WO2012106525A3 - Digital sequence analysis of dna methylation - Google Patents

Digital sequence analysis of dna methylation Download PDF

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Publication number
WO2012106525A3
WO2012106525A3 PCT/US2012/023646 US2012023646W WO2012106525A3 WO 2012106525 A3 WO2012106525 A3 WO 2012106525A3 US 2012023646 W US2012023646 W US 2012023646W WO 2012106525 A3 WO2012106525 A3 WO 2012106525A3
Authority
WO
WIPO (PCT)
Prior art keywords
sequence analysis
dna methylation
digital sequence
methods
adenoma
Prior art date
Application number
PCT/US2012/023646
Other languages
French (fr)
Other versions
WO2012106525A2 (en
Inventor
David A. Ahlquist
William R. Taylor
Hongzhi Zou
Graham P. Lidgard
Original Assignee
Exact Sciences Corporation
Mayo Foundation For Medical Education And Research
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 Exact Sciences Corporation, Mayo Foundation For Medical Education And Research filed Critical Exact Sciences Corporation
Priority to CN201280016745.6A priority Critical patent/CN103703173A/en
Priority to JP2013552632A priority patent/JP2014519310A/en
Priority to EP18179746.5A priority patent/EP3441479B1/en
Priority to EP20193533.5A priority patent/EP3795699B1/en
Priority to CA2826696A priority patent/CA2826696C/en
Priority to EP12742758.1A priority patent/EP2670893B1/en
Priority to ES12742758.1T priority patent/ES2686309T3/en
Priority to AU2012212127A priority patent/AU2012212127B2/en
Publication of WO2012106525A2 publication Critical patent/WO2012106525A2/en
Publication of WO2012106525A3 publication Critical patent/WO2012106525A3/en

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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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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
    • C12Q1/6844—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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Immunology (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • General Chemical & Material Sciences (AREA)

Abstract

The present invention relates to methods and compositions for determination of and uses of specific methylation patterns indicative of adenoma and carcinoma. In particular, the invention relates to analysis of defined CpG loci that are coordinately methylated in DNAs from cancer and adenoma samples, methods for identifying coordinately methylated loci, and methods of using analysis of coordinately methylated loci in one or more marker regions in the design of assays for adenoma and cancer.
PCT/US2012/023646 2011-02-02 2012-02-02 Digital sequence analysis of dna methylation WO2012106525A2 (en)

Priority Applications (8)

Application Number Priority Date Filing Date Title
CN201280016745.6A CN103703173A (en) 2011-02-02 2012-02-02 Digital sequence analysis of dna methylation
JP2013552632A JP2014519310A (en) 2011-02-02 2012-02-02 Digital sequence analysis of DNA methylation
EP18179746.5A EP3441479B1 (en) 2011-02-02 2012-02-02 Digital sequence analysis of dna methylation
EP20193533.5A EP3795699B1 (en) 2011-02-02 2012-02-02 Digital sequence analysis of dna methylation
CA2826696A CA2826696C (en) 2011-02-02 2012-02-02 Digital sequence analysis of dna methylation
EP12742758.1A EP2670893B1 (en) 2011-02-02 2012-02-02 Digital sequence analysis of dna methylation
ES12742758.1T ES2686309T3 (en) 2011-02-02 2012-02-02 Digital sequence analysis of DNA methylation
AU2012212127A AU2012212127B2 (en) 2011-02-02 2012-02-02 Digital sequence analysis of DNA methylation

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201161438649P 2011-02-02 2011-02-02
US61/438,649 2011-02-02

Publications (2)

Publication Number Publication Date
WO2012106525A2 WO2012106525A2 (en) 2012-08-09
WO2012106525A3 true WO2012106525A3 (en) 2014-02-20

Family

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Family Applications (1)

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PCT/US2012/023646 WO2012106525A2 (en) 2011-02-02 2012-02-02 Digital sequence analysis of dna methylation

Country Status (8)

Country Link
US (5) US9637792B2 (en)
EP (3) EP3795699B1 (en)
JP (1) JP2014519310A (en)
CN (2) CN110129436A (en)
AU (1) AU2012212127B2 (en)
CA (1) CA2826696C (en)
ES (2) ES2829198T3 (en)
WO (1) WO2012106525A2 (en)

