[go: up one dir, main page]

WO2008079374A3 - Methods and compositions for selecting and using single nucleotide polymorphisms - Google Patents

Methods and compositions for selecting and using single nucleotide polymorphisms Download PDF

Info

Publication number
WO2008079374A3
WO2008079374A3 PCT/US2007/026241 US2007026241W WO2008079374A3 WO 2008079374 A3 WO2008079374 A3 WO 2008079374A3 US 2007026241 W US2007026241 W US 2007026241W WO 2008079374 A3 WO2008079374 A3 WO 2008079374A3
Authority
WO
WIPO (PCT)
Prior art keywords
methods
snps
compositions
selecting
single nucleotide
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
PCT/US2007/026241
Other languages
French (fr)
Other versions
WO2008079374A2 (en
Inventor
Eric T Wang
Pierre Baldi
Robert K Moyzis
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.)
Individual
Original Assignee
Individual
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 Individual filed Critical Individual
Publication of WO2008079374A2 publication Critical patent/WO2008079374A2/en
Publication of WO2008079374A3 publication Critical patent/WO2008079374A3/en
Anticipated expiration legal-status Critical
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
    • 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
    • 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
    • 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
    • C12Q2600/156—Polymorphic or mutational 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
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • 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

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The invention provides methods of characterizing SNPs, sets of SNPs, genes, and/or gene fragments characterized by such methods, reagents and compositions using SNPs and sets of SNPs, genes, and/or gene fragments characterized by such methods, methods of assigning predictive value to characterized SNPs, diagnostic, prognostic, and treatment methods and compositions based on such predictive values, and business methods.
PCT/US2007/026241 2006-12-21 2007-12-21 Methods and compositions for selecting and using single nucleotide polymorphisms Ceased WO2008079374A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US87667406P 2006-12-21 2006-12-21
US60/876,674 2006-12-21

Publications (2)

Publication Number Publication Date
WO2008079374A2 WO2008079374A2 (en) 2008-07-03
WO2008079374A3 true WO2008079374A3 (en) 2008-10-30

Family

ID=39563117

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2007/026241 Ceased WO2008079374A2 (en) 2006-12-21 2007-12-21 Methods and compositions for selecting and using single nucleotide polymorphisms

Country Status (1)

Country Link
WO (1) WO2008079374A2 (en)

Families Citing this family (35)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11111544B2 (en) 2005-07-29 2021-09-07 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US9424392B2 (en) 2005-11-26 2016-08-23 Natera, Inc. System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals
US9218451B2 (en) * 2008-08-26 2015-12-22 23Andme, Inc. Processing data from genotyping chips
WO2010024894A1 (en) * 2008-08-26 2010-03-04 23Andme, Inc. Processing data from genotyping chips
PT2496720T (en) 2009-11-06 2020-10-12 Univ Leland Stanford Junior NON-INVASIVE GRAFT REJECTION DIAGNOSIS IN PATIENTS SUBJECT TO ORGAN TRANSPLANTS
US11408031B2 (en) 2010-05-18 2022-08-09 Natera, Inc. Methods for non-invasive prenatal paternity testing
US12221653B2 (en) 2010-05-18 2025-02-11 Natera, Inc. Methods for simultaneous amplification of target loci
US11332785B2 (en) 2010-05-18 2022-05-17 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11332793B2 (en) 2010-05-18 2022-05-17 Natera, Inc. Methods for simultaneous amplification of target loci
AU2011255641A1 (en) 2010-05-18 2012-12-06 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US12152275B2 (en) 2010-05-18 2024-11-26 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US20190010543A1 (en) 2010-05-18 2019-01-10 Natera, Inc. Methods for simultaneous amplification of target loci
US10316362B2 (en) 2010-05-18 2019-06-11 Natera, Inc. Methods for simultaneous amplification of target loci
US11939634B2 (en) 2010-05-18 2024-03-26 Natera, Inc. Methods for simultaneous amplification of target loci
US11339429B2 (en) 2010-05-18 2022-05-24 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US9677118B2 (en) 2014-04-21 2017-06-13 Natera, Inc. Methods for simultaneous amplification of target loci
US11322224B2 (en) 2010-05-18 2022-05-03 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11326208B2 (en) 2010-05-18 2022-05-10 Natera, Inc. Methods for nested PCR amplification of cell-free DNA
EP2673729B1 (en) 2011-02-09 2018-10-17 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US20140100126A1 (en) 2012-08-17 2014-04-10 Natera, Inc. Method for Non-Invasive Prenatal Testing Using Parental Mosaicism Data
CN113774132A (en) 2014-04-21 2021-12-10 纳特拉公司 Detection of mutations and ploidy in chromosomal segments
US20180173845A1 (en) 2014-06-05 2018-06-21 Natera, Inc. Systems and Methods for Detection of Aneuploidy
DK3294906T3 (en) 2015-05-11 2024-08-05 Natera Inc Methods for determining ploidy
ES2913468T3 (en) 2016-04-15 2022-06-02 Natera Inc Methods for the detection of lung cancer.
US11485996B2 (en) 2016-10-04 2022-11-01 Natera, Inc. Methods for characterizing copy number variation using proximity-litigation sequencing
GB201618485D0 (en) 2016-11-02 2016-12-14 Ucl Business Plc Method of detecting tumour recurrence
US10011870B2 (en) 2016-12-07 2018-07-03 Natera, Inc. Compositions and methods for identifying nucleic acid molecules
WO2018183493A1 (en) * 2017-03-29 2018-10-04 Nantomics, Llc Signature-hash for multi-sequence files
US12084720B2 (en) 2017-12-14 2024-09-10 Natera, Inc. Assessing graft suitability for transplantation
WO2019200228A1 (en) 2018-04-14 2019-10-17 Natera, Inc. Methods for cancer detection and monitoring by means of personalized detection of circulating tumor dna
US12234509B2 (en) 2018-07-03 2025-02-25 Natera, Inc. Methods for detection of donor-derived cell-free DNA
WO2020247263A1 (en) 2019-06-06 2020-12-10 Natera, Inc. Methods for detecting immune cell dna and monitoring immune system
CN111199773B (en) * 2020-01-20 2023-03-28 中国农业科学院北京畜牧兽医研究所 Evaluation method for fine positioning character associated genome homozygous fragments
WO2023215618A2 (en) * 2022-05-06 2023-11-09 Ampel Biosolutions, Llc Methods for identifying shared biological pathways between diseases using mendelian randomization
CN115188414A (en) * 2022-07-20 2022-10-14 湖南工商大学 SNP genotype coding method based on genome annotation

