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

Publications (2)

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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)

Families Citing this family (49)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20060183128A1 (en) * 2003-08-12 2006-08-17 Epigenomics Ag Methods and compositions for differentiating tissues for cell types using epigenetic markers
DE10338308B4 (en) * 2003-08-15 2006-10-19 Epigenomics Ag Method for the detection of cytosine methylations in DNA
EP2471924A1 (en) 2004-05-28 2012-07-04 Asuragen, INC. Methods and compositions involving microRNA
ES2534300T3 (en) 2004-11-12 2015-04-21 Asuragen, Inc. Procedures and compositions involving miRNA and miRNA inhibitor molecules
EP1748080A3 (en) * 2005-03-11 2007-04-11 Epiontis GmbH Specific DNAs for epigenetic characterisation of cells and tissues
EP1934369A2 (en) * 2005-09-29 2008-06-25 Epigenomics AG Methods and nucleic acids for the analysis of gene expression associated with tissue classification
US20080163824A1 (en) * 2006-09-01 2008-07-10 Innovative Dairy Products Pty Ltd, An Australian Company, Acn 098 382 784 Whole genome based genetic evaluation and selection process
CA2664383C (en) * 2006-09-19 2017-08-22 Asuragen, Inc. Micrornas differentially expressed in pancreatic diseases and uses thereof
JP2008136404A (en) * 2006-11-30 2008-06-19 Sysmex Corp Method for confirming amount of dna after conversion treatment of non-methylated cytosine in dna methylation detection
US20090049856A1 (en) * 2007-08-20 2009-02-26 Honeywell International Inc. Working fluid of a blend of 1,1,1,3,3-pentafluoropane, 1,1,1,2,3,3-hexafluoropropane, and 1,1,1,2-tetrafluoroethane and method and apparatus for using
US8361714B2 (en) 2007-09-14 2013-01-29 Asuragen, Inc. Micrornas differentially expressed in cervical cancer and uses thereof
WO2009070805A2 (en) 2007-12-01 2009-06-04 Asuragen, Inc. Mir-124 regulated genes and pathways as targets for therapeutic intervention
US7888127B2 (en) 2008-01-15 2011-02-15 Sequenom, Inc. Methods for reducing adduct formation for mass spectrometry analysis
US8258111B2 (en) 2008-05-08 2012-09-04 The Johns Hopkins University Compositions and methods related to miRNA modulation of neovascularization or angiogenesis
WO2010037001A2 (en) 2008-09-26 2010-04-01 Immune Disease Institute, Inc. Selective oxidation of 5-methylcytosine by tet-family proteins
US10927415B2 (en) * 2008-11-26 2021-02-23 The Johns Hopkins University Methods for identifying cancer risk
US8497066B2 (en) 2008-12-04 2013-07-30 Rush University Medical Center DNA methylation based test for monitoring efficacy of treatment
US20120221249A1 (en) * 2009-05-15 2012-08-30 The Trustees of The Uniiversity of Pennsylvania Long Hepitype Distribution (LHD)
WO2011008541A2 (en) * 2009-06-29 2011-01-20 The Regents Of The University Of California Molecular markers and assay methods for characterizing cells
US20120164110A1 (en) * 2009-10-14 2012-06-28 Feinberg Andrew P Differentially methylated regions of reprogrammed induced pluripotent stem cells, method and compositions thereof
GB201007944D0 (en) 2010-05-12 2010-06-30 Univ Aberystwyth Methods
US9644241B2 (en) 2011-09-13 2017-05-09 Interpace Diagnostics, Llc Methods and compositions involving miR-135B for distinguishing pancreatic cancer from benign pancreatic disease
