EP2714933A4 - Methods using dna methylation for identifying a cell or a mixture of cells for prognosis and diagnosis of diseases, and for cell remediation therapies - Google Patents

Methods using dna methylation for identifying a cell or a mixture of cells for prognosis and diagnosis of diseases, and for cell remediation therapies

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
cell
prognosis
therapies
diagnosis
diseases
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Withdrawn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
German (de)
French (fr)
Other versions
EP2714933A2 (en
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.)
University of California
Brown University
Original Assignee
University of California
Brown University
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 University of California, Brown University filed Critical University of California
Publication of EP2714933A2 publication Critical patent/EP2714933A2/en
Publication of EP2714933A4 publication Critical patent/EP2714933A4/en
Withdrawn legal-status Critical Current

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
    • C12Q1/6876—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)
  • Zoology (AREA)
  • Public Health (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Software Systems (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Pathology (AREA)
  • Microbiology (AREA)
  • Immunology (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 Methods using dna methylation for identifying a cell or a mixture of cells for prognosis and diagnosis of diseases, and for cell remediation therapies Withdrawn EP2714933A4 (en)

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 (en) 2014-04-09
EP2714933A4 true EP2714933A4 (en) 2014-12-31

Family

ID=47218125

Family Applications (1)

Application Number Title Priority Date Filing Date
EP12789375.8A Withdrawn EP2714933A4 (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

Country Status (3)

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

Families Citing this family (19)

* 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 (en) * 2017-03-30 2020-08-05 Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen Method for determining blood counts based on dna methylation
DE102017125013B4 (en) 2017-10-25 2019-10-17 Epiontis Gmbh MCC as an epigenetic marker for the identification of immune cells, in particular basophilic granulocytes
DE102017125019B4 (en) 2017-10-25 2019-10-17 Epiontis Gmbh PDCD1 as an epigenetic marker for the identification of immune cells, in particular PD1 + cells
DE102017125150B4 (en) 2017-10-26 2019-10-10 Epiontis Gmbh Endosialin (CD248) as an epigenetic marker for the identification of immune cells, in particular naïver CD8 + T cells
DE102017125335B4 (en) 2017-10-27 2019-10-17 Epiontis Gmbh Amplicon region as an epigenetic marker for the identification of immune cells, especially non-classical monocytes
DE102017126248B4 (en) 2017-11-09 2019-10-17 Epiontis Gmbh ERGIC1 as epigenetic marker for the identification of immune cells, in particular monocytic myeloid-derived suppressor cells (mMDSCs)
DE102018112644B4 (en) 2018-05-25 2020-06-10 Epiontis Gmbh CXCR3 as an epigenetic marker for the identification of inflammatory immune cells, in particular CD8 + memory T cells
US20230183804A1 (en) 2018-07-05 2023-06-15 Precision For Medicine Gmbh Epigenetic method to detect and distinguish ipex and ipex-like syndromes, in particular in newborns
DE102020108560B4 (en) 2020-03-27 2022-03-03 Precision For Medicine Gmbh CBX6 as an epigenetic marker for the identification of immune cells, especially memory B cells
DE102020111423B4 (en) 2020-04-27 2022-03-03 Precision For Medicine Gmbh MYH11/NDE1 region as an epigenetic marker for the identification of endothelial progenitor cells (EPCs)
WO2022132666A1 (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 (en) * 2022-04-15 2022-07-05 北京莱盟君泰国际医疗技术开发有限公司 Blood free DNA methylation quantitative detection method and application thereof
WO2024073508A2 (en) * 2022-09-27 2024-04-04 Guardant Health, Inc. Methods and compositions for quantifying immune cell dna
CN116312794B (en) * 2023-01-09 2023-11-14 哈尔滨医科大学 Methylation sample clustering method fused with single cell analysis method
DE102023114004B3 (en) 2023-05-26 2024-09-12 Precision For Medicine Gmbh GATA 3 as an epigenetic marker for the identification of immune cells
DE102023114016B3 (en) 2023-05-26 2024-09-12 Precision For Medicine Gmbh LAG3 as an epigenetic marker for the identification of immune cells
DE102023114008B3 (en) 2023-05-26 2024-09-12 Precision For Medicine Gmbh CRTH2 (PTGDR2) as an epigenetic marker for the identification of immune cells
CN116949156B (en) * 2023-09-19 2023-12-08 美迪西普亚医药科技(上海)有限公司 Analysis method for detecting human T cells in general way based on nucleic acid variants

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1826278A1 (en) * 2006-02-28 2007-08-29 Epiontis GmbH Epigenetic modification of the loci for camta1 and/or foxp3 as a marker for cancer treatment

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1826278A1 (en) * 2006-02-28 2007-08-29 Epiontis GmbH Epigenetic modification of the loci for camta1 and/or foxp3 as a marker for cancer treatment

Non-Patent Citations (4)

* 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 *
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
CA2869295A1 (en) 2012-11-29
WO2012162660A2 (en) 2012-11-29
EP2714933A2 (en) 2014-04-09
WO2012162660A3 (en) 2013-03-28

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