acid amplification
GB9620209D0 (en) 1996-09-27 1996-11-13 Cemu Bioteknik Ab Method of sequencing DNA
GB9626815D0 (en) 1996-12-23 1997-02-12 Cemu Bioteknik Ab Method of sequencing DNA
EP2319854B1 (en) 1997-01-08 2016-11-30 Sigma-Aldrich Co. LLC Bioconjugation Of Macromolecules
JP2002503954A (ja) 1997-04-01 2002-02-05 グラクソ、グループ、リミテッド 核酸増幅法
US7427678B2 (en) 1998-01-08 2008-09-23 Sigma-Aldrich Co. Method for immobilizing oligonucleotides employing the cycloaddition bioconjugation method
AR021833A1 (es) 1998-09-30 2002-08-07 Applied Research Systems Metodos de amplificacion y secuenciacion de acido nucleico
US20060275782A1 (en) 1999-04-20 2006-12-07 Illumina, Inc. Detection of nucleic acid reactions on bead arrays
US6355431B1 (en) 1999-04-20 2002-03-12 Illumina, Inc. Detection of nucleic acid amplification reactions using bead arrays
US20050244870A1 (en) 1999-04-20 2005-11-03 Illumina, Inc. Nucleic acid sequencing using microsphere arrays
US7244559B2 (en) 1999-09-16 2007-07-17 454 Life Sciences Corporation Method of sequencing a nucleic acid
US6274320B1 (en) 1999-09-16 2001-08-14 Curagen Corporation Method of sequencing a nucleic acid
US7955794B2 (en) 2000-09-21 2011-06-07 Illumina, Inc. Multiplex nucleic acid reactions
US6913884B2 (en) 2001-08-16 2005-07-05 Illumina, Inc. Compositions and methods for repetitive use of genomic DNA
US7611869B2 (en) 2000-02-07 2009-11-03 Illumina, Inc. Multiplexed methylation detection methods
US7582420B2 (en) 2001-07-12 2009-09-01 Illumina, Inc. Multiplex nucleic acid reactions
DK1259643T3 (da) 2000-02-07 2009-02-23 Illumina Inc Fremgangsmåde til detektion af nukleinsyre ved anvendelse af universel priming
US7001792B2 (en) 2000-04-24 2006-02-21 Eagle Research & Development, Llc Ultra-fast nucleic acid sequencing device and a method for making and using the same
ATE377093T1 (de) 2000-07-07 2007-11-15 Visigen Biotechnologies Inc Sequenzbestimmung in echtzeit
AU2002227156A1 (en) 2000-12-01 2002-06-11 Visigen Biotechnologies, Inc. Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
US7057026B2 (en) 2001-12-04 2006-06-06 Solexa Limited Labelled nucleotides
JP4638225B2 (ja) 2002-05-30 2011-02-23 ザ スクリプス リサーチ インスティテュート 銅を触媒とするアジドとアセチレンのライゲーション
WO2004018497A2 (en) 2002-08-23 2004-03-04 Solexa Limited Modified nucleotides for polynucleotide sequencing
US7595883B1 (en) 2002-09-16 2009-09-29 The Board Of Trustees Of The Leland Stanford Junior University Biological analysis arrangement and approach therefor
WO2005003304A2 (en) 2003-06-20 2005-01-13 Illumina, Inc. Methods and compositions for whole genome amplification and genotyping
US7259258B2 (en) 2003-12-17 2007-08-21 Illumina, Inc. Methods of attaching biological compounds to solid supports using triazine
EP1701785A1 (en) 2004-01-07 2006-09-20 Solexa Ltd. Modified molecular arrays
CA2579150C (en) 2004-09-17 2014-11-25 Pacific Biosciences Of California, Inc. Apparatus and method for analysis of molecules
GB0427236D0 (en) 2004-12-13 2005-01-12 Solexa Ltd Improved method of nucleotide detection
US7405281B2 (en) 2005-09-29 2008-07-29 Pacific Biosciences Of California, Inc. Fluorescent nucleotide analogs and uses therefor
GB0522310D0 (en) 2005-11-01 2005-12-07 Solexa Ltd Methods of preparing libraries of template polynucleotides
CA2648149A1 (en) 2006-03-31 2007-11-01 Solexa, Inc. Systems and devices for sequence by synthesis analysis
