JP2022533801A - 合成による高速フォワードシークエンシング - Google Patents

合成による高速フォワードシークエンシング Download PDF

Info

Publication number
JP2022533801A
JP2022533801A JP2022512704A JP2022512704A JP2022533801A JP 2022533801 A JP2022533801 A JP 2022533801A JP 2022512704 A JP2022512704 A JP 2022512704A JP 2022512704 A JP2022512704 A JP 2022512704A JP 2022533801 A JP2022533801 A JP 2022533801A
Authority
JP
Japan
Prior art keywords
region
polynucleotide
sequence
primer
sequencing
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
JP2022512704A
Other languages
English (en)
Japanese (ja)
Other versions
JP2022533801A5 (https=
Inventor
マーク プラット，
ギラッド アルモジー，
ドミトル ブリンザ，
エリアン トレパグニア，
オマー バラド，
ヨアヴ エツィオーニ，
フロリアン オーバーストラス，
Original Assignee
ウルティマ ジェノミクス， インコーポレイテッド
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 ウルティマ ジェノミクス， インコーポレイテッド filed Critical ウルティマ ジェノミクス， インコーポレイテッド
Publication of JP2022533801A publication Critical patent/JP2022533801A/ja
Publication of JP2022533801A5 publication Critical patent/JP2022533801A5/ja
Pending legal-status Critical Current

Links

Images

Classifications

    • 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
    • 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
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino 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
    • 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)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
JP2022512704A 2019-05-03 2020-05-01 合成による高速フォワードシークエンシング Pending JP2022533801A (ja)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US201962842534P 2019-05-03 2019-05-03
US62/842,534 2019-05-03
US201962904274P 2019-09-23 2019-09-23
US62/904,274 2019-09-23
US202062971530P 2020-02-07 2020-02-07
US62/971,530 2020-02-07
PCT/US2020/031163 WO2020227143A1 (en) 2019-05-03 2020-05-01 Fast-forward sequencing by synthesis methods

Publications (2)

Publication Number Publication Date
JP2022533801A true JP2022533801A (ja) 2022-07-25
JP2022533801A5 JP2022533801A5 (https=) 2023-05-11

Family

ID=73050882

Family Applications (1)

Application Number Title Priority Date Filing Date
JP2022512704A Pending JP2022533801A (ja) 2019-05-03 2020-05-01 合成による高速フォワードシークエンシング

Country Status (8)

Country Link
US (5) US20200377937A1 (https=)
EP (1) EP3963104A4 (https=)
JP (1) JP2022533801A (https=)
KR (1) KR102937518B1 (https=)
CN (1) CN114096682B (https=)
AU (2) AU2020269377C1 (https=)
IL (1) IL287707A (https=)
WO (1) WO2020227143A1 (https=)

Families Citing this family (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN120412737A (zh) 2019-05-03 2025-08-01 阿尔缇玛基因组学公司 用于检测核酸变体的方法
US20200377937A1 (en) * 2019-05-03 2020-12-03 Ultima Genomics, Inc. Fast-forward sequencing by synthesis methods
US12437839B2 (en) 2019-05-03 2025-10-07 Ultima Genomics, Inc. Methods for detecting nucleic acid variants
CN114423873B (zh) 2019-07-10 2025-06-13 阿尔缇玛基因组学公司 Rna测序方法
EP4081653B1 (en) 2019-12-23 2024-07-03 Singular Genomics Systems, Inc. Methods for long read sequencing
US20230407385A1 (en) * 2020-11-04 2023-12-21 Ultima Genomics, Inc. Methods and systems for phasing sequencing strands and long-range sequencing
EP4247979A4 (en) * 2020-11-18 2024-09-25 Ultima Genomics, Inc. METHODS AND SYSTEMS FOR DETECTION OF RESIDUAL DISEASE
WO2022204685A1 (en) * 2021-03-23 2022-09-29 Ultima Genomics, Inc. Methods for sequencing nucleic acid molecules with sequential barcodes
WO2024137873A1 (en) * 2022-12-22 2024-06-27 Ultima Genomics, Inc. Quantification of co-localized tag sequences using orthogonal sequence encoding
CN118581200A (zh) * 2023-03-01 2024-09-03 体学生物科技股份有限公司 核酸分子的检测方法、检测套组及检测卡匣
WO2025007019A2 (en) * 2023-06-30 2025-01-02 Ultima Genomics, Inc. Nucleic acid molecule sequencing systems and methods

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2001517948A (ja) * 1997-04-01 2001-10-09 グラクソ、グループ、リミテッド 核酸配列決定法
US20120252682A1 (en) * 2011-04-01 2012-10-04 Maples Corporate Services Limited Methods and systems for sequencing nucleic acids

