WO2005001142A3 - Methods and nucleic acids for the analysis of colorectal cell proliferative disorders - Google Patents

Methods and nucleic acids for the analysis of colorectal cell proliferative disorders Download PDF

Info

Publication number
WO2005001142A3
WO2005001142A3 PCT/US2004/020356 US2004020356W WO2005001142A3 WO 2005001142 A3 WO2005001142 A3 WO 2005001142A3 US 2004020356 W US2004020356 W US 2004020356W WO 2005001142 A3 WO2005001142 A3 WO 2005001142A3
Authority
WO
WIPO (PCT)
Prior art keywords
cell proliferative
proliferative disorders
methods
detecting
colorectal cell
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.)
Ceased
Application number
PCT/US2004/020356
Other languages
French (fr)
Other versions
WO2005001142A2 (en
Inventor
Cathy Lofton-Day
Andrew Sledziewski
Jeff Thomas
Robert W Day
Lori Tonnes-Priddy
Karen Cardon
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.)
Epigenomics AG
Original Assignee
Epigenomics AG
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 Epigenomics AG filed Critical Epigenomics AG
Priority to EP04777063A priority Critical patent/EP1636387A2/en
Priority to US10/562,377 priority patent/US20070184438A1/en
Publication of WO2005001142A2 publication Critical patent/WO2005001142A2/en
Publication of WO2005001142A3 publication Critical patent/WO2005001142A3/en
Anticipated expiration legal-status Critical
Ceased 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
    • 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
    • C12Q2600/112—Disease subtyping, staging or classification
    • 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

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • Wood Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Hospice & Palliative Care (AREA)
  • Biophysics (AREA)
  • Oncology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Various aspects of the present invention provide novel diagnostic and prognostic methods for detecting, or for detecting and differentiating between or among colorectal cell proliferative disorders. Preferably, said colorectal cell proliferative disorders are selected from the group consisting of colorectal carcinoma, colon adenomas, and colon polyps. The inventive methods are based on analysis of differential CpG dinucleotide methylation of genomic DNA between or among normal and disease states. Additional embodiments provide nucleic acids and oligomers (including oligonucleotides and peptide nucleic acid (PNA)-oligomers), nucleic acid arrays and kits useful for practicing said methods, and in otherwise detecting, or detecting and differentiating between or among colorectal cell proliferative disorders.
PCT/US2004/020356 2003-06-23 2004-06-23 Methods and nucleic acids for the analysis of colorectal cell proliferative disorders Ceased WO2005001142A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP04777063A EP1636387A2 (en) 2003-06-23 2004-06-23 Methods and nucleic acids for the analysis of colorectal cell proliferative disorders
US10/562,377 US20070184438A1 (en) 2003-06-23 2004-06-23 Methods and nucleic acids for the analysis of colorectal cell proliferative disorders

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US10/602,494 US20040265833A1 (en) 2003-06-23 2003-06-23 Methods and nucleic acids for the analysis of colorectal cell proliferative disorders
US10/602,494 2003-06-23

Publications (2)

Publication Number Publication Date
WO2005001142A2 WO2005001142A2 (en) 2005-01-06
WO2005001142A3 true WO2005001142A3 (en) 2005-12-15

Family

ID=33539559

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2004/020356 Ceased WO2005001142A2 (en) 2003-06-23 2004-06-23 Methods and nucleic acids for the analysis of colorectal cell proliferative disorders

Country Status (3)

Country Link
US (2) US20040265833A1 (en)
EP (1) EP1636387A2 (en)
WO (1) WO2005001142A2 (en)

