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WO2008155549A3 - Improved urine sample collecting and processing - Google Patents

Improved urine sample collecting and processing Download PDF

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Publication number
WO2008155549A3
WO2008155549A3 PCT/GB2008/002093 GB2008002093W WO2008155549A3 WO 2008155549 A3 WO2008155549 A3 WO 2008155549A3 GB 2008002093 W GB2008002093 W GB 2008002093W WO 2008155549 A3 WO2008155549 A3 WO 2008155549A3
Authority
WO
WIPO (PCT)
Prior art keywords
neoplasia
urine sample
dna
processing
characterising
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/GB2008/002093
Other languages
French (fr)
Other versions
WO2008155549A2 (en
Inventor
Katja Bierau
Madeleine Grooteclaes
Gaetan Otto
Joost Louwagie
Isabelle Renard
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.)
MDxHealth SA
Original Assignee
OncoMethylome Sciences SA
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 OncoMethylome Sciences SA filed Critical OncoMethylome Sciences SA
Priority to EP08762410A priority Critical patent/EP2173897A2/en
Priority to PL08802026T priority patent/PL2198042T3/en
Priority to ES08802026.8T priority patent/ES2605237T3/en
Priority to DK08802026.8T priority patent/DK2198042T3/en
Priority to JP2010524399A priority patent/JP5697448B2/en
Priority to EP08802026.8A priority patent/EP2198042B1/en
Priority to CA2699606A priority patent/CA2699606C/en
Priority to US12/678,696 priority patent/US9322065B2/en
Priority to PCT/EP2008/007465 priority patent/WO2009036922A2/en
Priority to EP16196638.7A priority patent/EP3147375A1/en
Publication of WO2008155549A2 publication Critical patent/WO2008155549A2/en
Publication of WO2008155549A3 publication Critical patent/WO2008155549A3/en
Anticipated expiration legal-status Critical
Priority to JP2014208231A priority patent/JP2015051006A/en
Priority to US15/079,948 priority patent/US10113202B2/en
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
    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • 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
    • 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
    • C12Q2600/158—Expression 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)
  • Investigating Or Analysing Biological Materials (AREA)

Abstract

A method for identifying, diagnosing and/or staging or otherwise characterising a urologic cancer or neoplasia in a subject comprises isolating cell-free DNA from a urine sample taken from the subject and analysing the DNA to determine whether the DNA contains an epigenetic modification. The epigenetic modification is indicative of the presence or stage or other characteristic of the urologic cancer or neoplasia and thus facilitates diagnosis, staging or otherwise characterising the urologic cancer or neoplasia. Stabilising buffers may be added to collected urine samples to enhance storage stability, even without the need for centrifugation, at various temperatures. Cell-free DNA may be isolated through appropriate filtration or capture.
PCT/GB2008/002093 2007-06-19 2008-06-19 Improved urine sample collecting and processing Ceased WO2008155549A2 (en)

Priority Applications (12)

Application Number Priority Date Filing Date Title
EP08762410A EP2173897A2 (en) 2007-06-19 2008-06-19 Improved urine sample collecting and processing
US12/678,696 US9322065B2 (en) 2007-09-17 2008-09-11 Methods for determining methylation of the TWIST1 gene for bladder cancer detection
PCT/EP2008/007465 WO2009036922A2 (en) 2007-09-17 2008-09-11 Novel markers for bladder cancer detection
DK08802026.8T DK2198042T3 (en) 2007-09-17 2008-09-11 New markers for bladder cancer detection
JP2010524399A JP5697448B2 (en) 2007-09-17 2008-09-11 A novel marker for detection of bladder cancer
EP08802026.8A EP2198042B1 (en) 2007-09-17 2008-09-11 Novel markers for bladder cancer detection
CA2699606A CA2699606C (en) 2007-09-17 2008-09-11 Novel markers for bladder cancer detection
PL08802026T PL2198042T3 (en) 2007-09-17 2008-09-11 Novel markers for bladder cancer detection
ES08802026.8T ES2605237T3 (en) 2007-09-17 2008-09-11 Novel markers for bladder cancer detection
EP16196638.7A EP3147375A1 (en) 2007-09-17 2008-09-11 Novel markers for bladder cancer detection
JP2014208231A JP2015051006A (en) 2007-09-17 2014-10-09 A novel marker for detection of bladder cancer
US15/079,948 US10113202B2 (en) 2007-09-17 2016-03-24 Method for determining the methylation status of the promoter region of the TWIST1 gene in genomic DNA from bladder cells

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US92924207P 2007-06-19 2007-06-19
US60/929,242 2007-06-19

Publications (2)

Publication Number Publication Date
WO2008155549A2 WO2008155549A2 (en) 2008-12-24
WO2008155549A3 true WO2008155549A3 (en) 2009-02-26

Family

ID=39743144

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/GB2008/002093 Ceased WO2008155549A2 (en) 2007-06-19 2008-06-19 Improved urine sample collecting and processing

Country Status (2)

Country Link
EP (1) EP2173897A2 (en)
WO (1) WO2008155549A2 (en)