US8343746B2 (en) 2006-10-23 2013-01-01 Pacific Biosciences Of California, Inc. Polymerase enzymes and reagents for enhanced nucleic acid sequencing
GB2457851B (en) 2006-12-14 2011-01-05 Ion Torrent Systems Inc Methods and apparatus for measuring analytes using large scale fet arrays
US8349167B2 (en) 2006-12-14 2013-01-08 Life Technologies Corporation Methods and apparatus for detecting molecular interactions using FET arrays
US8262900B2 (en) 2006-12-14 2012-09-11 Life Technologies Corporation Methods and apparatus for measuring analytes using large scale FET arrays
WO2008093098A2 (en) 2007-02-02 2008-08-07 Illumina Cambridge Limited Methods for indexing samples and sequencing multiple nucleotide templates
WO2008096146A1 (en) 2007-02-07 2008-08-14 Solexa Limited Preparation of templates for methylation analysis
US20100137143A1 (en) 2008-10-22 2010-06-03 Ion Torrent Systems Incorporated Methods and apparatus for measuring analytes
US9080211B2 (en) 2008-10-24 2015-07-14 Epicentre Technologies Corporation Transposon end compositions and methods for modifying nucleic acids
EP2718465B1 (en) 2011-06-09 2022-04-13 Illumina, Inc. Method of making an analyte array
US9683230B2 (en) 2013-01-09 2017-06-20 Illumina Cambridge Limited Sample preparation on a solid support
WO2015160895A2 (en) 2014-04-15 2015-10-22 Illumina, Inc. Modified transposases for improved insertion sequence bias and increased dna input tolerance
US10844428B2 (en) 2015-04-28 2020-11-24 Illumina, Inc. Error suppression in sequenced DNA fragments using redundant reads with unique molecular indices (UMIS)
WO2017048993A1 (en) * 2015-09-15 2017-03-23 Takara Bio Usa, Inc. Methods for preparing a next generation sequencing (ngs) library from a ribonucleic acid (rna) sample and compositions for practicing the same
SG11201906428SA (en) 2017-01-18 2019-08-27 Illumina Inc Methods and systems for generation and error-correction of unique molecular index sets with heterogeneous molecular lengths
KR102866805B1 (ko) * 2017-02-21 2025-09-30 일루미나, 인코포레이티드 링커를 갖는 고정된 트랜스포좀을 사용한 태그먼트화
AU2018261332B2 (en) 2017-05-01 2024-12-05 Illumina, Inc. Optimal index sequences for multiplex massively parallel sequencing
EP3622089B1 (en) 2017-05-08 2024-07-17 Illumina, Inc. Method for sequencing using universal short adapters for indexing of polynucleotide samples
US11447818B2 (en) 2017-09-15 2022-09-20 Illumina, Inc. Universal short adapters with variable length non-random unique molecular identifiers
CN110870016B (zh) 2017-11-30 2024-09-06 伊鲁米那股份有限公司 用于序列变体呼出的验证方法和系统

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2017514487A (ja) * 2014-04-29 2017-06-08 イルミナ インコーポレイテッド 鋳型切換え及びタグメンテーションを用いる単一細胞の遺伝子発現の多重分析
JP2018526026A (ja) * 2015-08-28 2018-09-13 イルミナ インコーポレイテッド 単一細胞の核酸配列分析
JP2020533272A (ja) * 2018-05-17 2020-11-19 イルミナ インコーポレイテッド 低減した増幅バイアスによるハイスループット単一細胞シークエンシング
WO2020144373A1 (en) * 2019-01-11 2020-07-16 Illumina Cambridge Limited Complex surface-bound transposome complexes
CN112251422A (zh) * 2020-10-21 2021-01-22 华中农业大学 含独特分子标签序列的转座酶复合体及其应用

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AU2022249289A1 (en) 2023-08-17
US20240026348A1 (en) 2024-01-25
WO2022212402A1 (en) 2022-10-06
CA3211172A1 (en) 2022-10-06
EP4314283A1 (en) 2024-02-07
CN117015603A (zh) 2023-11-07
IL307164A (en) 2023-11-01
BR112023019945A2 (pt) 2023-11-14
KR20230164668A (ko) 2023-12-04
MX2023011218A (es) 2023-10-02

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