JP2022548504A - 低頻度バリアントの検出およびレポートを容易にするためのｄｎａライブラリー生成方法 - Google Patents

低頻度バリアントの検出およびレポートを容易にするためのｄｎａライブラリー生成方法 Download PDF

Info

Publication number
JP2022548504A
JP2022548504A JP2022512862A JP2022512862A JP2022548504A JP 2022548504 A JP2022548504 A JP 2022548504A JP 2022512862 A JP2022512862 A JP 2022512862A JP 2022512862 A JP2022512862 A JP 2022512862A JP 2022548504 A JP2022548504 A JP 2022548504A
Authority
JP
Japan
Prior art keywords
dna
sequencing
adapter
read
sequence
Prior art date
Legal status (The legal status 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 status listed.)
Pending
Application number
JP2022512862A
Other languages
English (en)
Japanese (ja)
Other versions
JP2022548504A5 (https=
Inventor
モルガーヌ、マシェレット
クリスティアン、ポッツォリーニ
アードリアン、ウィリグ
ヨナタン、ビーラー
チェンユ、シュ
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.)
Sophia Genetics SA
Original Assignee
Sophia Genetics SA
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 Sophia Genetics SA filed Critical Sophia Genetics SA
Publication of JP2022548504A publication Critical patent/JP2022548504A/ja
Publication of JP2022548504A5 publication Critical patent/JP2022548504A5/ja
Pending legal-status Critical Current

Links

Images

Classifications

    • 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
    • C12Q1/6869—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
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/191—Modifications characterised by incorporating an adaptor
    • 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
    • C12Q2525/204—Modifications characterised by specific length of the oligonucleotides
    • 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
    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122—Massive parallel sequencing

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Microbiology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biomedical Technology (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
JP2022512862A 2019-09-20 2020-09-21 低頻度バリアントの検出およびレポートを容易にするためのｄｎａライブラリー生成方法 Pending JP2022548504A (ja)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
EP19198542.3A EP3795685A1 (en) 2019-09-20 2019-09-20 Methods for dna library generation to facilitate the detection and reporting of low frequency variants
EP19198542.3 2019-09-20
PCT/EP2020/076246 WO2021053208A1 (en) 2019-09-20 2020-09-21 Methods for dna library generation to facilitate the detection and reporting of low frequency variants

Publications (2)

Publication Number Publication Date
JP2022548504A true JP2022548504A (ja) 2022-11-21
JP2022548504A5 JP2022548504A5 (https=) 2023-09-08

Family

ID=67998258

Family Applications (1)

Application Number Title Priority Date Filing Date
JP2022512862A Pending JP2022548504A (ja) 2019-09-20 2020-09-21 低頻度バリアントの検出およびレポートを容易にするためのｄｎａライブラリー生成方法

Country Status (8)

Country Link
US (1) US20220364080A1 (https=)
EP (3) EP3795685A1 (https=)
JP (1) JP2022548504A (https=)
KR (1) KR20220064959A (https=)
AU (1) AU2020349622A1 (https=)
BR (1) BR112022004821A2 (https=)
CA (1) CA3149056A1 (https=)
WO (1) WO2021053208A1 (https=)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
IT202200027138A1 (it) 2022-12-29 2024-06-29 Centro Di Riferimento Oncologico Metodo per la correzione di errori nel sequenziamento di acidi nucleici
CN117437978A (zh) * 2023-12-12 2024-01-23 北京旌准医疗科技有限公司 一种二代测序数据的低频基因突变分析方法、装置及其应用
US20260049302A1 (en) 2024-08-14 2026-02-19 Sophia Genetics S.A. Systems and methods for assaying various regions of a genome at different resolutions

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20160319345A1 (en) * 2015-04-28 2016-11-03 Illumina, Inc. Error suppression in sequenced dna fragments using redundant reads with unique molecular indices (umis)
WO2018144159A1 (en) * 2017-01-31 2018-08-09 Counsyl, Inc. Capture probes using positive and negative strands for duplex sequencing
WO2019002366A1 (en) * 2017-06-27 2019-01-03 F. Hoffmann-La Roche Ag MODULAR ADAPTERS OF NUCLEIC ACID
WO2019084245A1 (en) * 2017-10-27 2019-05-02 Myriad Women's Health, Inc. METHODS AND COMPOSITIONS FOR PREPARING NUCLEIC ACID LIBRARIES

