EP2714933A4 - Verfahren mit dna-methylierung zur identifizierung einer zelle oder einer mischung von zellen zur prognose und diagnose von erkrankungen sowie für zellheilungstherapien - Google Patents

Verfahren mit dna-methylierung zur identifizierung einer zelle oder einer mischung von zellen zur prognose und diagnose von erkrankungen sowie für zellheilungstherapien

Info

Publication number
EP2714933A4
EP2714933A4 EP12789375.8A EP12789375A EP2714933A4 EP 2714933 A4 EP2714933 A4 EP 2714933A4 EP 12789375 A EP12789375 A EP 12789375A EP 2714933 A4 EP2714933 A4 EP 2714933A4
Authority
EP
European Patent Office
Prior art keywords
prognose
methylation
dna
cells
mixture
Prior art date
Legal status (The legal status 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 status listed.)
Withdrawn
Application number
EP12789375.8A
Other languages
English (en)
French (fr)
Other versions
EP2714933A2 (de
Inventor
Karl Kelsey
Eugene Andres Houseman
John Wiencke
William P Accomando Jr
Carmen Marsit
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Brown University
University of California Berkeley
University of California San Diego UCSD
Original Assignee
Brown University
University of California Berkeley
University of California San Diego UCSD
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 Brown University, University of California Berkeley, University of California San Diego UCSD filed Critical Brown University
Publication of EP2714933A2 publication Critical patent/EP2714933A2/de
Publication of EP2714933A4 publication Critical patent/EP2714933A4/de
Withdrawn legal-status Critical Current

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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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/10—Ploidy or copy number detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/30—Unsupervised data analysis
    • 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
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Chemical & Material Sciences (AREA)
  • Medical Informatics (AREA)
  • Biotechnology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Analytical Chemistry (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Molecular Biology (AREA)
  • Data Mining & Analysis (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Zoology (AREA)
  • Artificial Intelligence (AREA)
  • Software Systems (AREA)
  • Pathology (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
EP12789375.8A 2011-05-25 2012-05-25 Verfahren mit dna-methylierung zur identifizierung einer zelle oder einer mischung von zellen zur prognose und diagnose von erkrankungen sowie für zellheilungstherapien Withdrawn EP2714933A4 (de)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201161489883P 2011-05-25 2011-05-25
US201161509644P 2011-07-20 2011-07-20
US201261585892P 2012-01-12 2012-01-12
US201261619663P 2012-04-03 2012-04-03
PCT/US2012/039699 WO2012162660A2 (en) 2011-05-25 2012-05-25 Methods using dna methylation for identifying a cell or a mixture of cells for prognosis and diagnosis of diseases, and for cell remediation therapies

Publications (2)

Publication Number Publication Date
EP2714933A2 EP2714933A2 (de) 2014-04-09
EP2714933A4 true EP2714933A4 (de) 2014-12-31

Family

ID=47218125

Family Applications (1)

Application Number Title Priority Date Filing Date
EP12789375.8A Withdrawn EP2714933A4 (de) 2011-05-25 2012-05-25 Verfahren mit dna-methylierung zur identifizierung einer zelle oder einer mischung von zellen zur prognose und diagnose von erkrankungen sowie für zellheilungstherapien

Country Status (3)

Country Link
EP (1) EP2714933A4 (de)
CA (1) CA2869295A1 (de)
WO (1) WO2012162660A2 (de)

