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Article: OpenADAM: an open source genome-wide association data management system for Affymetrix SNP arrays.

TitleOpenADAM: an open source genome-wide association data management system for Affymetrix SNP arrays.
Authors
Issue Date2008
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/
Citation
Bmc Genomics, 2008, v. 9, p. 636 How to Cite?
AbstractBACKGROUND: Large scale genome-wide association studies have become popular since the introduction of high throughput genotyping platforms. Efficient management of the vast array of data generated poses many challenges. DESCRIPTION: We have developed an open source web-based data management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Affymetrix Genome-Wide Human SNP Array platforms. The database supports genotype calling using DM, BRLMM, BRLMM-P or Birdseed algorithms provided by the Affymetrix Power Tools. The genotype and corresponding pedigree data are stored in a relational database for efficient downstream data manipulation and analysis, such as calculation of allele and genotype frequencies, sample identity checking, and export of genotype data in various file formats for analysis using commonly-available software. A novel method for genotyping error estimation is implemented using linkage disequilibrium information from the HapMap project. All functionalities are accessible via a web-based user interface. CONCLUSION: OpenADAM provides an open source database system for management of Affymetrix genome-wide association SNP data.
Persistent Identifierhttp://hdl.handle.net/10722/59700
ISSN
2015 Impact Factor: 3.867
2015 SCImago Journal Rankings: 2.343
PubMed Central ID
ISI Accession Number ID
Funding AgencyGrant Number
The University of Hong Kong's strategic research theme of Genomics, Proteomics and Bio-Informatics
National Insitutes of Health, USAEY-12562
Funding Information:

Some of this work was done while JMYY was a Research Assistant in our group at the Genome Research Centre and partially supported by The University of Hong Kong's strategic research theme of Genomics, Proteomics and Bio-Informatics. We acknowledge support from grant EY-12562 from the National Insitutes of Health, USA, to PCS and SSC.

 

DC FieldValueLanguage
dc.contributor.authorYeung, JMen_HK
dc.contributor.authorSham, PCen_HK
dc.contributor.authorChan, ASen_HK
dc.contributor.authorCherny, SSen_HK
dc.date.accessioned2010-05-31T03:55:41Z-
dc.date.available2010-05-31T03:55:41Z-
dc.date.issued2008en_HK
dc.identifier.citationBmc Genomics, 2008, v. 9, p. 636en_HK
dc.identifier.issn1471-2164en_HK
dc.identifier.urihttp://hdl.handle.net/10722/59700-
dc.description.abstractBACKGROUND: Large scale genome-wide association studies have become popular since the introduction of high throughput genotyping platforms. Efficient management of the vast array of data generated poses many challenges. DESCRIPTION: We have developed an open source web-based data management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Affymetrix Genome-Wide Human SNP Array platforms. The database supports genotype calling using DM, BRLMM, BRLMM-P or Birdseed algorithms provided by the Affymetrix Power Tools. The genotype and corresponding pedigree data are stored in a relational database for efficient downstream data manipulation and analysis, such as calculation of allele and genotype frequencies, sample identity checking, and export of genotype data in various file formats for analysis using commonly-available software. A novel method for genotyping error estimation is implemented using linkage disequilibrium information from the HapMap project. All functionalities are accessible via a web-based user interface. CONCLUSION: OpenADAM provides an open source database system for management of Affymetrix genome-wide association SNP data.en_HK
dc.languageengen_HK
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenomics/en_HK
dc.relation.ispartofBMC genomicsen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rightsB M C Genomics. Copyright © BioMed Central Ltd.en_HK
dc.titleOpenADAM: an open source genome-wide association data management system for Affymetrix SNP arrays.en_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1471-2164&volume=9&spage=636&epage=&date=2008&atitle=OpenADAM:+an+open+source+genome-wide+association+data+management+system+for+Affymetrix+SNP+arraysen_HK
dc.identifier.emailSham, PC: pcsham@hku.hken_HK
dc.identifier.emailChan, AS: chansw3@hku.hken_HK
dc.identifier.emailCherny, SS: cherny@hku.hken_HK
dc.identifier.authoritySham, PC=rp00459en_HK
dc.identifier.authorityChan, AS=rp00288en_HK
dc.identifier.authorityCherny, SS=rp00232en_HK
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/1471-2164-9-636-
dc.identifier.pmid19117518-
dc.identifier.pmcidPMC2636804-
dc.identifier.scopuseid_2-s2.0-63149152765en_HK
dc.identifier.hkuros154398en_HK
dc.identifier.volume9en_HK
dc.identifier.spage636en_HK
dc.identifier.epage636en_HK
dc.identifier.eissn1471-2164-
dc.identifier.isiWOS:000263110600001-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridYeung, JM=36818580500en_HK
dc.identifier.scopusauthoridSham, PC=34573429300en_HK
dc.identifier.scopusauthoridChan, AS=37019607500en_HK
dc.identifier.scopusauthoridCherny, SS=7004670001en_HK
dc.identifier.citeulike3841310-

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