EP2714933A4 - METHODS USING METHYLATION OF DNA TO IDENTIFY CELL OR MIXTURE OF CELLS TO PROGNOSE AND DIAGNOSE DISEASES AND TO PERFORM CELL REPAIR TREATMENTS - Google Patents

METHODS USING METHYLATION OF DNA TO IDENTIFY CELL OR MIXTURE OF CELLS TO PROGNOSE AND DIAGNOSE DISEASES AND TO PERFORM CELL REPAIR TREATMENTS

Info

Publication number: EP2714933A4
Authority: EP; European Patent Office
Prior art keywords: prognose; methylation; dna; cells; mixture
Prior art date: 2011-05-25
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 Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.): Withdrawn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.)

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.)

2011-05-25

Filing date

2012-05-25

Publication date

2014-12-31

2012-05-25 Application filed by Brown University, University of California Berkeley, University of California San Diego UCSD filed Critical Brown University

2014-04-09 Publication of EP2714933A2 publication Critical patent/EP2714933A2/en

2014-12-31 Publication of EP2714933A4 publication Critical patent/EP2714933A4/en

Status Withdrawn legal-status Critical Current

Links

201000010099 disease Diseases 0.000 title 1
208000037265 diseases, disorders, signs and symptoms Diseases 0.000 title 1
238000000034 method Methods 0.000 title 1
230000011987 methylation Effects 0.000 title 1
238000007069 methylation reaction Methods 0.000 title 1
239000000203 mixture Substances 0.000 title 1
238000011282 treatment Methods 0.000 title 1

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 METHODS USING METHYLATION OF DNA TO IDENTIFY CELL OR MIXTURE OF CELLS TO PROGNOSE AND DIAGNOSE DISEASES AND TO PERFORM CELL REPAIR TREATMENTS 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 METHYLATION OF DNA TO IDENTIFY CELL OR MIXTURE OF CELLS TO PROGNOSE AND DIAGNOSE DISEASES AND TO PERFORM CELL REPAIR TREATMENTS

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
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
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
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)
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 (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
EP4594522A2 (en) *	2022-09-27	2025-08-06	Guardant Health, Inc.	Methods 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
DE102023114015B3 (en)	2023-05-26	2024-09-12	Precision For Medicine Gmbh	ITGA4 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
DE102023114004B3 (en)	2023-05-26	2024-09-12	Precision For Medicine Gmbh	GATA 3 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
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 (2)

* 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
EP2199411A1 (en) *	2008-12-16	2010-06-23	Epiontis GmbH	Epigenetic markers for the identification of CD3 positive T-lymphocytes

2012
- 2012-05-25 CA CA2869295A patent/CA2869295A1/en not_active Abandoned
- 2012-05-25 EP EP12789375.8A patent/EP2714933A4/en not_active Withdrawn
- 2012-05-25 WO PCT/US2012/039699 patent/WO2012162660A2/en not_active Ceased

Patent Citations (2)

* 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
EP2199411A1 (en) *	2008-12-16	2010-06-23	Epiontis GmbH	Epigenetic markers for the identification of CD3 positive T-lymphocytes

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

Legal Events

Date	Code	Title	Description
2014-03-07	PUAI	Public reference made under article 153(3) epc to a published international application that has entered the european phase	Free format text: ORIGINAL CODE: 0009012
2014-04-09	17P	Request for examination filed	Effective date: 20140102
2014-04-09	AK	Designated contracting states	Kind code of ref document: A2 Designated state(s): AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR
2014-09-03	DAX	Request for extension of the european patent (deleted)
2014-12-17	RIC1	Information provided on ipc code assigned before grant	Ipc: C12N 15/11 20060101ALI20141110BHEP Ipc: G06F 17/10 20060101ALI20141110BHEP Ipc: C12Q 1/68 20060101AFI20141110BHEP
2014-12-31	A4	Supplementary search report drawn up and despatched	Effective date: 20141203
2014-12-31	RIC1	Information provided on ipc code assigned before grant	Ipc: G06F 17/10 20060101ALI20141126BHEP Ipc: C12Q 1/68 20060101AFI20141126BHEP Ipc: C12N 15/11 20060101ALI20141126BHEP
2015-09-09	17Q	First examination report despatched	Effective date: 20150806
2017-06-07	STAA	Information on the status of an ep patent application or granted ep patent	Free format text: STATUS: EXAMINATION IS IN PROGRESS
2020-06-26	STAA	Information on the status of an ep patent application or granted ep patent	Free format text: STATUS: THE APPLICATION IS DEEMED TO BE WITHDRAWN
2020-07-29	18D	Application deemed to be withdrawn	Effective date: 20200114

