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WO2009051842A3 - Detection of cancer by measuring genomic copy number and strand length in cell-free dna - Google Patents

Detection of cancer by measuring genomic copy number and strand length in cell-free dna Download PDF

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Publication number
WO2009051842A3
WO2009051842A3 PCT/US2008/011948 US2008011948W WO2009051842A3 WO 2009051842 A3 WO2009051842 A3 WO 2009051842A3 US 2008011948 W US2008011948 W US 2008011948W WO 2009051842 A3 WO2009051842 A3 WO 2009051842A3
Authority
WO
WIPO (PCT)
Prior art keywords
cancer
dna
strand length
cell
subject
Prior art date
Application number
PCT/US2008/011948
Other languages
French (fr)
Other versions
WO2009051842A2 (en
Inventor
Ie-Ming Shih
Bai-Ling Lin
Tian-Li Wang
Original Assignee
Univ Johns Hopkins
Ie-Ming Shih
Bai-Ling Lin
Tian-Li Wang
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 Johns Hopkins, Ie-Ming Shih, Bai-Ling Lin, Tian-Li Wang filed Critical Univ Johns Hopkins
Publication of WO2009051842A2 publication Critical patent/WO2009051842A2/en
Publication of WO2009051842A3 publication Critical patent/WO2009051842A3/en

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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
    • C12Q2600/16—Primer sets for multiplex assays

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

The present invention relates, e.g., to a method for diagnosing a cancer in a subject, comprising measuring in a cell-free body fluid of the subject a) the amount of DNA in the body fluid from an amplified cancer-associated chromosomal locus, compared to a positive and/or a negative reference standard, wherein the positive and negative standards reflect the amount of the DNA in the body fluid of a subject having the cancer, or not having the cancer, respectively, and b) the strand length integrity index of the DNA in the body fluid from the amplified cancer-associated chromosomal locus compared to a baseline value, wherein if the amount of the measured DNA is statistically significantly increased compared to the negative reference standard, and/or is statistically the same as the positive reference standard, and if the strand length integrity index is at least about 0.65, this is indicative that the subject has the cancer.
PCT/US2008/011948 2007-10-18 2008-10-20 Detection of cancer by measuring genomic copy number and strand length in cell-free dna WO2009051842A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US99941407P 2007-10-18 2007-10-18
US60/999,414 2007-10-18

Publications (2)

Publication Number Publication Date
WO2009051842A2 WO2009051842A2 (en) 2009-04-23
WO2009051842A3 true WO2009051842A3 (en) 2009-08-13

Family

ID=40568037

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2008/011948 WO2009051842A2 (en) 2007-10-18 2008-10-20 Detection of cancer by measuring genomic copy number and strand length in cell-free dna

Country Status (1)

Country Link
WO (1) WO2009051842A2 (en)