Family Cites Families (52)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5714320A (en) 1993-04-15 1998-02-03 University Of Rochester Rolling circle synthesis of oligonucleotides and amplification of select randomized circular oligonucleotides
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
SG169356A1 (en) * 2006-02-08 2011-03-30 Illumina Cambridge Ltd Method for sequencing a polynucleotide template
US8364417B2 (en) 2007-02-15 2013-01-29 454 Life Sciences Corporation System and method to correct out of phase errors in DNA sequencing data by use of a recursive algorithm
US8301394B2 (en) 2006-02-16 2012-10-30 454 Life Sciences Corporation System and method for correcting primer extension errors in nucleic acid sequence data
US20100093986A1 (en) 2007-02-02 2010-04-15 Zwick Michael E Methods of direct genomic selection using high density oligonucleotide microarrays
US20090053724A1 (en) 2007-06-28 2009-02-26 454 Life Sciences Corporation System and method for adaptive reagent control in nucleic acid sequencing
EP2607496B1 (en) 2008-12-23 2014-07-16 Illumina, Inc. Methods useful in nucleic acid sequencing protocols
US8772473B2 (en) 2009-03-30 2014-07-08 The Regents Of The University Of California Mostly natural DNA sequencing by synthesis
US20100330569A1 (en) * 2009-04-23 2010-12-30 Intelligent Bio-Systems, Inc. Hydroxymethyl Linkers For Labeling Nucleotides
WO2011137368A2 (en) 2010-04-30 2011-11-03 Life Technologies Corporation Systems and methods for analyzing nucleic acid sequences
EP2633069B1 (en) 2010-10-26 2015-07-01 Illumina, Inc. Sequencing methods
US20130090860A1 (en) 2010-12-30 2013-04-11 Life Technologies Corporation Methods, systems, and computer readable media for making base calls in nucleic acid sequencing
US20190360034A1 (en) 2011-04-01 2019-11-28 Centrillion Technology Holdings Corporation Methods and systems for sequencing nucleic acids
CN103764845B (zh) 2011-04-08 2016-02-17 生命科技股份有限公司 用于合成测序中的相保护试剂流排序
KR101940833B1 (ko) * 2011-05-27 2019-01-21 제납시스 인크. 유전자 및 생물학적 분석을 위한 시스템 및 방법
US20130345066A1 (en) 2012-05-09 2013-12-26 Life Technologies Corporation Systems and methods for identifying sequence variation
US10192024B2 (en) 2012-05-18 2019-01-29 454 Life Sciences Corporation System and method for generation and use of optimal nucleotide flow orders
US20140052381A1 (en) 2012-08-14 2014-02-20 Life Technologies Corporation Systems and Methods for Detecting Homopolymer Insertions/Deletions
US20140296080A1 (en) 2013-03-14 2014-10-02 Life Technologies Corporation Methods, Systems, and Computer Readable Media for Evaluating Variant Likelihood
WO2015031689A1 (en) 2013-08-30 2015-03-05 Personalis, Inc. Methods and systems for genomic analysis
US9817944B2 (en) 2014-02-11 2017-11-14 Seven Bridges Genomics Inc. Systems and methods for analyzing sequence data
WO2016064703A1 (en) * 2014-10-21 2016-04-28 Life Technologies Corporation Methods, systems, and computer-readable media for blind deconvolution dephasing of nucleic acid sequencing data
CN106434873B (zh) 2015-08-13 2021-08-27 生捷科技控股公司 使核酸分子同步化的方法
EP3700856A4 (en) 2017-10-26 2021-12-15 Ultima Genomics, Inc. METHODS AND SYSTEMS FOR SEQUENCE CALL
US10344328B2 (en) 2017-11-17 2019-07-09 Ultima Genomics, Inc. Methods for biological sample processing and analysis
WO2019191003A1 (en) 2018-03-26 2019-10-03 Ultima Genomics, Inc. Methods of sequencing nucleic acid molecules
CN112654714B (zh) 2018-12-17 2024-10-11 伊卢米纳剑桥有限公司 用于测序的引物寡核苷酸
KR20260033107A (ko) 2019-02-19 2026-03-10 울티마 제노믹스, 인크. 광학 검출 및 시퀀싱을 위한 링커 및 방법
WO2020185790A1 (en) 2019-03-10 2020-09-17 Ultima Genomics, Inc. Methods and systems for sequence calling
EP3938832A4 (en) 2019-03-14 2023-03-22 Ultima Genomics, Inc. METHODS, DEVICES AND SYSTEMS FOR THE DETECTION AND ANALYSIS OF ANALYTES
CN120412737A (zh) 2019-05-03 2025-08-01 阿尔缇玛基因组学公司 用于检测核酸变体的方法
US20200377937A1 (en) 2019-05-03 2020-12-03 Ultima Genomics, Inc. Fast-forward sequencing by synthesis methods
CA3139535A1 (en) 2019-05-17 2020-11-26 Ultima Genomics, Inc. Methods and systems for detecting residual disease
CN119220641A (zh) 2019-05-31 2024-12-31 10X基因组学有限公司 检测目标核酸分子的方法
CN114423873B (zh) 2019-07-10 2025-06-13 阿尔缇玛基因组学公司 Rna测序方法
WO2022051296A1 (en) 2020-09-01 2022-03-10 Ultima Genomics, Inc. Methods and systems for reducing particle aggregation
US20230343416A1 (en) 2020-09-10 2023-10-26 Ultima Genomics, Inc. Methods and systems for sequence and variant calling
US20230407385A1 (en) 2020-11-04 2023-12-21 Ultima Genomics, Inc. Methods and systems for phasing sequencing strands and long-range sequencing
US20240043918A1 (en) 2020-11-04 2024-02-08 Ultima Genomics, Inc. Methods and systems for determinng sequencing read distances
EP4247979A4 (en) 2020-11-18 2024-09-25 Ultima Genomics, Inc. METHODS AND SYSTEMS FOR DETECTION OF RESIDUAL DISEASE
WO2022204685A1 (en) 2021-03-23 2022-09-29 Ultima Genomics, Inc. Methods for sequencing nucleic acid molecules with sequential barcodes
WO2023288319A1 (en) 2021-07-16 2023-01-19 Ultima Genomics, Inc. Polymerase assay
WO2023004421A1 (en) 2021-07-23 2023-01-26 Ultima Genomics, Inc. Methods and systems for increasing sequencing quality
WO2023010069A1 (en) 2021-07-29 2023-02-02 Ultima Genomics, Inc. Adaptive base calling systems and methods
WO2023010131A1 (en) 2021-07-30 2023-02-02 Ultima Genomics, Inc. Methods and systems for obtaining and processing sequencing data
WO2023060091A1 (en) 2021-10-04 2023-04-13 Ultima Genomics, Inc. Enhanced resolution imaging
WO2023081653A1 (en) 2021-11-02 2023-05-11 Ultima Genomics, Inc. Nucleic acid polymerase for incorporating labeled nucleotides
WO2023081883A2 (en) 2021-11-08 2023-05-11 Ultima Genomics, Inc. Methylation sequencing methods and compositions
WO2023141430A1 (en) 2022-01-18 2023-07-27 Ultima Genomics, Inc. Use of ethylene carbonate in nucleic acid sequencing methods
WO2023164505A2 (en) 2022-02-23 2023-08-31 Ultima Genomics, Inc. Methods and compositions for simultaneously sequencing a nucleic acid template sequence and copy sequence
WO2024102889A1 (en) 2022-11-10 2024-05-16 Ultima Genomics, Inc. Methods and systems for counter scan area mode imaging