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020098498A1 (en) * 2000-09-29 2002-07-25 Bader Joel S. Method of identifying genetic regions associated with disease and predicting responsiveness to therapeutic agents
US20030032015A1 (en) * 2001-06-08 2003-02-13 Toivonen Hannu T.T. Method for gene mapping from chromosome and phenotype data
US20030186280A1 (en) * 2002-03-28 2003-10-02 Affymetrix, Inc. Methods for detecting genomic regions of biological significance

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020098498A1 (en) * 2000-09-29 2002-07-25 Bader Joel S. Method of identifying genetic regions associated with disease and predicting responsiveness to therapeutic agents
US20030032015A1 (en) * 2001-06-08 2003-02-13 Toivonen Hannu T.T. Method for gene mapping from chromosome and phenotype data
US20030186280A1 (en) * 2002-03-28 2003-10-02 Affymetrix, Inc. Methods for detecting genomic regions of biological significance

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
HAWKS J. ET AL.: "Recent acceleration of human adaptive evolution", PNAS, vol. 104, no. 52, 26 December 2007 (2007-12-26), pages 20753 - 20758 *
SUNYAEV S.R. ET AL.: "SNP frequencies in human genes - an excess of rare alleles and differing modes of selection", TRENDS IN GENETICS, vol. 16, no. 8, 1 August 2000 (2000-08-01), pages 335 - 337, XP004215195 *

Also Published As

Publication number Publication date
WO2008079374A2 (en) 2008-07-03

Similar Documents

Publication Publication Date Title
WO2008079374A3 (en) Methods and compositions for selecting and using single nucleotide polymorphisms
WO2007146819A3 (en) Methods for identifying and using snp panels
WO2010018563A3 (en) Compositions and methods for the prognosis of lymphoma
WO2011056866A3 (en) Methods and kits for 3'-end-tagging of rna
WO2004023092A3 (en) Genetic analysis and authentication
WO2008069906A3 (en) Digital expression of gene analysis
WO2007087451A3 (en) Compositions and methods for enhancing discriminatory rna interference
WO2009124255A8 (en) Methods for transcript analysis
WO2007115205A3 (en) Improved methods, systems and compositions for monitoring enzyme activity and applications thereof
WO2008005562A3 (en) Rna silencing compositions and methods for the treatment of huntington's disease
WO2007139723A8 (en) Chemicallymodified oligonucleotide primers for nucleic acid amplification
GB2457402A (en) Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators
AU2009236219A8 (en) Silencing of CSN5 gene expression using interfering RNA
WO2009037473A3 (en) Nucleobase characterisation
WO2004003220A3 (en) Methods and composition for analyzing compromised samples using snps
WO2008067423A3 (en) Methods of improving the introduction of dna into bacterial cells
WO2007085497A3 (en) Markers for the prediction of outcome of anthracycline treatment
WO2008087641A3 (en) H19 silencing nucleic acid agents for treating rheumatoid arthritis
MX2022001710A (en) Chemically modified oligonucleotides targeting snps.
MX2007009809A (en) Selection probe amplification.
WO2008010085A3 (en) Prognostic method
WO2007058968A3 (en) Gene expression profiles and methods of use
SI1730315T1 (en) Polymorphisms in nod2/card15 gene
WO2009140679A3 (en) Genetic alterations on chromosomes 21q, 6q and 15q and methods of use thereof for the diagnosis and treatment of type i diabetes
WO2005073380A3 (en) Regulated polymerase iii expression systems and related methods

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 07863217

Country of ref document: EP

Kind code of ref document: A2

NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 07863217

Country of ref document: EP

Kind code of ref document: A2