Families Citing this family (23)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US12180549B2 (en) 2007-07-23 2024-12-31 The Chinese University Of Hong Kong Diagnosing fetal chromosomal aneuploidy using genomic sequencing
PL2557517T3 (en) 2007-07-23 2023-03-06 The Chinese University Of Hong Kong Determining a nucleic acid sequence imbalance
US10378064B1 (en) 2010-04-16 2019-08-13 Chronix Biomedical Analyzing circulating nucleic acids to identify a biomarker representative of cancer presented by a patient population
EP2558854B1 (en) * 2010-04-16 2018-10-10 Chronix Biomedical Breast cancer associated circulating nucleic acid biomarkers
US20130143214A1 (en) * 2010-06-04 2013-06-06 Chronix Biomedical Prostate cancer associated circulating nucleic acid biomarkers
EP2426217A1 (en) 2010-09-03 2012-03-07 Centre National de la Recherche Scientifique (CNRS) Analytical methods for cell free nucleic acids and applications
US9892230B2 (en) 2012-03-08 2018-02-13 The Chinese University Of Hong Kong Size-based analysis of fetal or tumor DNA fraction in plasma
WO2015061359A1 (en) 2013-10-21 2015-04-30 Verinata Health, Inc. Method for improving the sensitivity of detection in determining copy number variations
AU2014348428B2 (en) 2013-11-15 2020-12-17 Matthew BREEN Chromosomal assessment to diagnose urogenital malignancy in dogs
ES2637385T3 (en) * 2013-12-04 2017-10-13 Menarini Silicon Biosystems S.P.A. Method and kit to determine genome integrity and / or the quality of a library of DNA sequences obtained by complete genome amplification by deterministic restriction sites
US10501806B2 (en) 2014-04-15 2019-12-10 North Carolina State University Chromosomal assessment to differentiate histiocytic malignancy from lymphoma in dogs
KR102566176B1 (en) 2014-05-30 2023-08-10 베리나타 헬스, 인코포레이티드 Detecting fetal sub-chromosomal aneuploidies and copy number variations
US10513738B2 (en) 2014-07-24 2019-12-24 North Carolina State University Method to diagnose malignant melanoma in the domestic dog
KR102441391B1 (en) 2014-07-25 2022-09-07 유니버시티 오브 워싱톤 Methods of determining the tissue and/or cell type that produces cell-free DNA and methods of using the same to identify a disease or disorder
US11072814B2 (en) 2014-12-12 2021-07-27 Verinata Health, Inc. Using cell-free DNA fragment size to determine copy number variations
US10364467B2 (en) * 2015-01-13 2019-07-30 The Chinese University Of Hong Kong Using size and number aberrations in plasma DNA for detecting cancer
US10319463B2 (en) 2015-01-23 2019-06-11 The Chinese University Of Hong Kong Combined size- and count-based analysis of maternal plasma for detection of fetal subchromosomal aberrations
US10095831B2 (en) 2016-02-03 2018-10-09 Verinata Health, Inc. Using cell-free DNA fragment size to determine copy number variations
WO2017210115A1 (en) 2016-05-31 2017-12-07 North Carolina State University Methods of mast cell tumor prognosis and uses thereof
US11342047B2 (en) 2017-04-21 2022-05-24 Illumina, Inc. Using cell-free DNA fragment size to detect tumor-associated variant
US11168356B2 (en) 2017-11-02 2021-11-09 The Chinese University Of Hong Kong Using nucleic acid size range for noninvasive cancer detection
CN110894524B (en) * 2019-05-13 2023-05-05 嘉兴雅康博医学检验所有限公司 Method for rapidly preparing gene mutation reference
CN110878333A (en) * 2019-05-15 2020-03-13 嘉兴雅康博医学检验所有限公司 Method for preparing gene mutation reference substance

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6180349B1 (en) * 1999-05-18 2001-01-30 The Regents Of The University Of California Quantitative PCR method to enumerate DNA copy number
US20040014104A1 (en) * 1999-09-08 2004-01-22 Shuber Anthony P. Methods for disease detection

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6180349B1 (en) * 1999-05-18 2001-01-30 The Regents Of The University Of California Quantitative PCR method to enumerate DNA copy number
US20040014104A1 (en) * 1999-09-08 2004-01-22 Shuber Anthony P. Methods for disease detection

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
BEN DAVIDSON ET AL.: "Low-molecular weight forms of cyclin E differentiate ovarian carcinoma from cells of mesothelial origin and are associated with poor survival in ovarian carcinoma", CANCER, vol. 110, no. 6, 2007, pages 1264 - 1271 *
KENTARO NAKAYAMA ET AL.: "Amplicon profiles in ovarian serous carcinomas", INTERNATIONAL JOURNAL OF CANCER, vol. 120, no. 12, 9 March 2007 (2007-03-09), pages 2613 - 2617 *
RITU SALANI ET AL.: "Measurement of cylin E genomic copy number and strand length in cell-free DNA distinguish malignant versus benign effusions", CLINICAL CANCER RESEARCH, vol. 13, no. 19, 1 October 2007 (2007-10-01), pages 5805 - 5809 *

Also Published As

Publication number Publication date
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