CA3136034A1 - Methods of sequencing nucleic acid molecules - Google Patents

Methods of sequencing nucleic acid molecules Download PDF

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Publication number
CA3136034A1
CA3136034A1 CA3136034A CA3136034A CA3136034A1 CA 3136034 A1 CA3136034 A1 CA 3136034A1 CA 3136034 A CA3136034 A CA 3136034A CA 3136034 A CA3136034 A CA 3136034A CA 3136034 A1 CA3136034 A1 CA 3136034A1
Authority
CA
Canada
Prior art keywords
nucleotides
reaction mixture
nucleic acid
acid molecules
base type
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
CA3136034A
Other languages
English (en)
French (fr)
Inventor
Florian OBERSTRASS
Gilad Almogy
Linda Lee
Eliane Trepagnier
Geunwon JUNG
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.)
Ultima Genomics Inc
Original Assignee
Individual
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 Individual filed Critical Individual
Publication of CA3136034A1 publication Critical patent/CA3136034A1/en
Pending legal-status Critical Current

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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
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • 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
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • C12N9/1241—Nucleotidyltransferases (2.7.7)
    • C12N9/1252—DNA-directed DNA polymerase (2.7.7.7), i.e. DNA replicase
    • 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
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/6428—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • 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
    • C12Q2525/185—Modifications characterised by incorporating bases where the precise position of the bases in the nucleic acid string is important
    • 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
    • C12Q2525/186—Modifications characterised by incorporating a non-extendable or blocking moiety
    • 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
    • C12Q2539/00—Reactions characterised by analysis of gene expression or genome comparison
    • C12Q2539/10—The purpose being sequence identification by analysis of gene expression or genome comparison characterised by
    • C12Q2539/101—Subtraction analysis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence
    • G01N21/6428—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • G01N2021/6439—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" with indicators, stains, dyes, tags, labels, marks

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Genetics & Genomics (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Optics & Photonics (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Medicinal Chemistry (AREA)
  • Biomedical Technology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CA3136034A 2019-05-03 2020-05-01 Methods of sequencing nucleic acid molecules Pending CA3136034A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201962842534P 2019-05-03 2019-05-03
US62/842,534 2019-05-03
US201962909389P 2019-10-02 2019-10-02
US62/909,389 2019-10-02
PCT/US2020/031196 WO2020227161A1 (en) 2019-05-03 2020-05-01 Methods of sequencing nucleic acid molecules

Publications (1)

Publication Number Publication Date
CA3136034A1 true CA3136034A1 (en) 2020-11-12

Family

ID=73051356

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3136034A Pending CA3136034A1 (en) 2019-05-03 2020-05-01 Methods of sequencing nucleic acid molecules

Country Status (8)

Country Link
US (1) US20220154272A1 (https=)
EP (1) EP3963106A4 (https=)
JP (1) JP7556886B2 (https=)
KR (1) KR102934116B1 (https=)
CN (1) CN114222824B (https=)
AU (1) AU2020267371A1 (https=)
CA (1) CA3136034A1 (https=)
WO (1) WO2020227161A1 (https=)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
WO2022197942A1 (en) * 2021-03-17 2022-09-22 Singular Genomics Systems, Inc. Phase protective reagent flow ordering
CN115917006A (zh) * 2021-09-07 2023-04-04 深圳华大智造科技股份有限公司 一种用于分析靶多核苷酸的序列的方法
WO2024086277A1 (en) * 2022-10-20 2024-04-25 Ultima Genomics, Inc. Sequencing with concatemerization

Family Cites Families (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4962020A (en) 1988-07-12 1990-10-09 President And Fellows Of Harvard College DNA sequencing
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
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
US10597643B2 (en) * 2016-04-29 2020-03-24 Omniome, Inc. Polymerases engineered to reduce nucleotide-independent DNA binding
EP3449012B1 (en) * 2016-04-29 2020-12-23 Omniome, Inc. Sequencing method employing ternary complex destabilization to identify cognate nucleotides
WO2018064297A1 (en) * 2016-09-29 2018-04-05 Ultima Genomics, Inc. Systems and methods for nucleic acid sequencing
WO2019191003A1 (en) * 2018-03-26 2019-10-03 Ultima Genomics, Inc. Methods of sequencing nucleic acid molecules

Also Published As

Publication number Publication date
EP3963106A1 (en) 2022-03-09
CN114222824B (zh) 2024-07-30
CN114222824A (zh) 2022-03-22
JP7556886B2 (ja) 2024-09-26
JP2022531589A (ja) 2022-07-07
WO2020227161A1 (en) 2020-11-12
KR102934116B1 (ko) 2026-03-04
US20220154272A1 (en) 2022-05-19
EP3963106A4 (en) 2023-01-25
KR20220016078A (ko) 2022-02-08
AU2020267371A1 (en) 2021-12-02

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