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WO2016002875A1 - 核酸分子数計測法 - Google Patents

核酸分子数計測法 Download PDF

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Publication number
WO2016002875A1
WO2016002875A1 PCT/JP2015/069114 JP2015069114W WO2016002875A1 WO 2016002875 A1 WO2016002875 A1 WO 2016002875A1 JP 2015069114 W JP2015069114 W JP 2015069114W WO 2016002875 A1 WO2016002875 A1 WO 2016002875A1
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WO
WIPO (PCT)
Prior art keywords
nucleic acid
acid molecules
bar code
sequences
code sequences
Prior art date
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Ceased
Application number
PCT/JP2015/069114
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English (en)
French (fr)
Inventor
菊也 加藤
洋児 久木田
亮 的場
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
DNA Chip Research Inc
Osaka Prefectural Hospital Organization
Original Assignee
DNA Chip Research Inc
Osaka Prefectural Hospital Organization
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 DNA Chip Research Inc, Osaka Prefectural Hospital Organization filed Critical DNA Chip Research Inc
Priority to US15/322,883 priority Critical patent/US10584331B2/en
Priority to EP15815855.0A priority patent/EP3165612B1/en
Priority to JP2016531441A priority patent/JP6125731B2/ja
Publication of WO2016002875A1 publication Critical patent/WO2016002875A1/ja
Anticipated expiration legal-status Critical
Priority to US16/773,570 priority patent/US11332737B2/en
Ceased legal-status Critical Current

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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
    • C12Q1/6869—Methods for sequencing
    • 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
    • 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
    • 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
    • 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
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Physics & Mathematics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Engineering & Computer Science (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biomedical Technology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Immunology (AREA)
  • Plant Pathology (AREA)
  • Data Mining & Analysis (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

　複数の核酸分子の混合物における分子数を計測するために、核酸塩基配列を決定する際に生じるリードエラーを検出することによって高精度に核酸分子数を計測する方法であって、複数の核酸分子の混合物にバーコード配列生成オリゴヌクレオチドを加えることにより、各核酸分子を構成する塩基配列に、該核酸分子に固有のバーコード配列を連結する工程と、前記バーコード配列を連結した核酸分子の塩基配列を決定する工程と、塩基配列を決定したバーコード配列のリードエラーを検出する工程と、前記塩基配列を決定したバーコード配列のリード数に基いて、塩基配列を決定した全バーコード配列のうち、該バーコード配列にリードエラーが存在しないものの割合を算出する工程と、を有し、前記バーコード配列生成オリゴヌクレオチドは最多で５種類の塩基からなり、リードエラーが存在しないバーコード配列の数が前記混合物における核酸分子数を示す、方法を提供する。
PCT/JP2015/069114 2014-07-02 2015-07-02 核酸分子数計測法 Ceased WO2016002875A1 (ja)

Priority Applications (4)

Application Number Priority Date Filing Date Title
US15/322,883 US10584331B2 (en) 2014-07-02 2015-07-02 Method for counting number of nucleic acid molecules
EP15815855.0A EP3165612B1 (en) 2014-07-02 2015-07-02 Method for counting number of nucleic acid molecules
JP2016531441A JP6125731B2 (ja) 2014-07-02 2015-07-02 核酸分子数計測法
US16/773,570 US11332737B2 (en) 2014-07-02 2020-01-27 Method for counting number of nucleic acid molecules

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201462020210P 2014-07-02 2014-07-02
US62/020,210 2014-07-02

Related Child Applications (2)

Application Number Title Priority Date Filing Date
US15/322,883 A-371-Of-International US10584331B2 (en) 2014-07-02 2015-07-02 Method for counting number of nucleic acid molecules
US16/773,570 Division US11332737B2 (en) 2014-07-02 2020-01-27 Method for counting number of nucleic acid molecules

Publications (1)

Publication Number Publication Date
WO2016002875A1 true WO2016002875A1 (ja) 2016-01-07

Family

ID=55019402

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/JP2015/069114 Ceased WO2016002875A1 (ja) 2014-07-02 2015-07-02 核酸分子数計測法

Country Status (4)

