WO2003044226A3 - Method and nucleic acids for the analysis of a lymphoid cell proliferative disorder - Google Patents

Method and nucleic acids for the analysis of a lymphoid cell proliferative disorder Download PDF

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Publication number
WO2003044226A3
WO2003044226A3 PCT/EP2002/013265 EP0213265W WO03044226A3 WO 2003044226 A3 WO2003044226 A3 WO 2003044226A3 EP 0213265 W EP0213265 W EP 0213265W WO 03044226 A3 WO03044226 A3 WO 03044226A3
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WO
WIPO (PCT)
Prior art keywords
cell proliferative
lymphoid cell
analysis
nucleic acids
proliferative disorder
Prior art date
Application number
PCT/EP2002/013265
Other languages
French (fr)
Other versions
WO2003044226A2 (en
Inventor
Matthias Burger
Charles Caldwell
Buelent Genc
Evelyne Becker
Sabine Maier
Inko Nimmrich
Original Assignee
Epigenomics Ag
Matthias Burger
Charles Caldwell
Buelent Genc
Evelyne Becker
Sabine Maier
Inko Nimmrich
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
Priority claimed from DE10164501A external-priority patent/DE10164501A1/en
Application filed by Epigenomics Ag, Matthias Burger, Charles Caldwell, Buelent Genc, Evelyne Becker, Sabine Maier, Inko Nimmrich filed Critical Epigenomics Ag
Priority to EP02787817A priority Critical patent/EP1451354A2/en
Priority to AU2002352143A priority patent/AU2002352143A1/en
Publication of WO2003044226A2 publication Critical patent/WO2003044226A2/en
Publication of WO2003044226A3 publication Critical patent/WO2003044226A3/en

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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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • C12Q1/683—Hybridisation assays for detection of mutation or polymorphism involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • 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
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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
    • C12Q2600/156—Polymorphic or mutational markers

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (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 relates to modified and genomic sequences, to oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of genomic DNA, as well as to a method for ascertaining genetic and/or epigenetic parameters of genes for use in the differentiation, diagnosis, treatment and/or monitoring of lymphoid cell proliferative disorders, or the predisposition to lymphoid cell proliferative disorders.
PCT/EP2002/013265 2001-11-23 2002-11-25 Method and nucleic acids for the analysis of a lymphoid cell proliferative disorder WO2003044226A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP02787817A EP1451354A2 (en) 2001-11-23 2002-11-25 Method and nucleic acids for the analysis of a lymphoid cell proliferative disorder
AU2002352143A AU2002352143A1 (en) 2001-11-23 2002-11-25 Method and nucleic acids for the analysis of a lymphoid cell proliferative disorder

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
DE10157491 2001-11-23
DE10157491.6 2001-11-23
DE10164501.5 2001-12-28
DE10164501A DE10164501A1 (en) 2001-11-23 2001-12-28 Methods and nucleic acids for the analysis of a lymphoid cell division disorder

Publications (2)

Publication Number Publication Date
WO2003044226A2 WO2003044226A2 (en) 2003-05-30
WO2003044226A3 true WO2003044226A3 (en) 2004-03-11

Family

ID=26010632

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/EP2002/013265 WO2003044226A2 (en) 2001-11-23 2002-11-25 Method and nucleic acids for the analysis of a lymphoid cell proliferative disorder

Country Status (3)

Country Link
EP (1) EP1451354A2 (en)
AU (1) AU2002352143A1 (en)
WO (1) WO2003044226A2 (en)