Family Cites Families (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3475863B1 (en) 2016-06-22 2023-12-06 Sophia Genetics S.A. Methods for processing next-generation sequencing genomic data
GB201804642D0 (en) * 2018-03-22 2018-05-09 Inivata Ltd Methods of labelling nucleic acids
WO2019204702A1 (en) * 2018-04-20 2019-10-24 Board Of Regents, The University Of Texas System Error-correcting dna barcodes
WO2020043803A1 (en) * 2018-08-28 2020-03-05 Sophia Genetics S.A. Methods for asymmetric dna library generation and optionally integrated duplex sequencing

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20160319345A1 (en) * 2015-04-28 2016-11-03 Illumina, Inc. Error suppression in sequenced dna fragments using redundant reads with unique molecular indices (umis)
WO2018144159A1 (en) * 2017-01-31 2018-08-09 Counsyl, Inc. Capture probes using positive and negative strands for duplex sequencing
WO2019002366A1 (en) * 2017-06-27 2019-01-03 F. Hoffmann-La Roche Ag MODULAR ADAPTERS OF NUCLEIC ACID
WO2019084245A1 (en) * 2017-10-27 2019-05-02 Myriad Women's Health, Inc. METHODS AND COMPOSITIONS FOR PREPARING NUCLEIC ACID LIBRARIES

Also Published As

Publication number Publication date
EP4031664A1 (en) 2022-07-27
EP4031664C0 (en) 2025-02-26
CA3149056A1 (en) 2021-03-25
BR112022004821A2 (pt) 2022-08-23
WO2021053208A1 (en) 2021-03-25
EP3795685A1 (en) 2021-03-24
AU2020349622A1 (en) 2022-03-24
EP4570922A3 (en) 2025-09-17
EP4570922A2 (en) 2025-06-18
EP4031664B1 (en) 2025-02-26
KR20220064959A (ko) 2022-05-19
US20220364080A1 (en) 2022-11-17

Similar Documents

Publication Publication Date Title
US11898198B2 (en) Universal short adapters with variable length non-random unique molecular identifiers
AU2018210188B2 (en) Methods and systems for generation and error-correction of unique molecular index sets with heterogeneous molecular lengths
CN103484560B (zh) 精确序列信息及修饰碱基位置确定的方法
JP5389638B2 (ja) 制限断片に基づく分子マーカーのハイスループットな検出
CN105408496A (zh) 检测稀有突变和拷贝数变异的系统和方法
EP4031664B1 (en) Methods for dna library generation to facilitate the detection and reporting of low frequency variants
Saeed et al. Biological sequence analysis
US20240052339A1 (en) Rna probe for mutation profiling and use thereof
Esim et al. Determination of malignant melanoma by analysis of variation values
KR102942802B1 (ko) Ngs 분석에서의 itd 분석을 위한 씨드 서열의 생성 방법 및 장치
RU2766198C9 (ru) Способы и системы для получения наборов уникальных молекулярных индексов с гетерогенной длиной молекул и коррекции в них ошибок
Gulati et al. Computational and functional annotation at genomic scale: gene expression and analysis
HK40051826A (en) Methods and systems for generation and error-correction of unique molecular index sets with heterogeneous molecular lengths
HK40051826B (en) Methods and systems for generation and error-correction of unique molecular index sets with heterogeneous molecular lengths
HK40015418A (en) Methods and systems for generation and error-correction of unique molecular index sets with heterogeneous molecular lengths
HK40015418B (en) Methods and systems for generation and error-correction of unique molecular index sets with heterogeneous molecular lengths

Legal Events

Date Code Title Description
A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20230830

A621 Written request for application examination

Free format text: JAPANESE INTERMEDIATE CODE: A621

Effective date: 20230830

RD03 Notification of appointment of power of attorney

Free format text: JAPANESE INTERMEDIATE CODE: A7423

Effective date: 20240926

RD04 Notification of resignation of power of attorney

Free format text: JAPANESE INTERMEDIATE CODE: A7424

Effective date: 20241010

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20241119

A601 Written request for extension of time

Free format text: JAPANESE INTERMEDIATE CODE: A601

Effective date: 20250219

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20250418

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20250617

A601 Written request for extension of time

Free format text: JAPANESE INTERMEDIATE CODE: A601

Effective date: 20250917

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20251010

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20260127

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20260427