Families Citing this family (21)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9561006B2 (en) * 2008-10-15 2017-02-07 The United States Of America As Represented By The Secretary Of The Navy Bayesian modeling of pre-transplant variables accurately predicts kidney graft survival
EP3382033B1 (de) * 2017-03-30 2020-08-05 Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen Verfahren zur bestimmung von blutkörperchenzahlen auf der basis der dns methylierung
DE102017125019B4 (de) 2017-10-25 2019-10-17 Epiontis Gmbh PDCD1 als epigenetischer Marker zur Identifizierung von Immunzellen, insbesondere PD1+ Zellen
DE102017125013B4 (de) 2017-10-25 2019-10-17 Epiontis Gmbh MCC als epigenetischer Marker zur Identifizierung von Immunzellen, insbesondere basophiler Granulozyten
DE102017125150B4 (de) 2017-10-26 2019-10-10 Epiontis Gmbh Endosialin (CD248) als epigenetischer Marker zur Identifizierung von Immunzellen, insbesondere naïver CD8+ T-Zellen
DE102017125335B4 (de) 2017-10-27 2019-10-17 Epiontis Gmbh Amplikon-Region als epigenetischer Marker zur Identifizierung von Immunzellen, insbesondere nicht-klassischer Monozyten
DE102017126248B4 (de) 2017-11-09 2019-10-17 Epiontis Gmbh ERGIC1 als epigenetischer Marker zur Identifizierung von Immunzellen, insbesonderemonozytischem myeloid-abgeleiteten Suppressor-Zellen (mMDSCs)
DE102018112644B4 (de) 2018-05-25 2020-06-10 Epiontis Gmbh CXCR3 als epigenetischer Marker zur Identifizierung von inflammatorischen Immunzellen, insbesondere CD8+ Gedächnis-T-Zellen
WO2020007951A1 (en) 2018-07-05 2020-01-09 Epiontis Gmbh Epigenetic method to detect and distinguish ipex and ipex-like syndromes, in particular in newborns
DE102020108560B4 (de) 2020-03-27 2022-03-03 Precision For Medicine Gmbh CBX6 als epigenetischer Marker für die Identifizierung von Immunzellen, insbesondere Gedächtnis-B-Zellen
DE102020111423B4 (de) 2020-04-27 2022-03-03 Precision For Medicine Gmbh MYH11/NDE1 Region als epigenetischer Marker für die Identifizierung von Endothel-Vorläuferzellen (EPCs)
CA3201466A1 (en) 2020-12-14 2022-06-23 Regeneron Pharmaceuticals, Inc. Methods of treating metabolic disorders and cardiovascular disease with inhibin subunit beta e (inhbe) inhibitors
CN114703284A (zh) * 2022-04-15 2022-07-05 北京莱盟君泰国际医疗技术开发有限公司 一种血液游离dna甲基化定量检测方法及其应用
EP4594522A2 (de) * 2022-09-27 2025-08-06 Guardant Health, Inc. Verfahren zur quantifizierung von immunzellen-dna
CN116312794B (zh) * 2023-01-09 2023-11-14 哈尔滨医科大学 一种融合单细胞分析方法的甲基化样本聚类方法
DE102023114015B3 (de) 2023-05-26 2024-09-12 Precision For Medicine Gmbh ITGA4 als epigenetischer Marker für die Identifizierung von Immunzellen
DE102023114016B3 (de) 2023-05-26 2024-09-12 Precision For Medicine Gmbh LAG3 als epigenetischer Marker für die Identifizierung von Immunzellen
DE102023114004B3 (de) 2023-05-26 2024-09-12 Precision For Medicine Gmbh GATA 3 als epigenetischer Marker zur Identifizierung von Immunzellen
DE102023114008B3 (de) 2023-05-26 2024-09-12 Precision For Medicine Gmbh CRTH2 (PTGDR2) als epigenetischer Marker zur Identifizierung von Immunzellen
WO2024258948A1 (en) * 2023-06-12 2024-12-19 Tru Diagnostics, Inc. Method for predicting health of a human subject
CN116949156B (zh) * 2023-09-19 2023-12-08 美迪西普亚医药科技(上海)有限公司 一种基于核酸变体的通用型检测人t细胞的分析方法

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1826278A1 (de) * 2006-02-28 2007-08-29 Epiontis GmbH Epigenetische Modifikation der Loci für CAMTA1 und/oder FOXP3 als Markierung für die Krebsbehandlung
EP2199411A1 (de) * 2008-12-16 2010-06-23 Epiontis GmbH Epigenetische Marker zur Identifikation von CD3+ T-Lymphozyten

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1826278A1 (de) * 2006-02-28 2007-08-29 Epiontis GmbH Epigenetische Modifikation der Loci für CAMTA1 und/oder FOXP3 als Markierung für die Krebsbehandlung
EP2199411A1 (de) * 2008-12-16 2010-06-23 Epiontis GmbH Epigenetische Marker zur Identifikation von CD3+ T-Lymphozyten

Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
JOSE I. MARTIN-SUBERO ET AL: "A Comprehensive Microarray-Based DNA Methylation Study of 367 Hematological Neoplasms", PLOS ONE, vol. 4, no. 9, E6986, 11 September 2009 (2009-09-11), pages 1 - 11, XP055139130, DOI: 10.1371/journal.pone.0006986 *
KRISTI KERKEL ET AL: "Altered DNA Methylation in Leukocytes with Trisomy 21", PLOS GENETICS, vol. 6, no. 11, E1001212, 18 November 2010 (2010-11-18), pages 1 - 13, XP055139128, DOI: 10.1371/journal.pgen.1001212 *
See also references of WO2012162660A2 *
SEHOULI J ET AL: "Epigenetic quantification of tumor-infiltrating T-lymphocytes", EPIGENETICS, LANDES BIOSCIENCE, US, vol. 6, no. 2, 1 February 2011 (2011-02-01), pages 236 - 246, XP002639447, ISSN: 1559-2294, [retrieved on 20110201], DOI: 10.4161/EPI.6.2.13755 *
WU MINGQI ET AL: "Bayesian modeling of ChIP-chip data using latent variables.", BMC BIOINFORMATICS, vol. 10, 352, 2009, pages 13PP, XP002731974, ISSN: 1471-2105 *

Also Published As

Publication number Publication date
EP2714933A2 (de) 2014-04-09
WO2012162660A2 (en) 2012-11-29
CA2869295A1 (en) 2012-11-29
WO2012162660A3 (en) 2013-03-28

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