Families Citing this family (19)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6207646B1 (en) 1994-07-15 2001-03-27 University Of Iowa Research Foundation Immunostimulatory nucleic acid molecules
PT1456380E (en) * 2001-11-02 2012-07-23 Giuliani Int Ltd Smad7 inhibitors for the treatment of cns diseases
ITRM20030149A1 (en) 2003-04-02 2004-10-03 Giuliani Spa ANTISENSE OLIGONUCLEOTIDES (ODN) FOR SMAD7 AND THEIR USE IN THE MEDICAL FIELD
DE102005011398A1 (en) * 2005-03-03 2006-09-14 Epigenomics Ag Method for the investigation of cytosine methylations in DNA
KR101206028B1 (en) * 2005-03-05 2012-11-28 삼성전자주식회사 Method for diagnosing a breast cancer using a breast cancer specific polymorphic sequence, polynucleotide specific to a breast cancer and microarray immobilized with the polynucleotide
KR20130021400A (en) * 2005-04-15 2013-03-05 에피제노믹스 아게 Methods and nucleic acids for analyses of cellular proliferative disorders
ES2446250T3 (en) * 2005-05-02 2014-03-06 University Of Southern California DNA methylation markers associated with the CpG island methylation phenotype (CIMP) in human colorectal cancer
AU2006304883A1 (en) 2005-10-21 2007-04-26 Genenews Inc. Method and apparatus for correlating levels of biomarker products with disease
CA2676227A1 (en) * 2007-02-12 2008-08-21 The Johns Hopkins University Early detection and prognosis of colon cancers
WO2010099489A2 (en) * 2009-02-27 2010-09-02 The Johns Hopkins University Ovarian cancer methylome
ES2669439T3 (en) * 2009-06-26 2018-05-25 Epigenomics Ag Methods and nucleic acids for bladder carcinoma analysis
WO2012024535A2 (en) * 2010-08-18 2012-02-23 Fred Hutchinson Cancer Research Center Methods for determining the presence or risk of developing facioscapulohumeral dystrophy (fshd)
CN110055330B (en) * 2019-04-30 2022-10-11 上海奕谱生物科技有限公司 Tumor marker STAMP-EP9 based on methylation modification and application thereof
US11001898B2 (en) 2019-05-31 2021-05-11 Universal Diagnostics, S.L. Detection of colorectal cancer
US11396679B2 (en) 2019-05-31 2022-07-26 Universal Diagnostics, S.L. Detection of colorectal cancer
US11898199B2 (en) 2019-11-11 2024-02-13 Universal Diagnostics, S.A. Detection of colorectal cancer and/or advanced adenomas
WO2021228418A1 (en) 2020-05-15 2021-11-18 Universal Diagnostics, S.L. Methods and systems for identifying methylation biomarkers
WO2022002424A1 (en) 2020-06-30 2022-01-06 Universal Diagnostics, S.L. Systems and methods for detection of multiple cancer types
US12606872B2 (en) 2022-11-16 2026-04-21 Universal Diagnostics, S.A. Methods for stratification and early detection of advanced adenoma and/or colorectal cancer using DNA methylation markers

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002024056A2 (en) * 2000-09-20 2002-03-28 Case Western Reserve University METHODS AND COMPOSITIONS FOR DETECTING CANCERS ASSOCIATED WITH METHYLATION OF hMLH1PROMOTER DNA
WO2003014388A2 (en) * 2001-08-09 2003-02-20 Epigenomics Ag Method and nucleic acids for the analysis of colon cancer

Family Cites Families (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5567610A (en) * 1986-09-04 1996-10-22 Bioinvent International Ab Method of producing human monoclonal antibodies and kit therefor
US5585481A (en) * 1987-09-21 1996-12-17 Gen-Probe Incorporated Linking reagents for nucleotide probes
US5457183A (en) * 1989-03-06 1995-10-10 Board Of Regents, The University Of Texas System Hydroxylated texaphyrins
US6521594B1 (en) * 1990-04-06 2003-02-18 La Jolla Cancer Research Foundation Method and composition for treating thrombosis
US5565552A (en) * 1992-01-21 1996-10-15 Pharmacyclics, Inc. Method of expanded porphyrin-oligonucleotide conjugate synthesis
US5574142A (en) * 1992-12-15 1996-11-12 Microprobe Corporation Peptide linkers for improved oligonucleotide delivery
US5597696A (en) * 1994-07-18 1997-01-28 Becton Dickinson And Company Covalent cyanine dye oligonucleotide conjugates
US6017704A (en) * 1996-06-03 2000-01-25 The Johns Hopkins University School Of Medicine Method of detection of methylated nucleic acid using agents which modify unmethylated cytosine and distinguishing modified methylated and non-methylated nucleic acids
US5786146A (en) * 1996-06-03 1998-07-28 The Johns Hopkins University School Of Medicine Method of detection of methylated nucleic acid using agents which modify unmethylated cytosine and distinguishing modified methylated and non-methylated nucleic acids
US5958773A (en) * 1998-12-17 1999-09-28 Isis Pharmaceuticals Inc. Antisense modulation of AKT-1 expression
US6331393B1 (en) * 1999-05-14 2001-12-18 University Of Southern California Process for high-throughput DNA methylation analysis
US7473767B2 (en) * 2001-07-03 2009-01-06 The Institute For Systems Biology Methods for detection and quantification of analytes in complex mixtures

