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WO2012162660A3 - 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 Download PDF

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Publication number
WO2012162660A3
WO2012162660A3 PCT/US2012/039699 US2012039699W WO2012162660A3 WO 2012162660 A3 WO2012162660 A3 WO 2012162660A3 US 2012039699 W US2012039699 W US 2012039699W WO 2012162660 A3 WO2012162660 A3 WO 2012162660A3
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Prior art keywords
cell
cells
methods
identifying
mixture
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Ceased
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PCT/US2012/039699
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French (fr)
Other versions
WO2012162660A2 (en
Inventor
Karl KELSEY
Eugene Andres HOUSEMAN
John WIENCKE
William P. ACCOMANDO, Jr.
Carmen MARSIT
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Brown University
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Brown University
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Publication date
Application filed by Brown University filed Critical Brown University
Priority to EP12789375.8A priority Critical patent/EP2714933A4/en
Priority to CA2869295A priority patent/CA2869295A1/en
Publication of WO2012162660A2 publication Critical patent/WO2012162660A2/en
Publication of WO2012162660A3 publication Critical patent/WO2012162660A3/en
Priority to US14/089,398 priority patent/US20140178348A1/en
Anticipated expiration legal-status Critical
Priority to US15/271,909 priority patent/US10619211B2/en
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
    • C12Q1/6883—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

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  • 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)

Abstract

Methods using DNA Methylation arrays are provided for identifying a cell or mixture of cells and for quantification of alterations in distribution of cells in blood or in tissues, and for diagnosing, prognosing and treating disease conditions, particularly cancer. The methods use fresh and archival samples.
PCT/US2012/039699 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 Ceased WO2012162660A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
EP12789375.8A EP2714933A4 (en) 2011-05-25 2012-05-25 METHODS USING METHYLATION OF DNA TO IDENTIFY CELL OR MIXTURE OF CELLS TO PROGNOSE AND DIAGNOSE DISEASES AND TO PERFORM CELL REPAIR TREATMENTS
CA2869295A CA2869295A1 (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
US14/089,398 US20140178348A1 (en) 2011-05-25 2013-11-25 Methods using DNA methylation for identifying a cell or a mixture of cells for prognosis and diagnosis of diseases, and for cell remediation therapies
US15/271,909 US10619211B2 (en) 2011-05-25 2016-09-21 Methods using DNA methylation for identifying a cell or a mixture of cells for prognosis and diagnosis of diseases, and for cell remediation therapies

Applications Claiming Priority (8)

Application Number Priority Date Filing Date Title
US201161489883P 2011-05-25 2011-05-25
US61/489,883 2011-05-25
US201161509644P 2011-07-20 2011-07-20
US61/509,644 2011-07-20
US201261585892P 2012-01-12 2012-01-12
US61/585,892 2012-01-12
US201261619663P 2012-04-03 2012-04-03
US61/619,663 2012-04-03

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US14/089,398 Continuation-In-Part US20140178348A1 (en) 2011-05-25 2013-11-25 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
WO2012162660A2 WO2012162660A2 (en) 2012-11-29
WO2012162660A3 true WO2012162660A3 (en) 2013-03-28

Family

ID=47218125

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2012/039699 Ceased 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

Country Status (3)

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

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 (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
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 (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)
EP4259279A1 (en) 2020-12-14 2023-10-18 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
DE102023114008B3 (en) 2023-05-26 2024-09-12 Precision For Medicine Gmbh CRTH2 (PTGDR2) 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
DE102023114015B3 (en) 2023-05-26 2024-09-12 Precision For Medicine Gmbh ITGA4 as an epigenetic marker for the identification of immune cells
DE102023114004B3 (en) 2023-05-26 2024-09-12 Precision For Medicine Gmbh GATA 3 as an epigenetic marker for the identification of immune cells
WO2024258948A1 (en) * 2023-06-12 2024-12-19 Tru Diagnostics, Inc. Method for predicting health of a human subject
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)

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US20070269823A1 (en) * 2006-02-28 2007-11-22 Jochen Huehn Detection and quality control of regulatory T cells through DNA-methylation analysis of the Foxp3 gene

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2199411B1 (en) * 2008-12-16 2015-05-06 Epiontis GmbH Epigenetic markers for the identification of CD3 positive T-lymphocytes

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20070269823A1 (en) * 2006-02-28 2007-11-22 Jochen Huehn Detection and quality control of regulatory T cells through DNA-methylation analysis of the Foxp3 gene

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
KERKEL, K. ET AL.: "Altered DNA methylation in leukocytes with Trisomy 21", PLOS GENETICS, vol. 6, November 2010 (2010-11-01), pages E1001212, XP055139128 *
MARTIN-SUBERO, J. ET AL.: "A comprehensive microarray-based DNA methylation study of 367 hematological neoplasms", PLOS ONE, vol. 4, no. 9, September 2009 (2009-09-01), pages E6986, XP055139130 *
WANG, X. ET AL.: "Obesity related methylation changes in DNA of peripheral blood leukocytes", BMC MEDICINE, vol. 8, no. 87, 21 December 2010 (2010-12-21), XP021089557 *

Also Published As

Publication number Publication date
EP2714933A2 (en) 2014-04-09
WO2012162660A2 (en) 2012-11-29
CA2869295A1 (en) 2012-11-29
EP2714933A4 (en) 2014-12-31

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