WO2006053328A3 - Biomarkers for screening, predicting, and monitoring prostate disease - Google Patents

Biomarkers for screening, predicting, and monitoring prostate disease Download PDF

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Publication number
WO2006053328A3
WO2006053328A3 PCT/US2005/041442 US2005041442W WO2006053328A3 WO 2006053328 A3 WO2006053328 A3 WO 2006053328A3 US 2005041442 W US2005041442 W US 2005041442W WO 2006053328 A3 WO2006053328 A3 WO 2006053328A3
Authority
WO
WIPO (PCT)
Prior art keywords
biomarkers
predicting
screening
grade
prostate disease
Prior art date
Application number
PCT/US2005/041442
Other languages
French (fr)
Other versions
WO2006053328A2 (en
WO2006053328A8 (en
Inventor
Isabelle Guyon
Original Assignee
Health Discovery Corporation
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 Health Discovery Corporation filed Critical Health Discovery Corporation
Priority to EP05824959A priority Critical patent/EP1828917A4/en
Publication of WO2006053328A2 publication Critical patent/WO2006053328A2/en
Publication of WO2006053328A3 publication Critical patent/WO2006053328A3/en
Publication of WO2006053328A8 publication Critical patent/WO2006053328A8/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
    • G01N33/57434—Specifically defined cancers of prostate
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • 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
    • 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
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • 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
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/56—Staging of a disease; Further complications associated with the disease
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • 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

Abstract

Gene expression data are analyzed using learning machines such as support vector machines (SVM) and ridge regression classifiers to rank genes according to their ability to separate prostate cancer from BPH (benign prostatic hyperplasia) and to distinguish cancer volume. Other tests identify biomarker candidates for distinguishing between tumor (Grade 3 and Grade 4 (G3/4)) and normal tissue.
PCT/US2005/041442 2004-11-12 2005-11-14 Biomarkers for screening, predicting, and monitoring prostate disease WO2006053328A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
EP05824959A EP1828917A4 (en) 2004-11-12 2005-11-14 Biomarkers for screening, predicting, and monitoring prostate disease

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US62762604P 2004-11-12 2004-11-12
US60/627,626 2004-11-12
US65134005P 2005-02-09 2005-02-09
US60/651,340 2005-02-09

Publications (3)

Publication Number Publication Date
WO2006053328A2 WO2006053328A2 (en) 2006-05-18
WO2006053328A3 true WO2006053328A3 (en) 2010-10-28
WO2006053328A8 WO2006053328A8 (en) 2011-02-03

Family

ID=36337320

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2005/041442 WO2006053328A2 (en) 2004-11-12 2005-11-14 Biomarkers for screening, predicting, and monitoring prostate disease

Country Status (2)

Country Link
EP (1) EP1828917A4 (en)
WO (1) WO2006053328A2 (en)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN106909781A (en) * 2017-02-22 2017-06-30 北京航空航天大学 A kind of method for optimum option cerebral apoplexy associated biomarkers
CN108537003A (en) * 2018-03-30 2018-09-14 大连理工大学 Marker screening technique based on single argument and to variable

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2008067065A2 (en) * 2006-10-19 2008-06-05 Shiv Srivastava Methods, kits, and systems for diagnosing and prognosing prostate cancer using secreted biomarkers
GB201616912D0 (en) 2016-10-05 2016-11-16 University Of East Anglia Classification of cancer

Citations (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6566130B1 (en) * 2000-01-28 2003-05-20 Henry M. Jackson Foundation For The Advancement Of Military Medicine Androgen-regulated gene expressed in prostate tissue
US20030129629A1 (en) * 2000-02-17 2003-07-10 Millennium Pharmaceuticals, Inc. Methods and compositions for the identification, assessment, prevention, and therapy of human cancers
US20030228639A1 (en) * 2001-03-19 2003-12-11 Wright George L Prostate cancer markers
US20040018563A1 (en) * 2001-11-30 2004-01-29 Chemocentryx Inc. Compositions and methods for detecting and treating diseases and conditions related to chemokine receptors
US20040029114A1 (en) * 2001-01-24 2004-02-12 Eos Technology, Inc. Methods of diagnosis of breast cancer, compositions and methods of screening for modulators of breast cancer
US20040029151A1 (en) * 2002-04-09 2004-02-12 Affymetrix, Inc. Molecular genetic profiling of gleason grades 3 and 4/5 prostate cancer
US20040156854A1 (en) * 2002-12-06 2004-08-12 Millennium Pharmaceuticals, Inc. Methods for the identification, assessment, and treatment of patients with proteasome inhibition therapy

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002095534A2 (en) * 2001-05-18 2002-11-28 Biowulf Technologies, Llc Methods for feature selection in a learning machine
ATE496343T1 (en) * 2001-01-24 2011-02-15 Health Discovery Corp METHOD FOR IDENTIFYING PATTERNS IN BIOLOGICAL SYSTEMS AND THEIR APPLICATIONS

Patent Citations (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6566130B1 (en) * 2000-01-28 2003-05-20 Henry M. Jackson Foundation For The Advancement Of Military Medicine Androgen-regulated gene expressed in prostate tissue
US20030129629A1 (en) * 2000-02-17 2003-07-10 Millennium Pharmaceuticals, Inc. Methods and compositions for the identification, assessment, prevention, and therapy of human cancers
US20040029114A1 (en) * 2001-01-24 2004-02-12 Eos Technology, Inc. Methods of diagnosis of breast cancer, compositions and methods of screening for modulators of breast cancer
US20030228639A1 (en) * 2001-03-19 2003-12-11 Wright George L Prostate cancer markers
US20040018563A1 (en) * 2001-11-30 2004-01-29 Chemocentryx Inc. Compositions and methods for detecting and treating diseases and conditions related to chemokine receptors
US20040029151A1 (en) * 2002-04-09 2004-02-12 Affymetrix, Inc. Molecular genetic profiling of gleason grades 3 and 4/5 prostate cancer
US20040156854A1 (en) * 2002-12-06 2004-08-12 Millennium Pharmaceuticals, Inc. Methods for the identification, assessment, and treatment of patients with proteasome inhibition therapy

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN106909781A (en) * 2017-02-22 2017-06-30 北京航空航天大学 A kind of method for optimum option cerebral apoplexy associated biomarkers
CN106909781B (en) * 2017-02-22 2019-12-31 北京航空航天大学 Method for optimizing selection of stroke-related biomarkers
CN108537003A (en) * 2018-03-30 2018-09-14 大连理工大学 Marker screening technique based on single argument and to variable
CN108537003B (en) * 2018-03-30 2020-04-07 大连理工大学 Marker screening method based on univariate and paravariable

Also Published As

Publication number Publication date
EP1828917A4 (en) 2012-04-25
WO2006053328A2 (en) 2006-05-18
WO2006053328A8 (en) 2011-02-03
EP1828917A2 (en) 2007-09-05

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