WO2004037996A3 - Evaluation of breast cancer states and outcomes using gene expression profiles - Google Patents

Evaluation of breast cancer states and outcomes using gene expression profiles Download PDF

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Publication number
WO2004037996A3
WO2004037996A3 PCT/US2003/033656 US0333656W WO2004037996A3 WO 2004037996 A3 WO2004037996 A3 WO 2004037996A3 US 0333656 W US0333656 W US 0333656W WO 2004037996 A3 WO2004037996 A3 WO 2004037996A3
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WO
WIPO (PCT)
Prior art keywords
breast cancer
outcomes
methods
evaluation
gene expression
Prior art date
Application number
PCT/US2003/033656
Other languages
French (fr)
Other versions
WO2004037996A2 (en
Inventor
Mike West
Joseph R Nevins
Andrew Huang
Original Assignee
Univ Duke
Mike West
Joseph R Nevins
Andrew Huang
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
Priority claimed from PCT/US2002/038222 external-priority patent/WO2004038656A2/en
Priority claimed from PCT/US2002/038216 external-priority patent/WO2004044839A2/en
Priority claimed from US10/291,886 external-priority patent/US20040106113A1/en
Application filed by Univ Duke, Mike West, Joseph R Nevins, Andrew Huang filed Critical Univ Duke
Priority to AU2003284880A priority Critical patent/AU2003284880A1/en
Publication of WO2004037996A2 publication Critical patent/WO2004037996A2/en
Publication of WO2004037996A3 publication Critical patent/WO2004037996A3/en

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Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/30—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indices; for individual health risk assessment
    • 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
    • G01N33/57415—Specifically defined cancers of breast
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

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  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Biomedical Technology (AREA)
  • Medical Informatics (AREA)
  • Public Health (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Physics & Mathematics (AREA)
  • Primary Health Care (AREA)
  • Data Mining & Analysis (AREA)
  • Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Epidemiology (AREA)
  • Biotechnology (AREA)
  • Databases & Information Systems (AREA)
  • Urology & Nephrology (AREA)
  • Hematology (AREA)
  • Biochemistry (AREA)
  • Hospice & Palliative Care (AREA)
  • General Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Microbiology (AREA)
  • Oncology (AREA)
  • Medicinal Chemistry (AREA)
  • Cell Biology (AREA)
  • Food Science & Technology (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The present invention relates generally to a method for evaluating and/or predicting breast cancer states and outcomes by measuring gene and metagene expression levels and integrating such data with clinical risk factors. Genes and metagenes whose expressions are correlated with a particular breast cancer risk factor or phenotype are provided using binary prediction tree modelling. Methods of using the subject genes and metagenes in diagnosis and treatment methods, as well as drug screening methods, etc are also provided. In addition, reagents, media and kits that find use in practicing the subject methods are also provided.
PCT/US2003/033656 2002-10-24 2003-10-24 Evaluation of breast cancer states and outcomes using gene expression profiles WO2004037996A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2003284880A AU2003284880A1 (en) 2002-10-24 2003-10-24 Evaluation of breast cancer states and outcomes using gene expression profiles

Applications Claiming Priority (30)

Application Number Priority Date Filing Date Title
US42072902P 2002-10-24 2002-10-24
US60/420,729 2002-10-24
US42106202P 2002-10-25 2002-10-25
US42110202P 2002-10-25 2002-10-25
US60/421,102 2002-10-25
US60/421,062 2002-10-25
US42471502P 2002-11-08 2002-11-08
US42470102P 2002-11-08 2002-11-08
US42471802P 2002-11-08 2002-11-08
US60/424,701 2002-11-08
US60/424,715 2002-11-08
US60/424,718 2002-11-08
US42525602P 2002-11-12 2002-11-12
USPCTUS02/38216 2002-11-12
USPCTUS02/38222 2002-11-12
US10/291,886 2002-11-12
PCT/US2002/038222 WO2004038656A2 (en) 2002-10-24 2002-11-12 Binary prediction tree modeling with many predictors
PCT/US2002/038216 WO2004044839A2 (en) 2002-11-08 2002-11-12 Prediction of estrogen receptor status of brest tumors using binary prediction tree modeling
US10/291,878 US20040083084A1 (en) 2002-10-24 2002-11-12 Binary prediction tree modeling with many predictors
US10/291,878 2002-11-12
US10/291,886 US20040106113A1 (en) 2002-10-24 2002-11-12 Prediction of estrogen receptor status of breast tumors using binary prediction tree modeling
US60/425,256 2002-11-12
US44846103P 2003-02-21 2003-02-21
US44846203P 2003-02-21 2003-02-21
US60/448,462 2003-02-21
US60/448,461 2003-02-21
US45787703P 2003-03-27 2003-03-27
US60/457,877 2003-03-27
US45837303P 2003-03-31 2003-03-31
US60/458,373 2003-03-31