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
US10706957B2 (en) 2012-09-20 2020-07-07 The Chinese University Of Hong Kong Non-invasive determination of methylome of tumor from plasma
HUE053822T2 (en) 2012-09-20 2021-07-28 Univ Hong Kong Chinese Non-invasive method for the determination of tumor methylome from plasma
US20130189684A1 (en) * 2013-03-12 2013-07-25 Sequenom, Inc. Quantification of cell-specific nucleic acid markers
US9305756B2 (en) 2013-03-13 2016-04-05 Agena Bioscience, Inc. Preparation enhancements and methods of use for MALDI mass spectrometry
DE102013009654A1 (en) * 2013-06-07 2014-12-11 Klaus Olek A method for the detection and differentiation of body fluids from forensic material
TWI758011B (en) 2014-07-18 2022-03-11 香港中文大學 Methylation pattern analysis of tissues in a dna mixture
US9984201B2 (en) * 2015-01-18 2018-05-29 Youhealth Biotech, Limited Method and system for determining cancer status
WO2017193008A1 (en) * 2016-05-06 2017-11-09 Cedars-Sinai Medical Center Methods of diagnosing and treating cancer with micrornas
EP3481403B1 (en) 2016-07-06 2022-02-09 Youhealth Biotech, Limited Solid tumor methylation markers and uses thereof
IL266347B2 (en) 2016-11-30 2025-01-01 Univ Hong Kong Chinese Analysis of cell-free dna in urine and other samples
BR112019018272A2 (en) 2017-03-02 2020-07-28 Youhealth Oncotech, Limited methylation markers to diagnose hepatocellular carcinoma and cancer
DE102017004108A1 (en) * 2017-05-01 2018-11-08 Rheinisch-Westfälische Technische Hochschule (Rwth) Aachen Method for determining the cell number of eukaryotic cells
CN108103193A (en) * 2017-12-18 2018-06-01 东莞博奥木华基因科技有限公司 Methylation detecting method based on cervical carcinoma host cell
CN111989407B (en) 2018-03-13 2024-10-29 格里尔公司 Abnormal fragment detection and classification
CA3302676A1 (en) 2018-04-02 2026-05-13 Grail, Inc. Methylation markers and targeted methylation probe panels
EP3856903A4 (en) 2018-09-27 2022-07-27 Grail, LLC METHYLATION MARKERS AND TARGETED METHYLATION PROBE PANELS
AU2019384154B2 (en) 2018-11-21 2025-11-20 Agilent Technologies, Inc. Methods for targeted nucleic acid library formation
EP3899953A1 (en) 2018-12-21 2021-10-27 Grail, Inc. Source of origin deconvolution based on methylation fragments in cell-free-dna samples
GB2603051B (en) 2020-01-30 2023-04-26 Prognomiq Inc Lung biomarkers and methods of use thereof
CN115103909A (en) 2020-01-31 2022-09-23 艾维达生物医学公司 Systems and methods for targeted nucleic acid capture
CN115427587B (en) * 2020-03-25 2026-01-02 富士胶片株式会社 Methods and procedures for calculating the degree of methylation of bases
AU2022249074A1 (en) 2021-03-31 2023-09-21 PrognomIQ, Inc. Multi-omic assessment
WO2023039479A1 (en) 2021-09-10 2023-03-16 PrognomIQ, Inc. Direct classification of raw biomolecule measurement data
JP2024534992A (en) 2021-09-13 2024-09-26 プログノミック インコーポレイテッド Enhanced detection and quantification of biomolecules
WO2024112741A1 (en) * 2022-11-23 2024-05-30 Salk Institute For Biological Studies Dna methylation barcodes for identifying brain cells
WO2024184854A1 (en) 2023-03-07 2024-09-12 Pomorski Uniwersytet Medyczny W Szczecinie Methods, systems and assosiated computer program products for discriminating type of biological sample of an organism using epigenetic modification information

Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997046705A1 (en) * 1996-06-03 1997-12-11 The Johns Hopkins University School Of Medicine Methylation specific detection
WO1998056952A1 (en) * 1997-06-09 1998-12-17 University Of Southern California A cancer diagnostic method based upon dna methylation differences
US6214556B1 (en) * 1997-11-27 2001-04-10 Epigenomics Ag Method for producing complex DNA methylation fingerprints
US6310270B1 (en) * 1996-03-15 2001-10-30 The General Hospital Corporation Endothelial NOS knockout mice and methods of use
WO2002000932A2 (en) * 2000-06-30 2002-01-03 Epigenomics Ag Diagnosis of known genetic parameters within the mhc
WO2002034942A2 (en) * 2000-10-23 2002-05-02 Cancer Research Technology Limited Nucleic acid amplification-based methods for the determination of a methylation profile and reagents therefor
EP1213360A1 (en) * 2000-12-07 2002-06-12 The University of Tokyo Method of identifying cells using DNA methylation patterns
WO2003074730A1 (en) * 2002-03-05 2003-09-12 Epigenomics Ag Method and device for determination of tissue specificity of free floating dna in bodily fluids

Family Cites Families (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5585481A (en) * 1987-09-21 1996-12-17 Gen-Probe Incorporated Linking reagents for nucleotide probes
US5457183A (en) * 1989-03-06 1995-10-10 Board Of Regents, The University Of Texas System Hydroxylated texaphyrins
US5744101A (en) * 1989-06-07 1998-04-28 Affymax Technologies N.V. Photolabile nucleoside protecting groups
US5245022A (en) * 1990-08-03 1993-09-14 Sterling Drug, Inc. Exonuclease resistant terminally substituted oligonucleotides
US5565552A (en) * 1992-01-21 1996-10-15 Pharmacyclics, Inc. Method of expanded porphyrin-oligonucleotide conjugate synthesis
US5574142A (en) * 1992-12-15 1996-11-12 Microprobe Corporation Peptide linkers for improved oligonucleotide delivery
US5837832A (en) * 1993-06-25 1998-11-17 Affymetrix, Inc. Arrays of nucleic acid probes on biological chips
CH686982A5 (en) * 1993-12-16 1996-08-15 Maurice Stroun Method for diagnosis of cancers.
US5597696A (en) * 1994-07-18 1997-01-28 Becton Dickinson And Company Covalent cyanine dye oligonucleotide conjugates
US5552277A (en) * 1994-07-19 1996-09-03 The Johns Hopkins University School Of Medicine Genetic diagnosis of prostate cancer
US5786146A (en) * 1996-06-03 1998-07-28 The Johns Hopkins University School Of Medicine Method of detection of methylated nucleic acid using agents which modify unmethylated cytosine and distinguishing modified methylated and non-methylated nucleic acids
US5958773A (en) * 1998-12-17 1999-09-28 Isis Pharmaceuticals Inc. Antisense modulation of AKT-1 expression
US6581011B1 (en) * 1999-06-23 2003-06-17 Tissueinformatics, Inc. Online database that includes indices representative of a tissue population
US20060183128A1 (en) * 2003-08-12 2006-08-17 Epigenomics Ag Methods and compositions for differentiating tissues for cell types using epigenetic markers

Patent Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6310270B1 (en) * 1996-03-15 2001-10-30 The General Hospital Corporation Endothelial NOS knockout mice and methods of use
WO1997046705A1 (en) * 1996-06-03 1997-12-11 The Johns Hopkins University School Of Medicine Methylation specific detection
WO1998056952A1 (en) * 1997-06-09 1998-12-17 University Of Southern California A cancer diagnostic method based upon dna methylation differences
US6214556B1 (en) * 1997-11-27 2001-04-10 Epigenomics Ag Method for producing complex DNA methylation fingerprints
WO2002000932A2 (en) * 2000-06-30 2002-01-03 Epigenomics Ag Diagnosis of known genetic parameters within the mhc
WO2002034942A2 (en) * 2000-10-23 2002-05-02 Cancer Research Technology Limited Nucleic acid amplification-based methods for the determination of a methylation profile and reagents therefor
EP1213360A1 (en) * 2000-12-07 2002-06-12 The University of Tokyo Method of identifying cells using DNA methylation patterns
WO2003074730A1 (en) * 2002-03-05 2003-09-12 Epigenomics Ag Method and device for determination of tissue specificity of free floating dna in bodily fluids

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
SHIOTA K ET AL: "Epigenetic marks by DNA methylation specific to stem, germ and somatic cells in mice", GENES TO CELLS, OXFORD, GB, vol. 7, no. 9, September 2002 (2002-09-01), pages 961 - 969, XP002242365, ISSN: 1356-9597 *

Also Published As

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

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