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EP1960929A4 - System and method for cleaning noisy genetic data and using data to make predictions - Google Patents

System and method for cleaning noisy genetic data and using data to make predictions

Info

Publication number
EP1960929A4
EP1960929A4 EP06838311A EP06838311A EP1960929A4 EP 1960929 A4 EP1960929 A4 EP 1960929A4 EP 06838311 A EP06838311 A EP 06838311A EP 06838311 A EP06838311 A EP 06838311A EP 1960929 A4 EP1960929 A4 EP 1960929A4
Authority
EP
European Patent Office
Prior art keywords
data
make predictions
noisy genetic
cleaning
cleaning noisy
Prior art date
Legal status (The legal status 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 status listed.)
Ceased
Application number
EP06838311A
Other languages
German (de)
French (fr)
Other versions
EP1960929A2 (en
Inventor
Matthew Rabinowitz
Milena Banjevic
Zachary Paul Demko
David Scott Johnson
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Natera Inc
Original Assignee
Gene Security Network Inc
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 US11/496,982 external-priority patent/US20070027636A1/en
Application filed by Gene Security Network Inc filed Critical Gene Security Network Inc
Priority to EP11175867.8A priority Critical patent/EP2437191B1/en
Priority to EP18212459.4A priority patent/EP3599609A1/en
Priority to EP15199388.8A priority patent/EP3012760A1/en
Priority to EP17207702.6A priority patent/EP3373175A1/en
Publication of EP1960929A2 publication Critical patent/EP1960929A2/en
Publication of EP1960929A4 publication Critical patent/EP1960929A4/en
Ceased legal-status Critical Current

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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential 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
    • C12Q1/6869—Methods for sequencing
    • 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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • 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
    • 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
    • G16B40/20—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
    • 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
    • G16B20/10—Ploidy or copy number 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
    • G16B20/40—Population genetics; Linkage disequilibrium
    • 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

  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Medical Informatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Organic Chemistry (AREA)
  • Data Mining & Analysis (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Software Systems (AREA)
  • Public Health (AREA)
  • Artificial Intelligence (AREA)
  • Evolutionary Computation (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Epidemiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
EP06838311A 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions Ceased EP1960929A4 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
EP11175867.8A EP2437191B1 (en) 2005-11-26 2006-11-22 Method and system for detecting chromosomal abnormalities
EP18212459.4A EP3599609A1 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions
EP15199388.8A EP3012760A1 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions
EP17207702.6A EP3373175A1 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions

Applications Claiming Priority (9)

Application Number Priority Date Filing Date Title
US73988205P 2005-11-26 2005-11-26
US74230505P 2005-12-06 2005-12-06
US75439605P 2005-12-29 2005-12-29
US77497606P 2006-02-21 2006-02-21
US78950606P 2006-04-04 2006-04-04
US81774106P 2006-06-30 2006-06-30
US11/496,982 US20070027636A1 (en) 2005-07-29 2006-07-31 System and method for using genetic, phentoypic and clinical data to make predictions for clinical or lifestyle decisions
US84661006P 2006-09-22 2006-09-22
PCT/US2006/045281 WO2007062164A2 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions

Related Child Applications (4)

Application Number Title Priority Date Filing Date
EP18212459.4A Division EP3599609A1 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions
EP15199388.8A Division EP3012760A1 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions
EP11175867.8A Division EP2437191B1 (en) 2005-11-26 2006-11-22 Method and system for detecting chromosomal abnormalities
EP17207702.6A Division EP3373175A1 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions

Publications (2)

Publication Number Publication Date
EP1960929A2 EP1960929A2 (en) 2008-08-27
EP1960929A4 true EP1960929A4 (en) 2009-01-28

Family

ID=38067926

Family Applications (5)

Application Number Title Priority Date Filing Date
EP06838311A Ceased EP1960929A4 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions
EP18212459.4A Ceased EP3599609A1 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions
EP11175867.8A Active EP2437191B1 (en) 2005-11-26 2006-11-22 Method and system for detecting chromosomal abnormalities
EP17207702.6A Pending EP3373175A1 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions
EP15199388.8A Ceased EP3012760A1 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions

Family Applications After (4)

Application Number Title Priority Date Filing Date
EP18212459.4A Ceased EP3599609A1 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions
EP11175867.8A Active EP2437191B1 (en) 2005-11-26 2006-11-22 Method and system for detecting chromosomal abnormalities
EP17207702.6A Pending EP3373175A1 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions
EP15199388.8A Ceased EP3012760A1 (en) 2005-11-26 2006-11-22 System and method for cleaning noisy genetic data and using data to make predictions

Country Status (8)

Country Link
EP (5) EP1960929A4 (en)
JP (4) JP6121642B2 (en)
CN (1) CN101346724B (en)
AU (1) AU2006318425B2 (en)
CA (1) CA2632230C (en)
ES (1) ES2634665T3 (en)
HK (1) HK1224053A1 (en)
WO (1) WO2007062164A2 (en)

Families Citing this family (91)

* Cited by examiner, † Cited by third party
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