Families Citing this family (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2006088978A1 (en) 2005-02-16 2006-08-24 Epigenomics, Inc. Method for determining the methylation pattern of a polynucleic acid
US7932027B2 (en) 2005-02-16 2011-04-26 Epigenomics Ag Method for determining the methylation pattern of a polynucleic acid
SI1871912T1 (en) 2005-04-15 2012-06-29 Epigenomics Ag Method for determining DNA methylation in blood or urine samples
GB2435882A (en) * 2006-03-09 2007-09-12 Bioinvent Int Ab Detection and treatment of mantle cell lymphoma
WO2007137597A1 (en) * 2006-05-26 2007-12-06 Cnr Consiglio Nazionale Delle Ricerche Tests for detection of hot spot mutations and methylation of retinoblastoma-like 2 gene (rbl2) as diagnostic and prognostic markers of tumors
US20150259747A1 (en) 2007-03-29 2015-09-17 Vanda Pharmaceuticals Inc. Method of predicting a predisposition to qt prolongation
US9074254B2 (en) 2007-03-29 2015-07-07 Vanda Pharmaceuticals, Inc. Method of predicting a predisposition to QT prolongation
US8299237B2 (en) 2007-08-30 2012-10-30 Hadasit Medical Research Services & Development Ltd. Nucleic acid sequences comprising NF-κB binding site within O(6)-methylguanine-DNA-methyltransferase (MGMT) promoter region and uses thereof for the treatment of cancer and immune-related disorders
US8242243B2 (en) 2008-05-15 2012-08-14 Ribomed Biotechnologies, Inc. Methods and reagents for detecting CpG methylation with a methyl CpG binding protein (MBP)
CN102421914A (en) 2009-03-15 2012-04-18 里伯米德生物技术公司 Molecular detection based on abortive transcription
US9096905B2 (en) * 2012-02-23 2015-08-04 Medical Diagnostic Laboratories, Llc Detecting DNA methylation of BCL2, CDKN2A and NID2 genes to predict bladder cancer in humans
FI4026917T3 (en) * 2014-04-14 2024-02-14 Yissum Research And Development Company Of The Hebrew Univ Of Jerusalem Ltd A method and kit for determining the death of cells or tissue or the tissue or cell origin of dna by dna methylation analysis

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6077668A (en) * 1993-04-15 2000-06-20 University Of Rochester Highly sensitive multimeric nucleic acid probes
WO2001007647A2 (en) * 1999-07-26 2001-02-01 Epigenomics Ag Method for relative quantization of methylation of cytosin-type bases in dna samples
WO2002077272A2 (en) * 2001-03-26 2002-10-03 Epigenomics Ag Methods and nucleic acids for the analysis of hematopoietic cell proliferative disorders
WO2003052135A2 (en) * 2001-12-14 2003-06-26 Epigenomics Ag Method and nucleic acids for the analysis of a lung cell proliferative disorder

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6077668A (en) * 1993-04-15 2000-06-20 University Of Rochester Highly sensitive multimeric nucleic acid probes
WO2001007647A2 (en) * 1999-07-26 2001-02-01 Epigenomics Ag Method for relative quantization of methylation of cytosin-type bases in dna samples
WO2002077272A2 (en) * 2001-03-26 2002-10-03 Epigenomics Ag Methods and nucleic acids for the analysis of hematopoietic cell proliferative disorders
WO2003052135A2 (en) * 2001-12-14 2003-06-26 Epigenomics Ag Method and nucleic acids for the analysis of a lung cell proliferative disorder

Non-Patent Citations (10)