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CA2826696C (en) 2011-02-02 2019-12-03 Exact Sciences Corporation Digital sequence analysis of dna methylation
MX2015002637A (en) * 2012-08-31 2015-11-23 Nat Defense Medical Ct Method for screening cancer.
WO2014046197A1 (en) * 2012-09-19 2014-03-27 シスメックス株式会社 Method for obtaining information about colorectal cancer and marker and kit for obtaining information about colorectal cancer
CN106170558B (en) * 2013-10-21 2021-10-29 金圣千 Method and apparatus for analyzing biomolecules using oligonucleotide
US10253358B2 (en) 2013-11-04 2019-04-09 Exact Sciences Development Company, Llc Multiple-control calibrators for DNA quantitation
EP4209600A1 (en) 2013-12-19 2023-07-12 Exact Sciences Corporation Synthetic nucleic acid control molecules
CN106460046A (en) 2014-03-31 2017-02-22 梅奥医学教育和研究基金会 Detecting colorectal neoplasm
US10184154B2 (en) 2014-09-26 2019-01-22 Mayo Foundation For Medical Education And Research Detecting cholangiocarcinoma
US10704081B2 (en) 2015-10-30 2020-07-07 Exact Sciences Development Company, Llc Multiplex amplification detection assay
CN105603061A (en) * 2015-12-11 2016-05-25 宁云山 Method, probe, primer and kit for detecting methylation of human Septin 9 gene based on digital PCR technology
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WO2017201400A1 (en) * 2016-05-19 2017-11-23 The Regents Of The University Of California Determination of cell types in mixtures using targeted bisulfite sequencing
KR102667067B1 (en) 2017-01-27 2024-05-17 이그젝트 싸이언스 디블롭먼트 컴패니, 엘엘씨 Detection of colonic neoplasia by methylated DNA analysis.
JP7220200B2 (en) 2017-04-19 2023-02-09 シングレラ ジェノミクス， インコーポレイテッド Compositions and methods for library construction and sequence analysis
US10648025B2 (en) 2017-12-13 2020-05-12 Exact Sciences Development Company, Llc Multiplex amplification detection assay II
AU2019234843A1 (en) 2018-03-13 2020-09-24 GRAIL, Inc Anomalous fragment detection and classification
CN108676878B (en) * 2018-05-23 2019-12-17 杭州诺辉健康科技有限公司 Application of product for detecting NDRG4 gene methylation site in preparation of product for early detection of colorectal cancer
US12234514B2 (en) 2018-12-21 2025-02-25 Grail, Inc. Source of origin deconvolution based on methylation fragments in cell-free DNA samples
CN112195243A (en) * 2020-09-22 2021-01-08 北京华大吉比爱生物技术有限公司 Kit for detecting polygene methylation and application thereof
CN114561464A (en) * 2021-12-20 2022-05-31 上海锐翌生物科技有限公司 Primer probe set and kit for diagnosing, detecting or screening advanced adenoma
CN114317775B (en) * 2022-01-12 2023-06-30 中国人民解放军军事科学院军事医学研究院 Application of RNA m6A modification of NCOA4 as gamma-ray radiation marker

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Also Published As

Publication number Publication date
US9637792B2 (en) 2017-05-02
EP3795699B1 (en) 2023-12-20
ES2686309T3 (en) 2018-10-17
US20240368702A1 (en) 2024-11-07
CN103703173A (en) 2014-04-02
EP2670893B1 (en) 2018-06-27
US20120196756A1 (en) 2012-08-02
US10870893B2 (en) 2020-12-22
EP2670893A2 (en) 2013-12-11
ES2829198T3 (en) 2021-05-31
JP2014519310A (en) 2014-08-14
CA2826696A1 (en) 2012-08-09
AU2012212127B2 (en) 2016-06-02
EP2670893A4 (en) 2015-11-11
WO2012106525A2 (en) 2012-08-09
CN110129436A (en) 2019-08-16
EP3795699A1 (en) 2021-03-24
US20200048720A1 (en) 2020-02-13
EP3441479A1 (en) 2019-02-13
AU2012212127A1 (en) 2013-08-22
EP3441479B1 (en) 2020-09-02
US20170073771A1 (en) 2017-03-16
US10519510B2 (en) 2019-12-31
US20210095350A1 (en) 2021-04-01
CA2826696C (en) 2019-12-03
US11952633B2 (en) 2024-04-09

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