WO2003066895A3 - Quantitative methylation detection in dna samples - Google Patents

Quantitative methylation detection in dna samples Download PDF

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Publication number
WO2003066895A3
WO2003066895A3 PCT/EP2003/001218 EP0301218W WO03066895A3 WO 2003066895 A3 WO2003066895 A3 WO 2003066895A3 EP 0301218 W EP0301218 W EP 0301218W WO 03066895 A3 WO03066895 A3 WO 03066895A3
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WO
WIPO (PCT)
Prior art keywords
label
methylation detection
amplification product
sample
type
Prior art date
Application number
PCT/EP2003/001218
Other languages
French (fr)
Other versions
WO2003066895A2 (en
Inventor
Susan Cottrell
Original Assignee
Epigenomics Ag
Susan Cottrell
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 Epigenomics Ag, Susan Cottrell filed Critical Epigenomics Ag
Priority to EP03702610A priority Critical patent/EP1472369B1/en
Priority to JP2003566243A priority patent/JP2005516628A/en
Priority to AU2003205745A priority patent/AU2003205745A1/en
Priority to DE60305150T priority patent/DE60305150T2/en
Publication of WO2003066895A2 publication Critical patent/WO2003066895A2/en
Publication of WO2003066895A3 publication Critical patent/WO2003066895A3/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
    • C12Q1/6813—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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/6818—Hybridisation assays characterised by the detection means involving interaction of two or more labels, e.g. resonant energy transfer

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (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)
  • Investigating Or Analysing Biological Materials (AREA)

Abstract

Described is a method for methylation detection in a DNA sample. An isolated genomic DNA sample is treated in a manner capable of distinguishing methylated from unmethy-lated cytosine bases. The pretreated DNA is amplified us-ing at least one oligonucleotide primer, a polymerase and a set of nucleotides of which at least one is labeled with a first type of label. A sequence-specific oligonu-cleotide probe, marked with a second type of label, hy-bridizes to the amplification product and a FRET reaction occurs if a labeled oligonucleotide is present in close proximity in the amplification product. The method deter-mines the level of methylation of a sample by measuring the extent of fluorescence resonance energy transfer (FRET) between the donor and acceptor fluorophore.
PCT/EP2003/001218 2002-02-06 2003-02-06 Quantitative methylation detection in dna samples WO2003066895A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
EP03702610A EP1472369B1 (en) 2002-02-06 2003-02-06 Quantitative methylation detection in dna samples
JP2003566243A JP2005516628A (en) 2002-02-06 2003-02-06 Quantitative methylation detection of DNA samples
AU2003205745A AU2003205745A1 (en) 2002-02-06 2003-02-06 Quantitative methylation detection in dna samples
DE60305150T DE60305150T2 (en) 2002-02-06 2003-02-06 QUANTITATIVE DETECTION OF METHYLATION IN DNA SAMPLES

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US10/068,553 US6960436B2 (en) 2002-02-06 2002-02-06 Quantitative methylation detection in DNA samples
US10/068,553 2002-02-06

Publications (2)

Publication Number Publication Date
WO2003066895A2 WO2003066895A2 (en) 2003-08-14
WO2003066895A3 true WO2003066895A3 (en) 2003-11-20

Family

ID=27659063

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/EP2003/001218 WO2003066895A2 (en) 2002-02-06 2003-02-06 Quantitative methylation detection in dna samples

Country Status (7)

Country Link
US (2) US6960436B2 (en)
EP (1) EP1472369B1 (en)
JP (1) JP2005516628A (en)
AT (1) ATE325895T1 (en)
AU (1) AU2003205745A1 (en)
DE (1) DE60305150T2 (en)
WO (1) WO2003066895A2 (en)