Country Link
US (2) US10584331B2 (ja)
EP (1) EP3165612B1 (ja)
JP (2) JP6125731B2 (ja)
WO (1) WO2016002875A1 (ja)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2018235938A1 (ja) * 2017-06-23 2018-12-27 国立研究開発法人理化学研究所 核酸をシークエンシングする方法および解析する方法
US12257457B2 (en) 2019-04-30 2025-03-25 General Electric Company Neuromodulation techniques for perturbation of physiological systems

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP6125731B2 (ja) * 2014-07-02 2017-05-10 株式会社Ｄｎａチップ研究所 核酸分子数計測法
CN109074430B (zh) 2016-05-26 2022-03-29 贝克顿迪金森公司 分子标记计数调整方法
CN109906274B (zh) 2016-11-08 2023-08-25 贝克顿迪金森公司 用于细胞标记分类的方法
JP7232180B2 (ja) 2016-11-08 2023-03-02 ベクトン・ディキンソン・アンド・カンパニー 発現プロファイル分類の方法
US20190095578A1 (en) * 2017-09-25 2019-03-28 Cellular Research, Inc. Immune receptor-barcode error correction
WO2019132010A1 (ja) * 2017-12-28 2019-07-04 タカラバイオ株式会社 塩基配列における塩基種を推定する方法、装置及びプログラム
EP3670670A1 (en) 2018-12-18 2020-06-24 Ricoh Company, Ltd. Nucleic acid analysis method, nucleic acid analysis program, and device for library preparation
BR112020026133A2 (pt) * 2019-01-24 2021-07-27 Illumina, Inc. métodos e sistemas para monitorar a saúde e as doenças dos órgãos

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US20130053256A1 (en) * 2011-08-31 2013-02-28 Life Technologies Corporation Methods, systems, computer readable media, and kits for sample identification

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US9315857B2 (en) * 2009-12-15 2016-04-19 Cellular Research, Inc. Digital counting of individual molecules by stochastic attachment of diverse label-tags
CN103154273A (zh) * 2010-09-21 2013-06-12 群体遗传学科技有限公司 通过分子计数提高等位基因调用的置信度
US9260753B2 (en) * 2011-03-24 2016-02-16 President And Fellows Of Harvard College Single cell nucleic acid detection and analysis
WO2013033721A1 (en) * 2011-09-02 2013-03-07 Atreca, Inc. Dna barcodes for multiplexed sequencing
JP6125731B2 (ja) * 2014-07-02 2017-05-10 株式会社Ｄｎａチップ研究所 核酸分子数計測法

Patent Citations (1)

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Publication number Priority date Publication date Assignee Title
US20130053256A1 (en) * 2011-08-31 2013-02-28 Life Technologies Corporation Methods, systems, computer readable media, and kits for sample identification

Non-Patent Citations (4)

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Title
KUKITA Y. ET AL.: "High-fidelity target sequencing of individual molecules identified using barcode sequences: de novo detection and absolute quantitation of mutations in plasma cell -free DNA from cancer patients.", DNA RES, vol. 22, no. 4, 29 June 2015 (2015-06-29), pages 269 - 277, XP055249604 *
SCHMITT MW . ET AL.: "Detection of ultra-rare mutations by next-generation sequencing.", PROC NATL ACAD SCI USA, vol. 109, no. 36, 2012, pages 14508 - 14513, XP055161683 *
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SHIROGUCHI K. ET AL.: "Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single- molecule barcodes.", PROC NATL ACAD SCI USA, vol. 109, no. 4, 2012, pages 1347 - 1352, XP055037481 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2018235938A1 (ja) * 2017-06-23 2018-12-27 国立研究開発法人理化学研究所 核酸をシークエンシングする方法および解析する方法
US12257457B2 (en) 2019-04-30 2025-03-25 General Electric Company Neuromodulation techniques for perturbation of physiological systems

Also Published As

Publication number Publication date
JPWO2016002875A1 (ja) 2017-05-25
JP6664575B2 (ja) 2020-03-13
JP6125731B2 (ja) 2017-05-10
JP2017099400A (ja) 2017-06-08
EP3165612B1 (en) 2021-08-18
US11332737B2 (en) 2022-05-17
US20200385708A1 (en) 2020-12-10
US20170204406A1 (en) 2017-07-20
EP3165612A4 (en) 2018-01-03
EP3165612A1 (en) 2017-05-10
US10584331B2 (en) 2020-03-10

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