* Cited by examiner, † Cited by third party
Title
BAUR A S ET AL: "Frequent methylation silencing of p15(INK4b) (MTS2) and p16(INK4a) (MTS1) in B-cell and T-cell lymphomas.", BLOOD. UNITED STATES 1 SEP 1999, vol. 94, no. 5, 1 September 1999 (1999-09-01), pages 1773 - 1781, XP002255681, ISSN: 0006-4971 *
GARCIA-MANERO G ET AL: "CPG ISLAND METHYLATION PROFILE IN ACUTE LYMPHOCYTIC LEUKEMIA (ALL)", BLOOD, W.B.SAUNDERS COMPAGNY, ORLANDO, FL, US, vol. 96, no. 11, PART 1, 16 November 2000 (2000-11-16), pages 102A, XP009010440, ISSN: 0006-4971 *
GARCIA-MANERO GUILLERMO ET AL: "DNA methylation of multiple promoter-associated CpG islands in adult acute lymphocytic leukemia.", CLINICAL CANCER RESEARCH: AN OFFICIAL JOURNAL OF THE AMERICAN ASSOCIATION FOR CANCER RESEARCH. UNITED STATES JUL 2002, vol. 8, no. 7, July 2002 (2002-07-01), pages 2217 - 2224, XP002255684, ISSN: 1078-0432 *
KANTHARIDIS P ET AL: "Altered Methylation of the Human MDR1 Promoter is Associated with Aquired Multidrug Resistance", CLINICAL CANCER RESEARCH, vol. 3, pages 2025 - 2032, XP001155344 *
MODEL F ET AL: "Feature selection for DNA methylation based cancer classification.", BIOINFORMATICS (OXFORD, ENGLAND) ENGLAND 2001, vol. 17 Suppl 1, 2001, pages S157 - S164, XP001154594, ISSN: 1367-4803 *
SHANNON B A ET AL: "Methylation of the hMLH1, p16, and MDR1 genes in colorectal carcinoma: associations with clinicopathological features.", CANCER LETTERS. IRELAND 10 JUN 2001, vol. 167, no. 1, 10 June 2001 (2001-06-10), pages 91 - 97, XP002255680, ISSN: 0304-3835 *
TADA Y ET AL: "MDR1 gene overexpression and altered degree of methylation at the promoter region in bladder cancer during chemotherapeutic treatment.", CLINICAL CANCER RESEARCH: AN OFFICIAL JOURNAL OF THE AMERICAN ASSOCIATION FOR CANCER RESEARCH. UNITED STATES DEC 2000, vol. 6, no. 12, December 2000 (2000-12-01), pages 4618 - 4627, XP002255679, ISSN: 1078-0432 *
TAYLOR J M ET AL: "The diagnositc significance of Myf-3 hypermethylation in malignant lymphoproliferative disorders.", LEUKEMIA: OFFICIAL JOURNAL OF THE LEUKEMIA SOCIETY OF AMERICA, LEUKEMIA RESEARCH FUND, U.K. ENGLAND APR 2001, vol. 15, no. 4, April 2001 (2001-04-01), pages 583 - 589, XP001154596, ISSN: 0887-6924 *
VAN DEN HEUVEL-EIBRINK M M ET AL: "MDR1 expression in poor-risk acute myeloid leukemia with partial or complete monosomy 7.", LEUKEMIA: OFFICIAL JOURNAL OF THE LEUKEMIA SOCIETY OF AMERICA, LEUKEMIA RESEARCH FUND, U.K. ENGLAND MAR 2001, vol. 15, no. 3, March 2001 (2001-03-01), pages 398 - 405, XP002255678, ISSN: 0887-6924 *
WADA F ET AL: "5' CPG ISLAND DEMETHYLATION IS ASSOCIATED WITH TRANSCRIPTIONAL ACTIVATION OF THE HUMAN MULTIDRUG-RESISTANCE 1 (MDR1) GENE IN HUMAN TUMORS", PROCEEDINGS OF THE 88TH. ANNUAL MEETING OF THE AMERICAN ASSOCIATION FOR CANCER RESEARCH. SAN DIEGO, APR. 12 - 16, 1997, PROCEEDINGS OF THE ANNUAL MEETING OF THE AMERICAN ASSOCIATION FOR CANCER RESEARCH, PHILADELPHIA, AACR, US, vol. 38, March 1997 (1997-03-01), pages 480, XP001160788 *

Also Published As

Publication number Publication date
AU2002352143A1 (en) 2003-06-10
EP1451354A2 (en) 2004-09-01
WO2003044226A2 (en) 2003-05-30

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