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 PDFInfo
- 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
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
- C12Q1/6813—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
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- 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)
- Biotechnology (AREA)
- Molecular Biology (AREA)
- Biophysics (AREA)
- Analytical Chemistry (AREA)
- Physics & Mathematics (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.
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 |
---|---|---|---|
EP06090125.3 | 2006-07-18 | ||
EP06090125 | 2006-07-18 | ||
EP06120694 | 2006-09-14 | ||
EP06120694.2 | 2006-09-14 | ||
EP07109855.2 | 2007-06-08 | ||
EP07109855 | 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)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN101784673B (en) * | 2007-06-07 | 2013-03-27 | 西蒙斯单倍体有限公司 | 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 |
WO2014183093A1 (en) * | 2013-05-10 | 2014-11-13 | University Of Southern California | Dna methylation biomarkers for bladder cancer |
JP2022512848A (en) * | 2018-10-31 | 2022-02-07 | ガーダント ヘルス, インコーポレイテッド | Methods, compositions and systems for calibrating epigenetic compartment assays |
-
2007
- 2007-07-09 WO PCT/EP2007/006064 patent/WO2008009365A2/en active Application Filing
- 2007-07-09 EP EP07785943A patent/EP2044214A2/en not_active Withdrawn
Non-Patent Citations (5)
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 |
---|---|
EP2044214A2 (en) | 2009-04-08 |
WO2008009365A2 (en) | 2008-01-24 |
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