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WO2008009365A3 - A method for determining the methylation rate of a nucleic acid - Google Patents

A method for determining the methylation rate of a nucleic acid Download PDF

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Publication number
WO2008009365A3
WO2008009365A3 PCT/EP2007/006064 EP2007006064W WO2008009365A3 WO 2008009365 A3 WO2008009365 A3 WO 2008009365A3 EP 2007006064 W EP2007006064 W EP 2007006064W WO 2008009365 A3 WO2008009365 A3 WO 2008009365A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
base
signal
sequencing
cytosine bases
Prior art date
Application number
PCT/EP2007/006064
Other languages
French (fr)
Other versions
WO2008009365A2 (en
Inventor
Joern Lewin
Ralf Lesche
Matthias Schuster
Dimo Dietrich
Original Assignee
Epigenomics Ag
Joern Lewin
Ralf Lesche
Matthias Schuster
Dimo Dietrich
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
Priority to US12/309,555 priority Critical patent/US20100003680A1/en
Application filed by Epigenomics Ag, Joern Lewin, Ralf Lesche, Matthias Schuster, Dimo Dietrich filed Critical Epigenomics Ag
Priority to EP07785943A priority patent/EP2044214A2/en
Publication of WO2008009365A2 publication Critical patent/WO2008009365A2/en
Publication of WO2008009365A3 publication Critical patent/WO2008009365A3/en

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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
    • C12Q1/6813—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

Landscapes

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

Abstract

The invention relates to a method for quantitatively determining the methylation rate of a nucleic acid through sequencing. According to the invention, the method comprises at least the following steps: a) treating the nucleic acid with a chemical reagent or an enzyme containing solution, whereby the base pairing behavior of methylated cytosine bases and/or unmethylated cytosine bases of the nucleic acid are altered such that methylated cytosine bases become distinguishable from unmethylated cytosine bases, and b) introducing into the nucleic acid at least one base for generating a sequencing signal to be used as a reference signal for normalization, and c) sequencing the nucleic acid, whereby a signal from each cytosine base of the nucleic acid, or a signal from each guanine base of the nucleic acid and a reference signal from the at least on introduced base is obtained, and d) normalizing the signal obtained from each cytosine base of the nucleic acid, or the signal obtained from each guanine base of the nucleic acid to the reference signal from the at least one introduced base.
PCT/EP2007/006064 2006-07-18 2007-07-09 A method for determining the methylation rate of a nucleic acid WO2008009365A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
US12/309,555 US20100003680A1 (en) 2006-07-18 2006-07-18 Method For Determining The Methylation Rate of a Nucleic Acid
EP07785943A EP2044214A2 (en) 2006-07-18 2007-07-09 A method for determining the methylation rate of a nucleic acid

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
EP06090125 2006-07-18
EP06090125.3 2006-07-18
EP06120694.2 2006-09-14
EP06120694 2006-09-14
EP07109855 2007-06-08
EP07109855.2 2007-06-08

Publications (2)

Publication Number Publication Date
WO2008009365A2 WO2008009365A2 (en) 2008-01-24
WO2008009365A3 true WO2008009365A3 (en) 2008-04-17

Family

ID=38935863

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/EP2007/006064 WO2008009365A2 (en) 2006-07-18 2007-07-09 A method for determining the methylation rate of a nucleic acid

Country Status (2)

Country Link
EP (1) EP2044214A2 (en)
WO (1) WO2008009365A2 (en)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2008148159A1 (en) * 2007-06-07 2008-12-11 Simons Haplomics Limited Epigenetic methods
WO2011002029A1 (en) * 2009-07-03 2011-01-06 国立大学法人東京大学 Method for determination of presence of cancer cell, and method for determination of prognosis of cancer patient
US10570455B2 (en) 2013-05-10 2020-02-25 University Of Southern California DNA methylation biomarkers for bladder cancer
US20200131566A1 (en) * 2018-10-31 2020-04-30 Guardant Health, Inc. Methods, compositions and systems for calibrating epigenetic partitioning assays

Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
HAN ET AL: "DNA methylation mapping by tag-modified bisulfite genomic sequencing", ANALYTICAL BIOCHEMISTRY, ACADEMIC PRESS, SAN DIEGO, CA, US, vol. 355, no. 1, 2 June 2006 (2006-06-02), pages 50 - 61, XP005542202, ISSN: 0003-2697 *
JANG SE JIN ET AL: "Methylation patterns in human androgen receptor gene and clonality analysis", CANCER RESEARCH, vol. 60, no. 4, 15 February 2000 (2000-02-15), pages 864 - 866, XP002467560, ISSN: 0008-5472 *
LEWIN JOERN ET AL: "Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificates", BIOINFORMATICS (OXFORD), vol. 20, no. 17, 22 November 2004 (2004-11-22), pages 3005 - 3012, XP002467526, ISSN: 1367-4803 *
PAUL C L ET AL: "Cytosine methylation: quantitation by automated genomic sequencing and GENESCAN analysis", BIOTECHNIQUES, INFORMA LIFE SCIENCES PUBLISHING, WESTBOROUGH, MA, US, vol. 21, no. 1, July 1996 (1996-07-01), pages 126 - 133, XP002143107, ISSN: 0736-6205 *
YANG INCHUL ET AL: "Rapid quantification of DNA methylation through dNMP analysis following bisulfite-PCR.", NUCLEIC ACIDS RESEARCH 2006, vol. 34, no. 8, 2006, pages e61, XP002467528, ISSN: 1362-4962 *

Also Published As

Publication number Publication date
WO2008009365A2 (en) 2008-01-24
EP2044214A2 (en) 2009-04-08

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