LT3368688T - Kompozicijos ir būdai, skirti modifikuotų citozinų nustatymui sekvenavimu - Google Patents

Kompozicijos ir būdai, skirti modifikuotų citozinų nustatymui sekvenavimu

Info

Publication number
LT3368688T
LT3368688T LTEP16794858.7T LT16794858T LT3368688T LT 3368688 T LT3368688 T LT 3368688T LT 16794858 T LT16794858 T LT 16794858T LT 3368688 T LT3368688 T LT 3368688T
Authority
LT
Lithuania
Prior art keywords
sequencing
compositions
methods
modified cytosines
determining modified
Prior art date
Application number
LTEP16794858.7T
Other languages
English (en)
Inventor
Romualdas Vaisvila
Zhiyi Sun
Shengxi Guan
Lana SALEH
Laurence Ettwiller
Theodore Davis
Original Assignee
New England Biolabs, Inc.
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
Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=57286864&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=LT3368688(T) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Application filed by New England Biolabs, Inc. filed Critical New England Biolabs, Inc.
Publication of LT3368688T publication Critical patent/LT3368688T/lt

Links

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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6858—Allele-specific amplification
    • 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
    • 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
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0071—Oxidoreductases (1.) acting on paired donors with incorporation of molecular oxygen (1.14)
    • 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
    • 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
    • C12Q1/6872—Methods for sequencing involving mass spectrometry
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y114/00—Oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (1.14)
    • C12Y114/11—Oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (1.14) with 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (1.14.11)
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Immunology (AREA)
  • Biophysics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Medicinal Chemistry (AREA)
  • Biomedical Technology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
LTEP16794858.7T 2015-10-30 2016-10-28 Kompozicijos ir būdai, skirti modifikuotų citozinų nustatymui sekvenavimu LT3368688T (lt)

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US201562248872P 2015-10-30 2015-10-30
US201562257284P 2015-11-19 2015-11-19
US201562271679P 2015-12-28 2015-12-28
US201662300396P 2016-02-26 2016-02-26
US201662325626P 2016-04-21 2016-04-21
PCT/US2016/059447 WO2017075436A1 (en) 2015-10-30 2016-10-28 Compositions and methods for determining modified cytosines by sequencing

Publications (1)

Publication Number Publication Date
LT3368688T true LT3368688T (lt) 2021-03-10

Family

ID=57286864

Family Applications (1)

Application Number Title Priority Date Filing Date
LTEP16794858.7T LT3368688T (lt) 2015-10-30 2016-10-28 Kompozicijos ir būdai, skirti modifikuotų citozinų nustatymui sekvenavimu

Country Status (5)

Country Link
US (4) US10619200B2 (lt)
EP (2) EP3368688B1 (lt)
CN (2) CN108699598B (lt)
LT (1) LT3368688T (lt)
WO (1) WO2017075436A1 (lt)

Families Citing this family (30)

