WO2006002240A8 - Computer systems and methods for constructing biological classifiers and uses thereof - Google Patents

Computer systems and methods for constructing biological classifiers and uses thereof

Info

Publication number
WO2006002240A8
WO2006002240A8 PCT/US2005/022071 US2005022071W WO2006002240A8 WO 2006002240 A8 WO2006002240 A8 WO 2006002240A8 US 2005022071 W US2005022071 W US 2005022071W WO 2006002240 A8 WO2006002240 A8 WO 2006002240A8
Authority
WO
WIPO (PCT)
Prior art keywords
disease
classifiers
monitoring
molecular markers
treatment
Prior art date
Application number
PCT/US2005/022071
Other languages
French (fr)
Other versions
WO2006002240A3 (en
WO2006002240A2 (en
Inventor
Choong-Chin Liew
Tom Yager
Adam Dempsey
Samuel Chao
Original Assignee
Chondrogene Inc
Choong-Chin Liew
Tom Yager
Adam Dempsey
Samuel Chao
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 Chondrogene Inc, Choong-Chin Liew, Tom Yager, Adam Dempsey, Samuel Chao filed Critical Chondrogene Inc
Priority to EP05766673A priority Critical patent/EP1766043A4/en
Priority to CA002571180A priority patent/CA2571180A1/en
Priority to US10/568,264 priority patent/US7991557B2/en
Publication of WO2006002240A2 publication Critical patent/WO2006002240A2/en
Publication of WO2006002240A3 publication Critical patent/WO2006002240A3/en
Publication of WO2006002240A8 publication Critical patent/WO2006002240A8/en

Links

Classifications

    • 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
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F18/00—Pattern recognition
    • G06F18/20—Analysing
    • G06F18/21—Design or setup of recognition systems or techniques; Extraction of features in feature space; Blind source separation
    • G06F18/211—Selection of the most significant subset of features
    • 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
    • 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
    • G16B40/10—Signal processing, e.g. from mass spectrometry [MS] or from PCR
    • 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
    • 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

Landscapes

  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Data Mining & Analysis (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Chemical & Material Sciences (AREA)
  • Public Health (AREA)
  • Bioethics (AREA)
  • Genetics & Genomics (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Software Systems (AREA)
  • Signal Processing (AREA)
  • General Engineering & Computer Science (AREA)
  • General Physics & Mathematics (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The present invention provides systems and method for constructing classifiers that distinguish between trait subgroups using molecular marker data from blood samples. The invention further encompasses the use of the classifiers and combinations of molecular markers identified by the classifiers in a wide variety of applications including: diagnosis; prognosis; prediction of disease, stage of disease or disease risk; monitoring disease progression and/or regression; monitoring disease reoccurrence and identifying risk of disease reoccurrence; determining and/or predicting response to treatment and/or treatment outcomes; monitoring and/or predicting treatment compliance or non compliance and the like. The invention further provides a variety of selected molecular markers and a means to identify combinations of the selected molecular markers useful for diagnosing particular traits of interest.
PCT/US2005/022071 2004-06-19 2005-06-20 Computer systems and methods for constructing biological classifiers and uses thereof WO2006002240A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP05766673A EP1766043A4 (en) 2004-06-19 2005-06-20 Computer systems and methods for constructing biological classifiers and uses thereof
CA002571180A CA2571180A1 (en) 2004-06-19 2005-06-20 Computer systems and methods for constructing biological classifiers and uses thereof
US10/568,264 US7991557B2 (en) 2004-06-19 2005-06-20 Computer system and methods for constructing biological classifiers and uses thereof

Applications Claiming Priority (8)

Application Number Priority Date Filing Date Title
US58131204P 2004-06-19 2004-06-19
US60/581,312 2004-06-19
US58197704P 2004-06-21 2004-06-21
US60/581,977 2004-06-21
US64347505P 2005-01-12 2005-01-12
US60/643,475 2005-01-12
US66372205P 2005-03-22 2005-03-22
US60/663,722 2005-03-22

Publications (3)

Publication Number Publication Date
WO2006002240A2 WO2006002240A2 (en) 2006-01-05
WO2006002240A3 WO2006002240A3 (en) 2006-06-15
WO2006002240A8 true WO2006002240A8 (en) 2006-10-26

Family

ID=35782316

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2005/022071 WO2006002240A2 (en) 2004-06-19 2005-06-20 Computer systems and methods for constructing biological classifiers and uses thereof

Country Status (3)

Country Link
EP (1) EP1766043A4 (en)
CA (1) CA2571180A1 (en)
WO (1) WO2006002240A2 (en)

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2534661A1 (en) 2003-08-08 2005-02-17 Genenews Inc. Osteoarthritis biomarkers and uses thereof
US20100094560A1 (en) * 2006-08-15 2010-04-15 Prometheus Laboratories Inc. Methods for diagnosing irritable bowel syndrome
US20080085524A1 (en) * 2006-08-15 2008-04-10 Prometheus Laboratories Inc. Methods for diagnosing irritable bowel syndrome
JP5547639B2 (en) 2007-10-16 2014-07-16 コーニンクレッカ フィリップス エヌ ヴェ Estimating diagnostic markers
WO2009111891A1 (en) * 2008-03-12 2009-09-17 Mcmaster University Diagnostic method for peanut allergy
CA2776228A1 (en) 2009-10-01 2011-04-07 Chipdx Llc System and method for classification of patients
US20200026822A1 (en) * 2018-07-22 2020-01-23 LifeNome Inc. System and method for polygenic phenotypic trait predisposition assessment using a combination of dynamic network analysis and machine learning
CN111223520B (en) * 2019-11-20 2023-09-12 云南省烟草农业科学研究院 Whole genome selection model for predicting nicotine content in tobacco and application thereof
CN112232387B (en) * 2020-09-29 2024-02-06 南京财经大学 Effective characteristic identification method for disease symptoms of grain crops based on LSELM-RFE
CN113096734B (en) * 2021-05-11 2021-12-14 中国科学院水生生物研究所 Method for screening molecular marker combination for diploid population paternity test

Family Cites Families (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7324926B2 (en) * 1999-04-09 2008-01-29 Whitehead Institute For Biomedical Research Methods for predicting chemosensitivity or chemoresistance
CN1554025A (en) * 2001-03-12 2004-12-08 Īŵ���ɷ����޹�˾ Cell-based detection and differentiation of disease states
AU2003298689A1 (en) * 2002-11-21 2004-06-18 Wyeth Methods for diagnosing rcc and other solid tumors

Also Published As

Publication number Publication date
WO2006002240A3 (en) 2006-06-15
EP1766043A2 (en) 2007-03-28
CA2571180A1 (en) 2006-01-05
WO2006002240A2 (en) 2006-01-05
EP1766043A4 (en) 2012-05-30

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