WO2007059119A3 - Systems and methods for identifying diagnostic indicators - Google Patents

Systems and methods for identifying diagnostic indicators Download PDF

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Publication number
WO2007059119A3
WO2007059119A3 PCT/US2006/044170 US2006044170W WO2007059119A3 WO 2007059119 A3 WO2007059119 A3 WO 2007059119A3 US 2006044170 W US2006044170 W US 2006044170W WO 2007059119 A3 WO2007059119 A3 WO 2007059119A3
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WO
WIPO (PCT)
Prior art keywords
systems
methods
therapy
disease
diagnostic indicators
Prior art date
Application number
PCT/US2006/044170
Other languages
French (fr)
Other versions
WO2007059119A2 (en
Inventor
Ivan Borozan
Limin Chen
Aled M Edwards
Elizabeth J Heathcote
Ian D Mcgilvray
Original Assignee
Ivan Borozan
Limin Chen
Aled M Edwards
Elizabeth J Heathcote
Ian D Mcgilvray
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 Ivan Borozan, Limin Chen, Aled M Edwards, Elizabeth J Heathcote, Ian D Mcgilvray filed Critical Ivan Borozan
Publication of WO2007059119A2 publication Critical patent/WO2007059119A2/en
Publication of WO2007059119A3 publication Critical patent/WO2007059119A3/en

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    • 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
    • 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
    • G16B20/50—Mutagenesis
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/30—Detection of binding sites or motifs
    • 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
    • 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
    • G16B40/30—Unsupervised 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
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • 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
    • 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

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Genetics & Genomics (AREA)
  • Chemical & Material Sciences (AREA)
  • Data Mining & Analysis (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Software Systems (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Systems and methods are provided for predicting patient response to a therapy regimen for a liver disease or a disease that is treatable with an immunomodulatory disease therapy using gene expression classifiers. Systems and methods for screening for modulators of target gene expression are also provided. Systems and methods for developing therapeutics against one or more of the proteins coded for by genes of the present invention are also provided. Systems and methods for predicting a patient response to a regimen of interferon either alone or in conjuction with one or more therapeutic molecules, such as ribavirin, in a therapy for hepatitis C viral infection are also provided.
PCT/US2006/044170 2005-11-11 2006-11-13 Systems and methods for identifying diagnostic indicators WO2007059119A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US73556705P 2005-11-11 2005-11-11
US60/735,567 2005-11-11

Publications (2)

Publication Number Publication Date
WO2007059119A2 WO2007059119A2 (en) 2007-05-24
WO2007059119A3 true WO2007059119A3 (en) 2008-12-18

Family

ID=38049237

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2006/044170 WO2007059119A2 (en) 2005-11-11 2006-11-13 Systems and methods for identifying diagnostic indicators

Country Status (1)

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WO (1) WO2007059119A2 (en)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2010062676A1 (en) * 2008-10-30 2010-06-03 Vertex Pharmaceuticals Incorporated Modeling evolutionary dynamics of hepatitis-c resistant variants in patients dosed with telaprevir
EP2808402A3 (en) * 2008-12-29 2015-03-25 Yissum Research Development Company of the Hebrew University of Jerusalem Ltd. Methods of predicting responsiveness to interferon treatment
US8465413B2 (en) 2010-11-25 2013-06-18 Coloplast A/S Method of treating Peyronie's disease
KR20230049750A (en) * 2016-06-07 2023-04-13 더 보드 어브 트러스티스 어브 더 리랜드 스탠포드 주니어 유니버시티 Methods For Diagnosis of Bacterial and Viral Infection
CN107274386B (en) * 2017-05-18 2019-12-17 深思考人工智能机器人科技（北京）有限公司 artificial intelligent auxiliary cervical cell fluid-based smear reading system

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
HEDENFALK ET AL.: "Gene Expression Profiles in Hereditary Breast Cancer", N. ENGL. J. MED., vol. 1, 2001, pages 539 - 548, XP008074260 *
KORENBERG M.J.: "Prediction of Treatment Response Using Gene Expression Profiles", JOURNAL OF PROTEOME RESEARCH, vol. 1, 2002, pages 55 - 61, XP001196946 *
SHAUGNESSY ET AL.: "Integrating Cytogenetics and Gene Expression Profiling in the Molecular Analysis of Multiple Myeloma", INTERNATIONAL JOURNAL OF HEMATOLOGY, vol. 76, no. SUPPL. II, 2002, pages 59 - 64, XP008039054 *
ZALOUDIK ET AL.: "Biomarkers for Predicting Response to Regional Chemoimmunotherapy in Liver Metastases from Colorectal Carcinoma", INT. J. IMMUNOPHARMAC., vol. 19, 1997, pages 481 - 485, XP003005573 *

Also Published As

Publication number Publication date
WO2007059119A2 (en) 2007-05-24

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