Families Citing this family (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9322065B2 (en) 2007-09-17 2016-04-26 Mdxhealth Sa Methods for determining methylation of the TWIST1 gene for bladder cancer detection
WO2010102823A1 (en) * 2009-03-13 2010-09-16 Oncomethylome Sciences Sa Novel markers for bladder cancer detection
US9732390B2 (en) 2012-09-20 2017-08-15 The Chinese University Of Hong Kong Non-invasive determination of methylome of fetus or tumor from plasma
EP2898100B9 (en) 2012-09-20 2023-08-02 The Chinese University Of Hong Kong Non-invasive determination of methylome of fetus or tumor from plasma
WO2014182598A1 (en) * 2013-05-06 2014-11-13 Physicians Choice Laboratory Services, Llc Diagnostic assay combining cellular and cell free nucleic acid
EP3169813B1 (en) 2014-07-18 2019-06-12 The Chinese University Of Hong Kong Methylation pattern analysis of tissues in dna mixture
WO2017074926A1 (en) 2015-10-26 2017-05-04 Quest Diagnostics Investments Incorporated Methods for cell-free dna extraction for non-invasive prenatal screening
AU2017244280A1 (en) * 2016-04-01 2018-10-18 Nanomed Diagnostics B.V. Detection of cancer in urine
US10451544B2 (en) 2016-10-11 2019-10-22 Genotox Laboratories Methods of characterizing a urine sample
KR20230062684A (en) * 2016-11-30 2023-05-09 더 차이니즈 유니버시티 오브 홍콩 Analysis of cell-free dna in urine and other samples
CN108531594A (en) * 2018-04-19 2018-09-14 安徽达健医学科技有限公司 A kind of polygene combined non-invasive detection methods and its kit for carcinoma of urinary bladder early screening
CN120380342A (en) * 2023-01-20 2025-07-25 格里尔公司 Method for analyzing free nucleic acid in urine
EP4477751A1 (en) 2023-06-16 2024-12-18 QIAGEN GmbH Body fluid stabilization and processing

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007018602A1 (en) * 2005-08-02 2007-02-15 Rubicon Genomics, Inc. Isolation of cpg islands by thermal segregation and enzymatic selection-amplification method
WO2008021995A1 (en) * 2006-08-10 2008-02-21 Cohen Ariel B Methods and compositions for detecting an analyte in a biological sample

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007018602A1 (en) * 2005-08-02 2007-02-15 Rubicon Genomics, Inc. Isolation of cpg islands by thermal segregation and enzymatic selection-amplification method
WO2008021995A1 (en) * 2006-08-10 2008-02-21 Cohen Ariel B Methods and compositions for detecting an analyte in a biological sample

Non-Patent Citations (8)

* Cited by examiner, † Cited by third party
Title
BRYZGUNOVA O E ET AL: "Isolation and comparative study of cell-free nucleic acids from human urine", ANNALS OF THE NEW YORK ACADEMY OF SCIENCES - CIRCULATING NUCLEIC ACIDS IN PLASMA AND SERUM IV 200609 US, vol. 1075, September 2006 (2006-09-01), pages 334 - 340, XP002496413, ISSN: 0077-8923 1749-6632 1-57331-62 *
CHAN MICHAEL W Y ET AL: "Frequent hypermethylation of promoter region of RASSF1A in tumor tissues and voided urine of urinary bladder cancer patients.", INTERNATIONAL JOURNAL OF CANCER, vol. 104, no. 5, 1 May 2003 (2003-05-01), pages 611 - 616, XP002496412, ISSN: 0020-7136 *
CHANG H-W ET AL: "Urinary cell-free DNA as a potential tumor marker for bladder cancer", INTERNATIONAL JOURNAL OF BIOLOGICAL MARKERS, WICHTIG EDITORE, MILAN, IT, vol. 22, no. 4, October 2007 (2007-10-01), pages 287 - 294, XP009109607, ISSN: 0393-6155 *
DAS PARTHA M ET AL: "DNA methylation and cancer.", JOURNAL OF CLINICAL ONCOLOGY : OFFICIAL JOURNAL OF THE AMERICAN SOCIETY OF CLINICAL ONCOLOGY 15 NOV 2004, vol. 22, no. 22, 15 November 2004 (2004-11-15), pages 4632 - 4642, XP002496415, ISSN: 0732-183X *
HOQUE MOHAMMAD OBAIDUL ET AL: "Quantitative detection of promoter hypermethylation of multiple genes in the tumor, urine, and serum DNA of patients with renal cancer", CANCER RESEARCH, vol. 64, no. 15, 1 August 2004 (2004-08-01), pages 5511 - 5517, XP002496414, ISSN: 0008-5472 *
ROUPRÊT M ET AL: "Molecular detection of localized prostate cancer using quantitative methylation-specific PCR on urinary cells obtained following prostate massage", CLINICAL CANCER RESEARCH, THE AMERICAN ASSOCIATION FOR CANCER RESEARCH, US, vol. 13, no. 6, 15 March 2007 (2007-03-15), pages 1720 - 1725, XP002485530, ISSN: 1078-0432 *
UTTING M ET AL: "Detection of tumor genetic alterations of bladder carcinomas in body fluids depends on sample treatment before DNA isolation.", ANNALS OF THE NEW YORK ACADEMY OF SCIENCES APR 2000, vol. 906, April 2000 (2000-04-01), pages 67 - 71, XP002506790, ISSN: 0077-8923 *
UTTING MICHAEL ET AL: "Microsatellite analysis of free tumor DNA in urine, serum, and plasma of patients: a minimally invasive method for the detection of bladder cancer.", CLINICAL CANCER RESEARCH : AN OFFICIAL JOURNAL OF THE AMERICAN ASSOCIATION FOR CANCER RESEARCH JAN 2002, vol. 8, no. 1, January 2002 (2002-01-01), pages 35 - 40, XP002506789, ISSN: 1078-0432 *

Also Published As

Publication number Publication date
WO2008155549A2 (en) 2008-12-24
EP2173897A2 (en) 2010-04-14

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