WO2005019477A3 - Methods and compositions for differentiating tissues or cell types using epigenetic markers - Google Patents

Methods and compositions for differentiating tissues or cell types using epigenetic markers Download PDF

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Publication number
WO2005019477A3
WO2005019477A3 PCT/US2004/026071 US2004026071W WO2005019477A3 WO 2005019477 A3 WO2005019477 A3 WO 2005019477A3 US 2004026071 W US2004026071 W US 2004026071W WO 2005019477 A3 WO2005019477 A3 WO 2005019477A3
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WIPO (PCT)
Prior art keywords
mvp
types
sample types
distinguishing
cell
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Ceased
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PCT/US2004/026071
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French (fr)
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WO2005019477A2 (en
Inventor
Joern Lewin
Kurt Berlin
Thomas Hildmann
Alexander Olek
Stephan Beck
Karen Novik
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Epigenomics AG
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Epigenomics AG
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Priority to EP04780844A priority Critical patent/EP1660681A2/en
Priority to JP2006523343A priority patent/JP2007502113A/en
Publication of WO2005019477A2 publication Critical patent/WO2005019477A2/en
Publication of WO2005019477A3 publication Critical patent/WO2005019477A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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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
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • 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
    • 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
    • C12Q2600/16—Primer sets for multiplex assays

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Analytical Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Immunology (AREA)
  • Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Cell Biology (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 present invention provides, inter alia, a method for generating a genome-wide epigenomic map, comprising a correlation between methylation variable CpG positions (MVP) and genomic DNA sample types. MVP are those CpG positions that show a variable quantitative level of methylation between sample types. Particular genomic regions of interest (ROI) provide preferred marker sequences that comprise multiple, and preferably proximate MVP, and that have novel utility for distinguishing sample types. The epigenic maps have broad utility, for example, in identifying sample types, or for distinguishing between and among sample types. In a preferred embodiment the epigenomic map is based on methylation variable regions (MVP) within the major histocompatibility complex (MHC), and has utility, for example, in identifying the cell or tissue source of a genomic DNA sample, or for distinguishing one or more particular cell or tissue types among other cell or tissue types. Analysis of epigenetic characteristics of one, or of a set of nucleic acid sequences, in the context of an inventive epigenomic map, allows for the determination of an origin of the nucleic acids.
PCT/US2004/026071 2003-08-12 2004-08-12 Methods and compositions for differentiating tissues or cell types using epigenetic markers Ceased WO2005019477A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP04780844A EP1660681A2 (en) 2003-08-12 2004-08-12 Methods and compositions for differentiating tissues or cell types using epigenetic markers
JP2006523343A JP2007502113A (en) 2003-08-12 2004-08-12 Methods and compositions for differentiating tissue or cell types using epigenetic markers

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US10/641,321 US20060183128A1 (en) 2003-08-12 2003-08-12 Methods and compositions for differentiating tissues for cell types using epigenetic markers
US10/641,321 2003-08-12

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WO2005019477A2 WO2005019477A2 (en) 2005-03-03
WO2005019477A3 true WO2005019477A3 (en) 2005-06-16

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PCT/US2004/026071 Ceased WO2005019477A2 (en) 2003-08-12 2004-08-12 Methods and compositions for differentiating tissues or cell types using epigenetic markers

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US (2) US20060183128A1 (en)
EP (1) EP1660681A2 (en)
JP (1) JP2007502113A (en)
WO (1) WO2005019477A2 (en)

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US10706957B2 (en) 2012-09-20 2020-07-07 The Chinese University Of Hong Kong Non-invasive determination of methylome of tumor from plasma
US9732390B2 (en) 2012-09-20 2017-08-15 The Chinese University Of Hong Kong Non-invasive determination of methylome of fetus or tumor from plasma
US20130189684A1 (en) * 2013-03-12 2013-07-25 Sequenom, Inc. Quantification of cell-specific nucleic acid markers
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DE102013009654A1 (en) * 2013-06-07 2014-12-11 Klaus Olek A method for the detection and differentiation of body fluids from forensic material
EP3543356B1 (en) 2014-07-18 2021-06-30 The Chinese University of Hong Kong Methylation pattern analysis of tissues in dna mixture
US9984201B2 (en) * 2015-01-18 2018-05-29 Youhealth Biotech, Limited Method and system for determining cancer status
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WO2018009707A1 (en) 2016-07-06 2018-01-11 Youhealth Biotech, Limited Solid tumor methylation markers and uses thereof
KR20260032575A (en) 2016-11-30 2026-03-09 더 차이니즈 유니버시티 오브 홍콩 Analysis of cell-free dna in urine and other samples
WO2018161031A1 (en) 2017-03-02 2018-09-07 Youhealth Biotech, Limited Methylation markers for diagnosing hepatocellular carcinoma and lung cancer
DE102017004108A1 (en) * 2017-05-01 2018-11-08 Rheinisch-Westfälische Technische Hochschule (Rwth) Aachen Method for determining the cell number of eukaryotic cells
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Also Published As

Publication number Publication date
US20090170089A1 (en) 2009-07-02
EP1660681A2 (en) 2006-05-31
JP2007502113A (en) 2007-02-08
US20060183128A1 (en) 2006-08-17
WO2005019477A2 (en) 2005-03-03

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