WO2005017207A3 - Methods and compositions for detecting colon cancers - Google Patents

Methods and compositions for detecting colon cancers Download PDF

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Publication number
WO2005017207A3
WO2005017207A3 PCT/US2004/026478 US2004026478W WO2005017207A3 WO 2005017207 A3 WO2005017207 A3 WO 2005017207A3 US 2004026478 W US2004026478 W US 2004026478W WO 2005017207 A3 WO2005017207 A3 WO 2005017207A3
Authority
WO
WIPO (PCT)
Prior art keywords
compositions
methods
colon cancers
detecting colon
vimentin
Prior art date
Application number
PCT/US2004/026478
Other languages
French (fr)
Other versions
WO2005017207A2 (en
Inventor
Sanford D Markowitz
Original Assignee
Univ Case Western Reserve
Sanford D Markowitz
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 Univ Case Western Reserve, Sanford D Markowitz filed Critical Univ Case Western Reserve
Priority to EP04781201.1A priority Critical patent/EP1660683B1/en
Priority to CA2535910A priority patent/CA2535910C/en
Priority to JP2006523432A priority patent/JP4781267B2/en
Publication of WO2005017207A2 publication Critical patent/WO2005017207A2/en
Publication of WO2005017207A3 publication Critical patent/WO2005017207A3/en

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Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57419—Specifically defined cancers of colon
    • 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/5011—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing antineoplastic activity
    • 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
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • 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
    • C12Q2600/136—Screening for pharmacological compounds
    • 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

Abstract

This application describes methods and compositions for detecting and treating vimentin-associated neoplasia. Differential methylation of the vimentin nucleotide sequences has been observed in vimentin-associated neoplasia such as colon neoplasia.
PCT/US2004/026478 2003-08-14 2004-08-16 Methods and compositions for detecting colon cancers WO2005017207A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP04781201.1A EP1660683B1 (en) 2003-08-14 2004-08-16 Methods and compositions for detecting colon cancers
CA2535910A CA2535910C (en) 2003-08-14 2004-08-16 Methods and compositions for detecting colon cancers
JP2006523432A JP4781267B2 (en) 2003-08-14 2004-08-16 Method and composition for detecting colorectal cancer

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US49506403P 2003-08-14 2003-08-14
US60/495,064 2003-08-14

Publications (2)

Publication Number Publication Date
WO2005017207A2 WO2005017207A2 (en) 2005-02-24
WO2005017207A3 true WO2005017207A3 (en) 2005-10-27

Family

ID=34193270

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2004/026478 WO2005017207A2 (en) 2003-08-14 2004-08-16 Methods and compositions for detecting colon cancers

Country Status (5)

Country Link
US (4) US7485420B2 (en)
EP (1) EP1660683B1 (en)
JP (2) JP4781267B2 (en)
CA (1) CA2535910C (en)
WO (1) WO2005017207A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11845991B2 (en) 2009-02-03 2023-12-19 Exact Sciences Corporation Fecal sample processing and analysis comprising detection of blood