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002024056A2 (en) * 2000-09-20 2002-03-28 Case Western Reserve University METHODS AND COMPOSITIONS FOR DETECTING CANCERS ASSOCIATED WITH METHYLATION OF hMLH1PROMOTER DNA
WO2003014388A2 (en) * 2001-08-09 2003-02-20 Epigenomics Ag Method and nucleic acids for the analysis of colon cancer

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
DATABASE EMBL [online] 11 November 1999 (1999-11-11), "Homo sapiens BAC clone RP11-538J11 from 2, complete sequence.", XP002313106, retrieved from EBI accession no. EM_HUM:AC013413 Database accession no. AC013413 *
DATABASE EMBL [online] 16 July 2002 (2002-07-16), "Homo sapiens cDNA FLJ40417 fis, clone TESTI2038388, highly similar to Homo sapiens gamma cysteine string protein mRNA.", XP002313107, retrieved from EBI accession no. EM_HUM:AK097736 Database accession no. AK097736 *

Also Published As

Publication number Publication date
EP1636387A2 (en) 2006-03-22
WO2005001142A2 (en) 2005-01-06
US20040265833A1 (en) 2004-12-30
US20070184438A1 (en) 2007-08-09

Similar Documents

Publication Publication Date Title
WO2005001142A3 (en) Methods and nucleic acids for the analysis of colorectal cell proliferative disorders
WO2002002808A3 (en) Method and nucleic acids for the analysis of astrocytomas
CA2369045A1 (en) Methods for improving sensitivity and specificity of screening assays
JP2004527241A (en) Highly sensitive method to demonstrate cytosine methylated form
EP1241266A4 (en) Method of detecting nucleotide polymorphism
CA2172248A1 (en) Self-sustained sequence replication electrochemiluminescent nucleic acid assay
WO2000077260A8 (en) Genomic profiling: a rapid method for testing a complex biological sample for the presence of many types of organisms
ATE534748T1 (en) DIRECT SNP DETECTION USING NON-AMPLIFIED DNA
CA2396778A1 (en) Methods and kits for identifying elite event gat-zm1 in biological samples
WO2004099431A3 (en) Nucleic acid sequence detection using multiplexed oligonucleotide pcr
WO2005045060A3 (en) Multiplexed nucleic acid analysis by fragmentation of double-stranded dna
WO2001090419A3 (en) Methods for genetic analysis of dna to detect sequence variances
WO2003078587A3 (en) Nucleic acid detection method
WO2003072821A3 (en) Method and nucleic acids for the analysis of a colon cell proliferactive disorder
WO2005083115A3 (en) Method for the identification of sepsis
WO1996022392A3 (en) Nucleic acid amplification oligonucleotides and probes to lyme disease associated borrelia
CN113528621A (en) Probes for improved melt resolution and multiplexing in nucleic acid assays
WO2003052135A8 (en) Method and nucleic acids for the analysis of a lung cell proliferative disorder
WO2005001141A3 (en) Methods and nucleic acids for analyses of colorectal cell proliferative disorders
WO2003014388A3 (en) Method and nucleic acids for the analysis of colon cancer
WO2002031186A3 (en) Method for the detection of cytosine methylations
WO2006034879A3 (en) Epigenetic methods and nucleic acids for the detection of lung cell proliferative disorders
WO2003044226A3 (en) Method and nucleic acids for the analysis of a lymphoid cell proliferative disorder
WO2002012554A3 (en) Diagnosis of diseases which are associated with cd24
WO2002036814A3 (en) Diagnosis of diseases associated with cdk4 by determining the methylation state of the cdk4

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BW BY BZ CA CH CN CO CR CU CZ DE DK DM DZ EC EE EG ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NA NI NO NZ OM PG PH PL PT RO RU SC SD SE SG SK SL SY TJ TM TN TR TT TZ UA UG US UZ VC VN YU ZA ZM ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): BW GH GM KE LS MW MZ NA SD SL SZ TZ UG ZM ZW AM AZ BY KG KZ MD RU TJ TM AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HU IE IT LU MC NL PL PT RO SE SI SK TR BF BJ CF CG CI CM GA GN GQ GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
WWE Wipo information: entry into national phase

Ref document number: 2004777063

Country of ref document: EP

WWP Wipo information: published in national office

Ref document number: 2004777063

Country of ref document: EP

WWE Wipo information: entry into national phase

Ref document number: 10562377

Country of ref document: US

Ref document number: 2007184438

Country of ref document: US

WWP Wipo information: published in national office

Ref document number: 10562377

Country of ref document: US