A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies

Zuber, Verena; Silva, A. Pedro Duarte; Strimmer, Korbinian

Publication

A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies

2012Journal article

dc.contributor.author	Zuber, Verena
dc.contributor.author	Silva, A. Pedro Duarte
dc.contributor.author	Strimmer, Korbinian
dc.date.accessioned	2014-06-05T16:25:04Z
dc.date.available	2014-06-05T16:25:04Z
dc.date.issued	2012
dc.description.abstract	Background: Identification of causal SNPs in most genome wide association studies relies on approaches that consider each SNP individually. However, there is a strong correlation structure among SNPs that needs to be taken into account. Hence, increasingly modern computationally expensive regression methods are employed for SNP selection that consider all markers simultaneously and thus incorporate dependencies among SNPs. Results: We develop a novel multivariate algorithm for large scale SNP selection using CAR score regression, a promising new approach for prioritizing biomarkers. Specifically, we propose a computationally efficient procedure for shrinkage estimation of CAR scores from high-dimensional data. Subsequently, we conduct a comprehensive comparison study including five advanced regression approaches (boosting, lasso, NEG, MCP, and CAR score) and a univariate approach (marginal correlation) to determine the effectiveness in finding true causal SNPs. Conclusions: Simultaneous SNP selection is a challenging task. We demonstrate that our CAR score-based algorithm consistently outperforms all competing approaches, both uni- and multivariate, in terms of correctly recovered causal SNPs and SNP ranking. An R package implementing the approach as well as R code to reproduce the complete study presented here is available from http://strimmerlab.org/software/care/.	por
dc.description.version	info:eu-repo/semantics/publishedVersion
dc.identifier.citation	Zuber, Verena; Duarte Silva, A.P. Strimmer, Korbinian - A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies. BMC Bioinformatics. ISSN 1471-2105. Vol. 13, N.º 284 (2012), 8 p.	por
dc.identifier.doi	10.1186/1471-2105-13-284
dc.identifier.issn	1471-2105
dc.identifier.uri	http://hdl.handle.net/10400.14/14504
dc.identifier.wos	WOS:000314180800001
dc.language.iso	eng	por
dc.peerreviewed	yes	por
dc.relation	0315452A
dc.relation	R01 GM031575
dc.relation	R01 MH059490
dc.rights.uri	http://creativecommons.org/licenses/by/2.0
dc.title	A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies	por
dc.type	journal article
dspace.entity.type	Publication
oaire.citation.title	BMC Bioinformatics
oaire.citation.volume	13
person.familyName	Zuber
person.familyName	Duarte Silva
person.familyName	Strimmer
person.givenName	Verena
person.givenName	Pedro
person.givenName	Korbinian
person.identifier.ciencia-id	371F-636A-E2E9
person.identifier.orcid	0000-0001-9827-1877
person.identifier.orcid	0000-0003-1378-2403
person.identifier.orcid	0000-0001-7917-2056
person.identifier.rid	B-6168-2008
person.identifier.scopus-author-id	6602627961
rcaap.rights	openAccess	por
rcaap.type	article	por
relation.isAuthorOfPublication	60100d97-965f-4bce-b90c-9cab27bc86ff
relation.isAuthorOfPublication	2a796b4b-6325-4af6-a47e-d233ccde3b53
relation.isAuthorOfPublication	01ec2436-ac75-471b-9dfc-9f55bc87cb1e
relation.isAuthorOfPublication.latestForDiscovery	60100d97-965f-4bce-b90c-9cab27bc86ff