Families Citing this family (34)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2003213107A1 (en) 2002-02-15 2003-09-09 Exact Sciences Corporation Methods for analysis of molecular events
WO2003099313A1 (en) * 2002-05-23 2003-12-04 Purdue Research Foundation Low molecular weight protein tyrosine phosphatase (lmw-ptp) as a diagnostic and therapeutic target
JP4781267B2 (en) * 2003-08-14 2011-09-28 ケース ウエスタン リザーブ ユニバーシティ Method and composition for detecting colorectal cancer
US8415100B2 (en) * 2003-08-14 2013-04-09 Case Western Reserve University Methods and compositions for detecting gastrointestinal and other cancers
WO2005111244A2 (en) * 2004-05-10 2005-11-24 Exact Sciences Corporation Methods for detecting a mutant nucleic acid
WO2006026654A2 (en) 2004-08-27 2006-03-09 Exact Sciences Corporation Method for detecting a recombinant event
WO2006047787A2 (en) 2004-10-27 2006-05-04 Exact Sciences Corporation Method for monitoring disease progression or recurrence
WO2006094149A2 (en) * 2005-03-01 2006-09-08 Exact Sciences Corporation Methods and compositions for detecting adenoma
US9777314B2 (en) 2005-04-21 2017-10-03 Esoterix Genetic Laboratories, Llc Analysis of heterogeneous nucleic acid samples
WO2006128140A2 (en) * 2005-05-27 2006-11-30 Dana-Farber Cancer Institute, Inc. Gene methylation and expression
JP2011501674A (en) * 2007-10-23 2011-01-13 クリニカル・ジェノミックス・プロプライエタリー・リミテッド Diagnosis of type 2 neoplasia (NEOPLASMS-II)
JPWO2010113529A1 (en) 2009-04-03 2012-10-04 株式会社エイアンドティー Colorectal tumor detection method
EP3327139A1 (en) * 2009-04-06 2018-05-30 The Johns Hopkins University Digital quantification of dna methylation
US8642271B2 (en) * 2009-08-27 2014-02-04 Case Western Reserve University Aberrant methylation of C6Orf150 DNA sequences in human colorectal cancer
US20130012410A1 (en) * 2010-03-29 2013-01-10 Mayo Foundation For Medical Education And Research Methods and materials for detecting colorectal cancer and adenoma
WO2012052844A1 (en) * 2010-10-19 2012-04-26 Oslo Universitetssykehus Hf Methods and biomarkers for detection of bladder cancer
US8916344B2 (en) * 2010-11-15 2014-12-23 Exact Sciences Corporation Methylation assay
US9637792B2 (en) 2011-02-02 2017-05-02 Mayo Foundation For Medical Education And Research Digital sequence analysis of DNA methylation
GB201107466D0 (en) 2011-05-05 2011-06-15 Loktionov Alexandre Device and method for non-invasive collection of colorectal mucocellular layer and disease detection
US20150072866A1 (en) * 2012-03-20 2015-03-12 Exact Sciences Corporation Marker panel for detecting cancer
US9994911B2 (en) 2013-03-14 2018-06-12 Mayo Foundation For Medical Education And Research Detecting neoplasm
US10253358B2 (en) 2013-11-04 2019-04-09 Exact Sciences Development Company, Llc Multiple-control calibrators for DNA quantitation
CA3147619A1 (en) 2013-12-12 2015-06-18 Case Western Reserve University Device for collecting a biological sample
WO2015095689A1 (en) 2013-12-19 2015-06-25 Exact Sciences Corporation Synthetic nucleic acid control molecules
WO2015153284A1 (en) 2014-03-31 2015-10-08 Mayo Foundation For Medical Education And Research Detecting colorectal neoplasm
WO2016085944A1 (en) * 2014-11-24 2016-06-02 Case Western Reserve University Diagnostic and therapeutic targeting of dnmt-1 associated rna in human cancer
US10030272B2 (en) 2015-02-27 2018-07-24 Mayo Foundation For Medical Education And Research Detecting gastrointestinal neoplasms
CN108138235B (en) 2015-08-31 2022-04-15 梅约医药教育及研究基金会 Detection of gastric tumors
EP3443089A4 (en) 2016-04-14 2020-04-22 Mayo Foundation for Medical Education and Research Detecting pancreatic high-grade dysplasia
US10370726B2 (en) 2016-04-14 2019-08-06 Mayo Foundation For Medical Education And Research Detecting colorectal neoplasia
CA3029866A1 (en) * 2016-07-06 2018-01-11 Case Western Reserve University Methods and compositions for detecting esophageal neoplasias and/or metaplasias in the esophagus
JP7356349B2 (en) 2017-02-28 2023-10-04 マヨ ファウンデーション フォア メディカル エデュケーション アンド リサーチ prostate cancer detection
EP3717644A4 (en) 2017-11-30 2021-12-29 Mayo Foundation for Medical Education and Research Detecting breast cancer
EP3856903A4 (en) 2018-09-27 2022-07-27 Grail, LLC Methylation markers and targeted methylation probe panel

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030148327A1 (en) * 2000-04-06 2003-08-07 Alexander Olek Diagnosis of diseases associated with metastasis

