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Article: FAPI: Fast and Accurate P-value Imputation for genome-wide association study

TitleFAPI: Fast and Accurate P-value Imputation for genome-wide association study
Authors
Issue Date2015
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/ejhg
Citation
European Journal of Human Genetics, 2015 How to Cite?
AbstractImputing individual-level genotypes (or genotype imputation) is now a standard procedure in genome-wide association studies (GWAS) to examine disease associations at untyped common genetic variants. Meta-analysis of publicly available GWAS summary statistics can allow more disease-associated loci to be discovered, but these data are usually provided for various variant sets. Thus imputing these summary statistics of different variant sets into a common reference panel for meta-analyses is impossible using traditional genotype imputation methods. Here we develop a Fast and Accurate P-value Imputation (FAPI) method that utilizes summary statistics of common variants only. Its computational cost is linear with the number of untyped variants and has similar accuracy compared with IMPUTE2 with prephasing, one of the leading methods in genotype imputation. In addition, based on the FAPI idea, we develop a metric to detect abnormal association at a variant and showed that it had a significantly greater power compared with LD-PAC, a method that quantifies the evidence of spurious associations based on likelihood ratio. Our method is implemented in a user-friendly software tool, which is available at http://statgenpro.psychiatry.hku.hk/fapi.European Journal of Human Genetics advance online publication, 26 August 2015; doi:10.1038/ejhg.2015.190. © 2015 Macmillan Publishers Limited
Persistent Identifierhttp://hdl.handle.net/10722/218841
ISSN
2015 Impact Factor: 4.58
2015 SCImago Journal Rankings: 2.077

 

DC FieldValueLanguage
dc.contributor.authorKwan, SH-
dc.contributor.authorLi, M-
dc.contributor.authorDeng, SJ-
dc.contributor.authorSham, PC-
dc.date.accessioned2015-09-18T06:55:15Z-
dc.date.available2015-09-18T06:55:15Z-
dc.date.issued2015-
dc.identifier.citationEuropean Journal of Human Genetics, 2015-
dc.identifier.issn1018-4813-
dc.identifier.urihttp://hdl.handle.net/10722/218841-
dc.description.abstractImputing individual-level genotypes (or genotype imputation) is now a standard procedure in genome-wide association studies (GWAS) to examine disease associations at untyped common genetic variants. Meta-analysis of publicly available GWAS summary statistics can allow more disease-associated loci to be discovered, but these data are usually provided for various variant sets. Thus imputing these summary statistics of different variant sets into a common reference panel for meta-analyses is impossible using traditional genotype imputation methods. Here we develop a Fast and Accurate P-value Imputation (FAPI) method that utilizes summary statistics of common variants only. Its computational cost is linear with the number of untyped variants and has similar accuracy compared with IMPUTE2 with prephasing, one of the leading methods in genotype imputation. In addition, based on the FAPI idea, we develop a metric to detect abnormal association at a variant and showed that it had a significantly greater power compared with LD-PAC, a method that quantifies the evidence of spurious associations based on likelihood ratio. Our method is implemented in a user-friendly software tool, which is available at http://statgenpro.psychiatry.hku.hk/fapi.European Journal of Human Genetics advance online publication, 26 August 2015; doi:10.1038/ejhg.2015.190. © 2015 Macmillan Publishers Limited-
dc.languageeng-
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/ejhg-
dc.relation.ispartofEuropean Journal of Human Genetics-
dc.titleFAPI: Fast and Accurate P-value Imputation for genome-wide association study-
dc.typeArticle-
dc.identifier.emailKwan, SH: shkwan@hku.hk-
dc.identifier.emailLi, M: mxli@hku.hk-
dc.identifier.emailDeng, SJ: silviakt@hku.hk-
dc.identifier.emailSham, PC: pcsham@hku.hk-
dc.identifier.authorityLi, M=rp01722-
dc.identifier.authoritySham, PC=rp00459-
dc.identifier.doi10.1038/ejhg.2015.190-
dc.identifier.pmid26306642-
dc.identifier.scopuseid_2-s2.0-84940061697-
dc.identifier.hkuros252457-
dc.publisher.placeUnited Kingdom-

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