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Article: IGG3: A tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis

TitleIGG3: A tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis
Authors
Li, MXJiang, LKao, PYPSham, PCSong, YQ
Issue Date2009
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2009, v. 25 n. 11, p. 1449-1450 How to Cite?
DOI: http://dx.doi.org/10.1093/bioinformatics/btp183
AbstractSummary: There is an urgent and increasing demand for integrating large genotype datasets across genome-wide association studies and HapMap project for whole-genome imputation and individual-level meta-analysis. A new algorithm was developed to efficiently merge raw genotypes across large datasets and implemented in the latest version of IGG, IGG3. In addition, IGG3 can integrate the latest phased and unphased HapMap genotypes and can flexibly generate complete sets of input files for six popular genotype imputation tools. We demonstrated the efficiency of IGG3 by simulation tests, which could rapidly merge genotypes in tens of thousands of large genotype chips (e.g. Affymetrix Genome-Wide Human SNP Array 6.0 and Illumina Human1m-duo) and in HapMap III project on an ordinary desktop computer. © The Author 2009. Published by Oxford University Press. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/58279
ISSN
1367-4803
2021 Impact Factor: 6.931
2020 SCImago Journal Rankings: 3.599
ISI Accession Number ID
WOS:000266109500025
Funding AgencyGrant Number
Research Grant Council of Hong KongHKU7688/05M
HKU7752/08M
Research Fund for the Control of Infectious Diseases08070652
Funding Information:

Research Grant Council of Hong Kong (HKU7688/05M & HKU7752/08M, YQS); Research Fund for the Control of Infectious Diseases (No. 08070652, to Y.-Q.S.).

References
References in Scopus
Grants
Fine mapping candidate loci for nasopharyngeal carcinoma (NPC) in southern Chinese specifically linked to EBV aetiopathogenesis

 

DC FieldValueLanguage
dc.contributor.authorLi, MXen_HK
dc.contributor.authorJiang, Len_HK
dc.contributor.authorKao, PYPen_HK
dc.contributor.authorSham, PCen_HK
dc.contributor.authorSong, YQen_HK
dc.date.accessioned2010-05-31T03:27:19Z-
dc.date.available2010-05-31T03:27:19Z-
dc.date.issued2009en_HK
dc.identifier.citationBioinformatics, 2009, v. 25 n. 11, p. 1449-1450en_HK
dc.identifier.issn1367-4803en_HK
dc.identifier.urihttp://hdl.handle.net/10722/58279-
dc.description.abstractSummary: There is an urgent and increasing demand for integrating large genotype datasets across genome-wide association studies and HapMap project for whole-genome imputation and individual-level meta-analysis. A new algorithm was developed to efficiently merge raw genotypes across large datasets and implemented in the latest version of IGG, IGG3. In addition, IGG3 can integrate the latest phased and unphased HapMap genotypes and can flexibly generate complete sets of input files for six popular genotype imputation tools. We demonstrated the efficiency of IGG3 by simulation tests, which could rapidly merge genotypes in tens of thousands of large genotype chips (e.g. Affymetrix Genome-Wide Human SNP Array 6.0 and Illumina Human1m-duo) and in HapMap III project on an ordinary desktop computer. © The Author 2009. Published by Oxford University Press. All rights reserved.en_HK
dc.languageengen_HK
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/en_HK
dc.relation.ispartofBioinformaticsen_HK
dc.rightsBioinformatics. Copyright © Oxford University Press.en_HK
dc.subject.meshAlgorithmsen_HK
dc.subject.meshDatabases, Geneticen_HK
dc.subject.meshGenome - geneticsen_HK
dc.subject.meshGenome-Wide Association Studyen_HK
dc.subject.meshGenomics - methodsen_HK
dc.subject.meshGenotypeen_HK
dc.subject.meshInformation Storage and Retrieval - methodsen_HK
dc.subject.meshMeta-Analysis as Topicen_HK
dc.subject.meshSoftwareen_HK
dc.titleIGG3: A tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysisen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1367-4803&volume=25 &issue=11&spage=1449&epage=1450&date=2009&atitle=IGG3:+a+tool+to+rapidly+integrate+large+genotype+datasets+for+whole-genome+imputation+and+individual-level+meta-analysisen_HK
dc.identifier.emailLi, MX: mxli@hku.hken_HK
dc.identifier.emailSham, PC: pcsham@hku.hken_HK
dc.identifier.emailSong, YQ: songy@hku.hken_HK
dc.identifier.authorityLi, MX=rp01722en_HK
dc.identifier.authoritySham, PC=rp00459en_HK
dc.identifier.authoritySong, YQ=rp00488en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1093/bioinformatics/btp183en_HK
dc.identifier.pmid19346322-
dc.identifier.scopuseid_2-s2.0-65649085584en_HK
dc.identifier.hkuros158153en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-65649085584&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume25en_HK
dc.identifier.issue11en_HK
dc.identifier.spage1449en_HK
dc.identifier.epage1450en_HK
dc.identifier.eissn1460-2059-
dc.identifier.isiWOS:000266109500025-
dc.publisher.placeUnited Kingdomen_HK
dc.relation.projectFine mapping candidate loci for nasopharyngeal carcinoma (NPC) in southern Chinese specifically linked to EBV aetiopathogenesis-
dc.identifier.scopusauthoridLi, MX=17135391100en_HK
dc.identifier.scopusauthoridJiang, L=23012303800en_HK
dc.identifier.scopusauthoridKao, PYP=24280722500en_HK
dc.identifier.scopusauthoridSham, PC=34573429300en_HK
dc.identifier.scopusauthoridSong, YQ=7404921212en_HK
dc.identifier.citeulike4285138-

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