Publication	Publication Date	Title
EP2714933A4 (en)	2014-12-31	METHODS USING METHYLATION OF DNA TO IDENTIFY CELL OR MIXTURE OF CELLS TO PROGNOSE AND DIAGNOSE DISEASES AND TO PERFORM CELL REPAIR TREATMENTS
EP2485751A4 (en)	2013-03-13	METHODS OF TREATING DEPRESSION AND OTHER ASSOCIATED DISEASES
AR088514A1 (en)	2014-06-18	BISPECIFIC IMMUNOLIGANTS DIRECTED AGAINST TNF
EP2797416A4 (en)	2015-12-23	SUBSTITUTED BENZALDEHYDE COMPOUNDS AND METHODS OF USE THEREOF IN INCREASING TISSUE OXYGENATION
EP2517402A4 (en)	2014-01-08	ARCHITECTURE OF DECOUPLED CASCADE MIXERS AND RELATED METHODS
EP2637702A4 (en)	2014-11-26	METHODS, COMPOSITIONS, CELLS AND KITS FOR TREATING ISCHEMIC LESIONS
EP2435557A4 (en)	2014-05-07	GENETICALLY INDUCED INTRODUCED PLURIPOTENT CELLS OR TRANSDIFFERENCED CELLS AND METHODS OF PRODUCTION THEREOF
BR112014023353A2 (en)	2017-07-11	methods for modifying specific site of target dna molecule, to obtain complex in genetically modified microorganism, to cleave polynucleotide and nucleotide sequence, to cut specific site of polynucleotide and nucleotide sequences, in vitro to generate complexes, to reprogram specificity of cas9-crrna complex and to selectively modify site-specific target DNA molecule in vivo, rna-protein and cas9-crrna complexes, cas9-isolated protein and isolated crrna
EP2651565A4 (en)	2016-11-09	METHODS AND APPARATUS FOR ENHANCED RECOVERY OF CELLS AND CELL-ENRICHED MATRIX FROM TISSUE SAMPLES
EP2791325A4 (en)	2015-08-05	METHODS AND COMPOSITIONS FOR ANALYSIS OF AHASL GENES PRESENT IN WHEAT
AR089529A1 (en)	2014-08-27	UNION PROTEINS SPECIFIC DUALS DIRECTED AGAINST IL-13 AND / OR IL-17
EP2249644A4 (en)	2012-05-30	PICOPLATIN AND AMRUBICIN USEFUL IN THE TREATMENT OF LUNG CANCER
EP2294183A4 (en)	2012-08-15	MESENCHYMAL STEM CELLS, COMPOSITIONS AND METHODS FOR TREATMENT OF CARDIAC TISSUE LESIONS
EP2748333A4 (en)	2015-05-20	DNA METHYLATION IN DIAGNOSTIC METHODS OF COLORECTAL CANCER AND BREAST
EP2247750A4 (en)	2011-10-26	METHODS AND COMPOSITIONS RELATING TO CARCINOMA STEM CELLS
EP2866017A4 (en)	2016-02-24	METHOD FOR MAKING TRANSPARENT BIOLOGICAL SUBSTANCE AND TREATMENT KIT THEREFOR
EP2303310A4 (en)	2012-07-11	COMPOSITIONS AND METHODS FOR USING CELLS TO TREAT CARDIAC TISSUE
EP2274617A4 (en)	2011-11-09	METHODS FOR IDENTIFYING AND USING AGENTS TARGETING CANCER STEM CELLS
KR102112438B9 (en)	2024-08-22	Diagnosis of fetal chromosomal aneuploidy using massively parallel genome sequencing
EP2286217A4 (en)	2011-05-25	METHODS AND COMPOSITIONS OF INDIVIDUAL MOLECULE LOAD
EP2660331A4 (en)	2015-04-15	METHOD FOR SINGLE CELL GENOME ANALYSIS AND CORRESPONDING KIT
EP2683812A4 (en)	2014-12-03	METHODS FOR TRANSFECTING CELLS WITH NUCLEIC ACIDS
EP3699291C0 (en)	2024-08-07	SINGLE MOLECULE NUCLEIC ACID SEQUENCE ANALYSIS METHODS AND COMPOSITIONS
EP2523563A4 (en)	2013-08-07	METHOD OF TREATING NEUROLOGICAL DISEASES USING CARDIAC GLYCOSIDES
EP2503995A4 (en)	2014-05-21	METHODS, COMPOSITIONS AND LYOPHILIZATION KITS