WO2009105154A3 - Diagnostic and prognostic methods for cancer - Google Patents

Diagnostic and prognostic methods for cancer Download PDF

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Publication number
WO2009105154A3
WO2009105154A3 PCT/US2009/000695 US2009000695W WO2009105154A3 WO 2009105154 A3 WO2009105154 A3 WO 2009105154A3 US 2009000695 W US2009000695 W US 2009000695W WO 2009105154 A3 WO2009105154 A3 WO 2009105154A3
Authority
WO
WIPO (PCT)
Prior art keywords
methods
cancer
metagene
subject
score
Prior art date
Application number
PCT/US2009/000695
Other languages
French (fr)
Other versions
WO2009105154A2 (en
Inventor
Kevin Mills
Yong Woo
Original Assignee
The Jackson Laboratory
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 The Jackson Laboratory filed Critical The Jackson Laboratory
Publication of WO2009105154A2 publication Critical patent/WO2009105154A2/en
Publication of WO2009105154A3 publication Critical patent/WO2009105154A3/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
    • C12Q2600/118—Prognosis of disease development
    • 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)
  • Peptides Or Proteins (AREA)

Abstract

Described herein are methods for determining or predicting a prognosis for an individual having cancer. Also described are methods of determining a type or sub-type of a cancer. The methods are based upon the identification of genes or gene profiles that correlate with the aggressiveness and/or type of a cancer. The methods involve the measurement of the expression of a set of prognostic genes in a subject's tumor. In some embodiments, a metagene score is determined for the subject's tumor, and the metagene score is compared with a set or database of reference metagene scores from individuals with known diagnosis, prognosis or outcome. In such embodiments, the distance of the subject's metagene's score from the median reference metagene score is predictive of the relative aggressiveness of the subject's tumor. Also provided are methods of identifying genes prognostic or diagnostic for a given disease or disorder.
PCT/US2009/000695 2008-02-19 2009-02-03 Diagnostic and prognostic methods for cancer WO2009105154A2 (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US2973008P 2008-02-19 2008-02-19
US61/029,730 2008-02-19
US2999008P 2008-02-20 2008-02-20
US61/029,990 2008-02-20

Publications (2)

Publication Number Publication Date
WO2009105154A2 WO2009105154A2 (en) 2009-08-27
WO2009105154A3 true WO2009105154A3 (en) 2010-01-14

Family

ID=40986088

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2009/000695 WO2009105154A2 (en) 2008-02-19 2009-02-03 Diagnostic and prognostic methods for cancer

Country Status (1)

Country Link
WO (1) WO2009105154A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
RU2445632C1 (en) * 2010-08-03 2012-03-20 Федеральное государственное учреждение "Ростовский научно-исследовательский онкологический институт Федерального агентства по высокотехнологичной медицинской помощи" Method for prediction of metastases in patients with stomach cancer

Families Citing this family (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
FI20105347A0 (en) * 2010-04-06 2010-04-06 Medisapiens Oy Method, apparatus and computer program for the analysis of a cancerous tissue
EP2588866A4 (en) * 2010-07-02 2014-01-22 Welcome Receptor Antibodies Pty Ltd Diagnosis and treatment of brain tumors
MX338883B (en) 2010-07-27 2016-05-04 Genomic Health Inc Method for using gene expression to determine prognosis of prostate cancer.
CA2825894C (en) * 2011-02-02 2021-11-30 Amgen Inc. Prognosis of cancer using a circulating biomarker
SE536352C2 (en) 2011-10-24 2013-09-03 Chundsell Medicals Ab Cursor genes for classification of prostate cancer
WO2013071247A1 (en) 2011-11-10 2013-05-16 The United States Of America, As Represented By The Secretary, Department Of Health And Human Servic Gene expression signatures of neoplasm responsiveness to theraphy
KR101520615B1 (en) * 2013-03-20 2015-05-18 서울대학교산학협력단 Markers for diagnosis of liver cancer
WO2016153434A1 (en) * 2015-03-24 2016-09-29 Agency For Science, Technology And Research (A*Star) Normalization methods for measuring gene copy number and expression
CN105624324B (en) * 2016-03-31 2019-06-11 北京泱深生物信息技术有限公司 Hypophysoma diagnosis and treatment marker
CN111579786B (en) * 2020-05-27 2020-12-01 郑州大学第一附属医院 Test strip for screening early esophageal squamous carcinoma of high risk group
MX2023001914A (en) 2020-08-15 2023-03-13 Regeneron Pharma Treatment of obesity in subjects having variant nucleic acid molecules encoding calcitonin receptor (calcr).
CN113061658A (en) * 2021-04-14 2021-07-02 智乾生物科技(浙江)有限公司 Gene for breast cancer genetic screening and application thereof
WO2022266232A1 (en) * 2021-06-16 2022-12-22 Sanford Burnham Prebys Medical Discovery Institute Methods and compositions for treating chronic liver disease and hepatocellular carcinoma
EP4413151A1 (en) * 2021-10-04 2024-08-14 The Chinese University Of Hong Kong Sequencing of viral dna for predicting disease relapse
CN115537462B (en) * 2022-10-13 2023-08-11 深圳市儿童医院 Sequencing method for simultaneously detecting pathogenic bacteria and host gene expression quantity and application of sequencing method in diagnosis and prognosis of bacterial meningitis

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2003091410A2 (en) * 2002-04-26 2003-11-06 Children's Medical Center Corporation Method of fingerprinting tissue samples
JP2005270093A (en) * 2004-02-24 2005-10-06 Nippon Medical School Gene participating in estimating postoperative prognosis of breast cancer
US20070099197A1 (en) * 2002-06-24 2007-05-03 Afar Daniel E Methods of prognosis of prostate cancer

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2003091410A2 (en) * 2002-04-26 2003-11-06 Children's Medical Center Corporation Method of fingerprinting tissue samples
US20070275373A1 (en) * 2002-04-26 2007-11-29 Lois Smith Method of fingerprinting tissue samples
US20070099197A1 (en) * 2002-06-24 2007-05-03 Afar Daniel E Methods of prognosis of prostate cancer
JP2005270093A (en) * 2004-02-24 2005-10-06 Nippon Medical School Gene participating in estimating postoperative prognosis of breast cancer

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
JENNIFER PITTMAN ET AL.: "Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 101, no. 22, 1 June 2004 (2004-06-01), pages 8431 - 8436 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
RU2445632C1 (en) * 2010-08-03 2012-03-20 Федеральное государственное учреждение "Ростовский научно-исследовательский онкологический институт Федерального агентства по высокотехнологичной медицинской помощи" Method for prediction of metastases in patients with stomach cancer

Also Published As

Publication number Publication date
WO2009105154A2 (en) 2009-08-27

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