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2001517948A (ja) * 1997-04-01 2001-10-09 グラクソ、グループ、リミテッド 核酸配列決定法
US20120252682A1 (en) * 2011-04-01 2012-10-04 Maples Corporate Services Limited Methods and systems for sequencing nucleic acids

Also Published As

Publication number Publication date
US20230060685A1 (en) 2023-03-02
CN114096682B (zh) 2025-06-13
AU2020269377A1 (en) 2021-11-25
CN114096682A (zh) 2022-02-25
IL287707A (en) 2021-12-01
WO2020227143A1 (en) 2020-11-12
US20210054442A1 (en) 2021-02-25
US20250197928A1 (en) 2025-06-19
AU2024219619A1 (en) 2024-10-10
US20200377937A1 (en) 2020-12-03
EP3963104A4 (en) 2023-11-08
US12209278B2 (en) 2025-01-28
KR102937518B1 (ko) 2026-03-11
CA3138862A1 (en) 2020-12-10
AU2020269377B2 (en) 2024-06-13
US20220170089A1 (en) 2022-06-02
EP3963104A1 (en) 2022-03-09
AU2020269377C1 (en) 2024-12-12
US11459609B2 (en) 2022-10-04
KR20220032516A (ko) 2022-03-15

Similar Documents

Publication Publication Date Title
JP2022533801A (ja) 合成による高速フォワードシークエンシング
AU2023282274B2 (en) Variant classifier based on deep neural networks
US20260112449A1 (en) Methods for detecting nucleic acid variants
US20180165411A1 (en) Systems and methods for assembling fragmented information
JP2018513445A (ja) 構造変異の特定及びバリアントコールデータを用いたフェージングのためのシステム及び方法
CA2888779A1 (en) Validation of genetic tests
US20160055293A1 (en) Systems, Algorithms, and Software for Molecular Inversion Probe (MIP) Design
CA3138862C (en) Fast-forward sequencing by synthesis methods
Bolognini Unraveling tandem repeat variation in personal genomes with long reads
Heinrich Aspects of Quality Control for Next Generation Sequencing Data in Medical Genetics
Chiara BIOINFORMATIC TOOLS FOR NEXT GENERATION GENOMICS

Legal Events

Date Code Title Description
A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20230428

A621 Written request for application examination

Free format text: JAPANESE INTERMEDIATE CODE: A621

Effective date: 20230428

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20240531

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20240902

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20241025

A02 Decision of refusal

Free format text: JAPANESE INTERMEDIATE CODE: A02

Effective date: 20250415