Publications (2)

Publication Number Publication Date
WO2004037996A2 WO2004037996A2 (en) 2004-05-06
WO2004037996A3 true WO2004037996A3 (en) 2004-12-29

Family

ID=32180894

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2003/033656 WO2004037996A2 (en) 2002-10-24 2003-10-24 Evaluation of breast cancer states and outcomes using gene expression profiles

Country Status (2)

Country Link
AU (1) AU2003284880A1 (en)
WO (1) WO2004037996A2 (en)

Families Citing this family (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20050186577A1 (en) 2004-02-20 2005-08-25 Yixin Wang Breast cancer prognostics
JP5760247B2 (en) * 2005-12-28 2015-08-05 国立大学法人名古屋大学 Composition and method for predicting postoperative prognosis or metastatic potential of cancer patients
WO2009020028A1 (en) * 2007-08-03 2009-02-12 Konica Minolta Holdings, Inc. Determination and suppression of expression level of g protein-coupled receptor kinase 4 gene in breast cancer cell
GB201009798D0 (en) 2010-06-11 2010-07-21 Immunovia Ab Method,array and use thereof
RU2647159C2 (en) * 2011-12-30 2018-03-14 Конинклейке Филипс Н.В. Choice of clinical guidance for cervical cancer
ES2648176T3 (en) * 2012-07-12 2017-12-28 INSERM (Institut National de la Santé et de la Recherche Médicale) Methods for predicting survival time and response to treatment of a patient suffering from solid cancer with a hallmark of at least 7 genes
US10689701B2 (en) 2013-03-15 2020-06-23 Duke University Biomarkers for the molecular classification of bacterial infection
WO2020036571A1 (en) * 2018-08-16 2020-02-20 RICHARDSON, Paul, Stephen Systems and methods for automatic bias monitoring of cohort models and un-deployment of biased models
CN109801680B (en) * 2018-12-03 2023-02-28 广州中医药大学(广州中医药研究院) Tumor metastasis and recurrence prediction method and system based on TCGA database
CN112946695B (en) * 2021-03-01 2023-10-13 北京交通大学 Satellite positioning suppression interference identification method based on singular value decomposition
CN114974598B (en) * 2022-06-29 2024-04-16 山东大学 Method for constructing lung cancer prognosis prediction model and lung cancer prognosis prediction system

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
BENSON ET AL: "GenBank", NUCLEIC ACIDS RESEARCH, vol. 25, 1997, pages 1 - 6, XP002967189 *
FELLENBERG ET AL: "Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis", BIOINFORMATICS, vol. 18, 2002, pages 423 - 433, XP002978946 *
SORLIE ET AL: "Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications", PNAS, vol. 98, no. 19, 11 September 2001 (2001-09-11), pages 10869 - 10874, XP002215483 *
STOECKERT ET AL: "A relational schema for both array-based and SAGE gene expression experiments", BIOINFORMATICS, vol. 17, 2001, pages 300 - 308, XP001086454 *

Also Published As

Publication number Publication date
AU2003284880A8 (en) 2004-05-13
AU2003284880A1 (en) 2004-05-13
WO2004037996A2 (en) 2004-05-06

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