* Cited by examiner, † Cited by third party
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US9115386B2 (en) 2008-09-26 2015-08-25 Children's Medical Center Corporation Selective oxidation of 5-methylcytosine by TET-family proteins
EP3425065B1 (en) 2011-12-13 2021-04-21 Oslo Universitetssykehus HF Methods and kits for detection of methylation status
CN104955960A (zh) 2012-11-30 2015-09-30 剑桥表现遗传学有限公司 用于修饰的核苷酸的氧化剂
CN108350453A (zh) 2015-09-11 2018-07-31 通用医疗公司 核酸酶dsb的完全查询和测序(find-seq)
WO2017059245A2 (en) 2015-09-30 2017-04-06 Trustees Of Boston University Deadman and passcode microbial kill switches
US10260088B2 (en) * 2015-10-30 2019-04-16 New England Biolabs, Inc. Compositions and methods for analyzing modified nucleotides
CN108699598B (zh) * 2015-10-30 2022-11-15 新英格兰生物实验室公司 用于分析修饰的核苷酸的组合物和方法
WO2018031760A1 (en) 2016-08-10 2018-02-15 Grail, Inc. Methods of preparing dual-indexed dna libraries for bisulfite conversion sequencing
US10155939B1 (en) 2017-06-15 2018-12-18 New England Biolabs, Inc. Method for performing multiple enzyme reactions in a single tube
CN107447044A (zh) * 2017-08-09 2017-12-08 华子昂 一种检测大肠杆菌λ噬菌体全基因组碱基修饰单倍型的方法
US11286468B2 (en) 2017-08-23 2022-03-29 The General Hospital Corporation Engineered CRISPR-Cas9 nucleases with altered PAM specificity
US11725228B2 (en) 2017-10-11 2023-08-15 The General Hospital Corporation Methods for detecting site-specific and spurious genomic deamination induced by base editing technologies
WO2019204378A1 (en) * 2018-04-17 2019-10-24 The General Hospital Corporation Sensitive in vitro assays for substrate preferences and sites of nucleic acid binding, modifying, and cleaving agents
US11932899B2 (en) 2018-06-07 2024-03-19 10X Genomics, Inc. Methods and systems for characterizing nucleic acid molecules
WO2020069350A1 (en) 2018-09-27 2020-04-02 Grail, Inc. Methylation markers and targeted methylation probe panel
CA3111019A1 (en) * 2019-05-31 2020-12-03 Freenome Holdings, Inc. Methods and systems for high-depth sequencing of methylated nucleic acid
CN110358817B (zh) * 2019-06-25 2021-03-16 武汉大学 脱氨酶辅助的dna中5-羧基胞嘧啶修饰单碱基分辨率定位分析方法
US20220162676A1 (en) * 2019-12-23 2022-05-26 Active Motif, Inc. Methods and Kits for Detection of N-4-acetyldeoxycytidine in DNA
CN110982883A (zh) * 2019-12-30 2020-04-10 西安交通大学 一种高通量单细胞基因组5-羟甲基嘧啶单分子可视化分析方法
CN113088562A (zh) * 2020-01-08 2021-07-09 深圳华大基因股份有限公司 一种新型的低起始量dna甲基化建库方法
WO2022023753A1 (en) 2020-07-30 2022-02-03 Cambridge Epigenetix Limited Compositions and methods for nucleic acid analysis
CN112708661B (zh) * 2021-01-27 2022-07-12 西安交通大学 一种细胞内5-醛基尿嘧啶的可视化分析方法及系统
WO2022178093A1 (en) 2021-02-19 2022-08-25 New England Biolabs, Inc. Compositions and methods for labeling modified nucleotides in nucleic acids
WO2022236221A1 (en) * 2021-05-05 2022-11-10 The Board Of Trustees Of The Leland Stanford Junior University Methods and systems for analyzing nucleic acid molecules
GB202112817D0 (en) * 2021-09-08 2021-10-20 Mitra Bio Ltd Methods, compositions, and kits for characterizing skins
CN113846070B (zh) * 2021-10-18 2023-05-16 翌圣生物科技(上海)股份有限公司 高活性的mTET2酶突变体、其编码DNA及其应用
CN114134205B (zh) * 2021-11-25 2023-11-24 武汉大学 脱氨酶介导的dna中n4-甲基胞嘧啶的单碱基分辨率定位分析方法
CA3223653A1 (en) 2022-03-15 2023-09-21 Aathavan KARUNAKARAN Concurrent sequencing of forward and reverse complement strands on separate polynucleotides for methylation detection
WO2023175018A1 (en) 2022-03-15 2023-09-21 Illumina, Inc. Concurrent sequencing of forward and reverse complement strands on separate polynucleotides
CN115323035B (zh) * 2022-10-18 2023-02-10 翌圣生物科技(上海)股份有限公司 一种检测tet酶氧化能力的方法

Family Cites Families (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2009150229A1 (en) * 2008-06-12 2009-12-17 Institut National De La Sante Et De La Recherche Medicale (Inserm) Tet2 as a new diagnostic and pronostic marker in hematopoietic neoplasms
US9115386B2 (en) 2008-09-26 2015-08-25 Children's Medical Center Corporation Selective oxidation of 5-methylcytosine by TET-family proteins
US9175338B2 (en) * 2008-12-11 2015-11-03 Pacific Biosciences Of California, Inc. Methods for identifying nucleic acid modifications
EP3034628B1 (en) * 2010-09-13 2018-10-24 Clinical Genomics Pty Ltd Diagnosis of cancer by means of methylation marker
EP2694686B2 (en) 2011-04-06 2023-07-19 The University of Chicago COMPOSITION AND METHODS RELATED TO MODIFICATION OF 5-METHYLCYTOSINE (5mC)
US10081827B2 (en) * 2012-03-15 2018-09-25 New England Biolabs, Inc. Mapping cytosine modifications
WO2013138644A2 (en) 2012-03-15 2013-09-19 New England Biolabs, Inc. Methods and compositions for discrimination between cytosine and modifications thereof, and for methylome analysis
WO2013163207A1 (en) 2012-04-24 2013-10-31 Pacific Biosciences Of California, Inc. Identification of 5-methyl-c in nucleic acid templates
WO2014210444A1 (en) 2013-06-28 2014-12-31 New England Biolabs, Inc. Compositions and methods for identifying hydroxymethylcytosine in a dna
KR20180033454A (ko) * 2015-05-12 2018-04-03 웨이크 포리스트 유니버시티 헬스 사이언시즈 유전자 변형의 확인
US10260088B2 (en) * 2015-10-30 2019-04-16 New England Biolabs, Inc. Compositions and methods for analyzing modified nucleotides
CN108699598B (zh) * 2015-10-30 2022-11-15 新英格兰生物实验室公司 用于分析修饰的核苷酸的组合物和方法

Also Published As

Publication number Publication date
US11124825B2 (en) 2021-09-21
WO2017075436A1 (en) 2017-05-04
CN108699598B (zh) 2022-11-15
EP3368688A1 (en) 2018-09-05
US20180312914A1 (en) 2018-11-01
US10619200B2 (en) 2020-04-14
US20170198344A1 (en) 2017-07-13
EP3845668A1 (en) 2021-07-07
US20190100796A1 (en) 2019-04-04
EP3368688B1 (en) 2021-01-27
CN115927563A (zh) 2023-04-07
CN108699598A (zh) 2018-10-23
US20210388433A1 (en) 2021-12-16
US10227646B2 (en) 2019-03-12

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