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AU2003302146B2 (en) * 2002-06-26 2008-06-26 Cold Spring Harbor Laboratory Methods and compositions for determining methylation profiles
AU2003900368A0 (en) * 2003-01-24 2003-02-13 Human Genetic Signatures Pty Ltd Assay for nucleic acid molecules
DE10304219B3 (en) * 2003-01-30 2004-08-19 Epigenomics Ag Method for the detection of cytosine methylation patterns with high sensitivity
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US20050009059A1 (en) * 2003-05-07 2005-01-13 Affymetrix, Inc. Analysis of methylation status using oligonucleotide arrays
US7799525B2 (en) * 2003-06-17 2010-09-21 Human Genetic Signatures Pty Ltd. Methods for genome amplification
DE602004018801D1 (en) * 2003-09-04 2009-02-12 Human Genetic Signatures Pty NUCLEIC DETECTION TEST
AU2004284456B2 (en) 2003-10-21 2012-04-19 Orion Genomics Llc Methods for quantitative determination of methylation density in a DNA locus
WO2005085477A1 (en) * 2004-03-02 2005-09-15 Orion Genomics Llc Differential enzymatic fragmentation by whole genome amplification
ATE399884T1 (en) * 2004-03-24 2008-07-15 Applera Corp CODING AND DECODING REACTIONS FOR DETERMINING TARGET POLYNUCLEOTIDES
US8168777B2 (en) 2004-04-29 2012-05-01 Human Genetic Signatures Pty. Ltd. Bisulphite reagent treatment of nucleic acid
CN101056883B (en) * 2004-09-10 2012-10-10 人类遗传标记控股有限公司 Amplification blocker for intercalating nucleic acid (ina) containing intercalating pseudo nucleic acid (IPN)
WO2006040187A2 (en) * 2004-10-11 2006-04-20 Epigenomics Ag A method for the carry-over protection in dna amplification systems targeting methylation analysis achieved by a modified pre-treatment of nucleic acids
NZ555620A (en) * 2004-12-03 2008-08-29 Human Genetic Signatures Pty Methods for simplifying microbial nucleic acids by chemical modification of cytosines
AU2005312354B2 (en) * 2004-12-03 2007-05-03 Human Genetic Signatures Pty Ltd Methods for simplifying microbial nucleic acids by chemical modification of cytosines
JP2008524990A (en) * 2004-12-23 2008-07-17 ヒューマン ジェネティック シグネチャーズ ピーティーワイ リミテッド Detection of human papillomavirus
WO2006094149A2 (en) * 2005-03-01 2006-09-08 Exact Sciences Corporation Methods and compositions for detecting adenoma
KR100673811B1 (en) 2005-05-11 2007-01-24 한국표준과학연구원 Method for quantitative analysis of methyl cytosine in DNA and uses thereof
EP1883707B1 (en) * 2005-05-26 2014-04-09 Human Genetic Signatures PTY Ltd Isothermal strand displacement amplification using primers containing a non-regular base
US20060286577A1 (en) * 2005-06-17 2006-12-21 Xiyu Jia Methods for detection of methylated DNA
US20060292585A1 (en) * 2005-06-24 2006-12-28 Affymetrix, Inc. Analysis of methylation using nucleic acid arrays
US20070020667A1 (en) * 2005-06-30 2007-01-25 Ruff David W Methods and compositions for amplifying nucleic acids
DE102005034628B4 (en) * 2005-07-19 2007-08-23 Epigenomics Ag Method for the investigation of cytosine methylations in DNA
US8343738B2 (en) * 2005-09-14 2013-01-01 Human Genetic Signatures Pty. Ltd. Assay for screening for potential cervical cancer
DE102006001161A1 (en) * 2006-01-06 2007-07-12 Qiagen Gmbh Method for the detection of cytosine methylations
US7901882B2 (en) * 2006-03-31 2011-03-08 Affymetrix, Inc. Analysis of methylation using nucleic acid arrays
EP2016188B1 (en) * 2006-04-24 2015-10-21 Xiyu Jia Methods for detection of methylated dna
US20080050738A1 (en) * 2006-05-31 2008-02-28 Human Genetic Signatures Pty Ltd. Detection of target nucleic acid
US20080213870A1 (en) * 2007-03-01 2008-09-04 Sean Wuxiong Cao Methods for obtaining modified DNA from a biological specimen
AU2008229628A1 (en) * 2007-03-16 2008-09-25 Human Genetic Signatures Pty Ltd Assay for gene expression
EP2183391A4 (en) * 2007-07-31 2010-10-27 Quest Diagnostics Invest Inc Detection of methicillin-resistant and methicillin-sensitive staphylococcus aureus in biological samples
CA2706740C (en) * 2007-11-27 2017-01-17 Human Genetic Signatures Pty Ltd Enzymes for amplification and copying bisulphite modified nucleic acids
US20090137024A1 (en) * 2007-11-28 2009-05-28 Canon U.S. Life Sciences, Inc. Method of Separating Target DNA from Mixed DNA
JP2011505845A (en) * 2007-12-20 2011-03-03 ヒューマン ジェネティック シグネチャーズ ピーティーワイ リミテッド Eliminate contaminants associated with nucleic acid amplification
US20100159452A1 (en) * 2008-12-22 2010-06-24 Roche Molecular Systems, Inc. Method For Detecting a Target Nucleic Acid in a Sample
US9732375B2 (en) 2011-09-07 2017-08-15 Human Genetic Signatures Pty. Ltd. Molecular detection assay using direct treatment with a bisulphite reagent
US9428813B2 (en) 2012-03-26 2016-08-30 The United States Of America, As Represented By The Secretary, Dept. Of Health & Human Services DNA methylation analysis for the diagnosis, prognosis and treatment of adrenal neoplasms
GB201319180D0 (en) 2013-10-30 2013-12-11 Mast Group Ltd Nucleic acid probe
CN107918725B (en) * 2017-12-28 2021-09-07 大连海事大学 DNA methylation prediction method for selecting optimal features based on machine learning
WO2021050962A1 (en) 2019-09-11 2021-03-18 The United States Of America, As Represented By The Secretary, Department Of Health And Human Services Cancer detection and classification
JP7500727B2 (en) * 2019-12-18 2024-06-17 エフ． ホフマン－ラ ロシュ アーゲー Sequencing-by-synthesis method using sequential labeling schemes
CN114381497B (en) * 2021-12-31 2024-01-26 湖南中医药大学 Method for detecting methylation modification of DNA

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Title
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Also Published As

Publication number Publication date
US20060088866A1 (en) 2006-04-27
WO2003066895A2 (en) 2003-08-14
EP1472369A2 (en) 2004-11-03
EP1472369B1 (en) 2006-05-10
US6960436B2 (en) 2005-11-01
AU2003205745A1 (en) 2003-09-02
DE60305150D1 (en) 2006-06-14
JP2005516628A (en) 2005-06-09
DE60305150T2 (en) 2007-04-26
US20030148290A1 (en) 2003-08-07
ATE325895T1 (en) 2006-06-15

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