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WO2002008469A3 - Methods, systems, and articles of manufacture for evaluating biological data - Google Patents

Methods, systems, and articles of manufacture for evaluating biological data Download PDF

Info

Publication number
WO2002008469A3
WO2002008469A3 PCT/US2001/023629 US0123629W WO0208469A3 WO 2002008469 A3 WO2002008469 A3 WO 2002008469A3 US 0123629 W US0123629 W US 0123629W WO 0208469 A3 WO0208469 A3 WO 0208469A3
Authority
WO
WIPO (PCT)
Prior art keywords
algorithms
articles
systems
calls
methods
Prior art date
Application number
PCT/US2001/023629
Other languages
French (fr)
Other versions
WO2002008469A2 (en
WO2002008469A9 (en
Inventor
Heinz Breu
Hugh J Pasika
Yuandan Lou
David P Holden
Original Assignee
Applera Corp
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 Applera Corp filed Critical Applera Corp
Priority to CA002416764A priority Critical patent/CA2416764A1/en
Priority to AU2002211212A priority patent/AU2002211212A1/en
Priority to EP01979226A priority patent/EP1349960A2/en
Priority to JP2002513951A priority patent/JP2004516455A/en
Publication of WO2002008469A2 publication Critical patent/WO2002008469A2/en
Publication of WO2002008469A3 publication Critical patent/WO2002008469A3/en
Publication of WO2002008469A9 publication Critical patent/WO2002008469A9/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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids

Landscapes

  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Complex Calculations (AREA)
  • Measurement Of The Respiration, Hearing Ability, Form, And Blood Characteristics Of Living Organisms (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)

Abstract

Methods, systems, and articles of manufacture consistent with the present invention are provided for making allele calls. In certain embodiments, allele calling is accomplished by providing a committee machine that receives calls from several allele calling algorithms. By receiving calls from multiple allele calling algorithms, the committee machine makes calls containing a high level of confidence over a variety of conditions. Certain embodiments provide methods employing at least two algorithms and at least two quality values for allele calling. Unique individual algorithms for allele calling are also provided.
PCT/US2001/023629 2000-07-21 2001-07-23 Methods, systems, and articles of manufacture for evaluating biological data WO2002008469A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
CA002416764A CA2416764A1 (en) 2000-07-21 2001-07-23 Methods, systems, and articles of manufacture for evaluating biological data
AU2002211212A AU2002211212A1 (en) 2000-07-21 2001-07-23 Methods, systems, and articles of manufacture for evaluating biological data
EP01979226A EP1349960A2 (en) 2000-07-21 2001-07-23 Methods, systems, and articles of manufacture for evaluating biological data
JP2002513951A JP2004516455A (en) 2000-07-21 2001-07-23 Methods, systems, and products for evaluating biological data

Applications Claiming Priority (8)

Application Number Priority Date Filing Date Title
US21969700P 2000-07-21 2000-07-21
US60/219,697 2000-07-21
US22755600P 2000-08-23 2000-08-23
US60/227,556 2000-08-23
US72491000A 2000-11-28 2000-11-28
US09/724,910 2000-11-28
US29012901P 2001-05-10 2001-05-10
US60/290,129 2001-05-10

Publications (3)

Publication Number Publication Date
WO2002008469A2 WO2002008469A2 (en) 2002-01-31
WO2002008469A3 true WO2002008469A3 (en) 2003-07-17
WO2002008469A9 WO2002008469A9 (en) 2003-11-20

Family

ID=27499158

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/023629 WO2002008469A2 (en) 2000-07-21 2001-07-23 Methods, systems, and articles of manufacture for evaluating biological data

Country Status (5)

Country Link
EP (1) EP1349960A2 (en)
JP (1) JP2004516455A (en)
AU (1) AU2002211212A1 (en)
CA (1) CA2416764A1 (en)
WO (1) WO2002008469A2 (en)

Families Citing this family (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2005531853A (en) * 2002-06-28 2005-10-20 アプレラ コーポレイション System and method for SNP genotype clustering
JP4713138B2 (en) * 2004-12-06 2011-06-29 株式会社日立ソリューションズ Gene information display method, display apparatus, and program
EP1862929A1 (en) * 2006-02-28 2007-12-05 Hitachi Software Engineering Co., Ltd. Genotyping result evaluation method and system
CN101467032B (en) 2006-04-14 2013-03-27 日本电气株式会社 Individual discrimination method and apparatus
WO2015029670A1 (en) * 2013-08-27 2015-03-05 日産自動車株式会社 Multi-link piston-crank mechanism for internal combustion engine
JP2017532699A (en) * 2014-09-05 2017-11-02 ナントミクス，エルエルシー Systems and methods for origin determination

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5580728A (en) * 1994-06-17 1996-12-03 Perlin; Mark W. Method and system for genotyping
WO1999053423A1 (en) * 1998-04-16 1999-10-21 Northeastern University Expert system for analysis of dna sequencing electropherograms
US6019896A (en) * 1998-03-06 2000-02-01 Molecular Dynamics, Inc. Method for using a quality metric to assess the quality of biochemical separations

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5580728A (en) * 1994-06-17 1996-12-03 Perlin; Mark W. Method and system for genotyping
US6019896A (en) * 1998-03-06 2000-02-01 Molecular Dynamics, Inc. Method for using a quality metric to assess the quality of biochemical separations
WO1999053423A1 (en) * 1998-04-16 1999-10-21 Northeastern University Expert system for analysis of dna sequencing electropherograms

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
PALSSON B ET AL: "Using Quality Measures to Facilitate Allele Calling in High-Throughput Genotyping", GENOME RESEARCH, vol. 9, no. 10, October 1999 (1999-10-01), pages 1002 - 1012, XP002228698, Retrieved from the Internet <URL:http://www.genome.org/cgi/reprint/9/10/1002.pdf> [retrieved on 20030117] *
PERLIN M W: "An Expert System for Scoring DNA Database Profiles", GENETIC IDENTITY CONFERENCE PROCEEDINGS, ELEVENTH INTERNATIONAL SYMPOSIUM ON HUMAN IDENTIFICATION - 2000, 7 October 2000 (2000-10-07) - 14 October 2000 (2000-10-14), Biloxi, MS, XP002228697, Retrieved from the Internet <URL:http://www.promega.com/geneticidproc/ussymp11proc/content/perlin.pdf> [retrieved on 20030117] *
SEE-KIONG NG: "Automating Computational Molecular Genetics: Solving the Microsatellite Genotyping Problem", CMU-CS-98-105, 23 January 1998 (1998-01-23), Pittsburgh, PA, USA, XP002228696, Retrieved from the Internet <URL:http://reports-archive.adm.cs.cmu.edu/anon/1998/CMU-CS-98-105.ps> [retrieved on 20030117] *

Also Published As

Publication number Publication date
AU2002211212A1 (en) 2002-02-05
CA2416764A1 (en) 2002-01-31
WO2002008469A2 (en) 2002-01-31
EP1349960A2 (en) 2003-10-08
JP2004516455A (en) 2004-06-03
WO2002008469A9 (en) 2003-11-20

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