Family Cites Families (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5853975A (en) * 1994-08-23 1998-12-29 Millennium Pharmaceuticals, Inc. Methods for identifying compositions for the treatment of body weight disorders, including obesity
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
JP4151751B2 (en) * 1999-07-22 2008-09-17 第一三共株式会社 New bicyclonucleoside analogues
DE10019058A1 (en) * 2000-04-06 2001-12-20 Epigenomics Ag Designing primers and probes for analyzing diseases associated with cytosine methylation state e.g. arthritis, cancer, aging, arteriosclerosis comprising fragments of chemically modified genes associated with cell cycle
JP2004516821A (en) 2000-09-01 2004-06-10 エピゲノミクス アーゲー Method for quantifying the degree of methylation of specific cytosine in sequence context 5-CpG-3 on genomic DNA
AUPR142500A0 (en) * 2000-11-13 2000-12-07 Human Genetic Signatures Pty Ltd A peptide nucleic acid-based assay for the detection of specific nucleic acid sequences
DE10056802B4 (en) * 2000-11-14 2005-06-16 Epigenomics Ag Method for the detection of methylation conditions for toxicological diagnostics
JP4781267B2 (en) 2003-08-14 2011-09-28 ケース ウエスタン リザーブ ユニバーシティ Method and composition for detecting colorectal cancer
GB0700374D0 (en) * 2007-01-09 2007-02-14 Oncomethylome Sciences S A NDRG family methylation markers
US7785772B2 (en) * 2007-01-23 2010-08-31 Mayo Foundation For Medical Education And Research Detecting methylated mammalian nucleic acid in stool

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030148327A1 (en) * 2000-04-06 2003-08-07 Alexander Olek Diagnosis of diseases associated with metastasis

Non-Patent Citations (6)

* Cited by examiner, † Cited by third party
Title
DOMAGALA W ET AL: "VIMENTIN IS PREFERENTIALLY EXPRESSED IN HUMAN BREAST CARCINOMAS WITH LOW ESTROGEN RECEPTOR AND HIGH KI-67 GROWTH FRACTION", AMERICAN JOURNAL OF PATHOLOGY, PHILADELPHIA, PA, US, vol. 136, no. 1, January 1990 (1990-01-01), pages 219 - 227, XP008006515, ISSN: 0002-9440 *
EDEN SHARON ET AL: "Role of DNA methylation in the regulation of transcription", CURRENT OPINION IN GENETICS AND DEVELOPMENT, vol. 4, no. 2, 1994, pages 255 - 259, XP009044081, ISSN: 0959-437X *
IZMAILOVA E S ET AL: "A GC-box is required for expression of the human vimentin gene", GENE, ELSEVIER BIOMEDICAL PRESS. AMSTERDAM, NL, vol. 235, no. 1-2, 22 July 1999 (1999-07-22), pages 69 - 75, XP004174740, ISSN: 0378-1119 *
LANGA FRANCINA ET AL: "Teratocarcinomas induced by embryonic stem (ES) cells lacking vimentin: An approach to study the role of vimentin in tumorigenesis", JOURNAL OF CELL SCIENCE, vol. 113, no. 19, October 2000 (2000-10-01), pages 3463 - 3472, XP002318359, ISSN: 0021-9533 *
LI HUI ET AL: "SLC5A8, a sodium transporter, is a tumor suppressor gene silenced by methylation in human colon aberrant crypt foci and cancers.", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 100, no. 14, 8 July 2003 (2003-07-08), pages 8412 - 8417, XP001205249, ISSN: 0027-8424 *
PETKO ZSOLT ET AL: "Aberrantly methylated CDKN2A, MGMT and hMLH1 are biomarkers for colon adenomas and colon adenocarcinomas.", PROCEEDINGS OF THE AMERICAN ASSOCIATION FOR CANCER RESEARCH ANNUAL MEETING, vol. 44, July 2003 (2003-07-01), & 94TH ANNUAL MEETING OF THE AMERICAN ASSOCIATION FOR CANCER RESEARCH; WASHINGTON, DC, USA; JULY 11-14, 2003, pages 698, XP001205250, ISSN: 0197-016X *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11845991B2 (en) 2009-02-03 2023-12-19 Exact Sciences Corporation Fecal sample processing and analysis comprising detection of blood

Also Published As

Publication number Publication date
US20050106593A1 (en) 2005-05-19
US7964353B2 (en) 2011-06-21
JP2011200237A (en) 2011-10-13
US20110217708A1 (en) 2011-09-08
US7485420B2 (en) 2009-02-03
EP1660683A2 (en) 2006-05-31
US8221977B2 (en) 2012-07-17
US20100009359A1 (en) 2010-01-14
US8481707B2 (en) 2013-07-09
JP2007502121A (en) 2007-02-08
EP1660683B1 (en) 2017-04-19
JP5575053B2 (en) 2014-08-20
JP4781267B2 (en) 2011-09-28
US20100209906A1 (en) 2010-08-19
CA2535910C (en) 2016-04-26
WO2005017207A2 (en) 2005-02-24
CA2535910A1 (en) 2005-02-24

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