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Analysis of Genome-Wide Association Studies with Multiple Outcomes Using Penalization

Liu, Jin ; Huang, Jian ; Ma, Shuangge

PLoS One, Dec 2012, Vol.7(12), p.e51198 [Peer Reviewed Journal]

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  • Title:
    Analysis of Genome-Wide Association Studies with Multiple Outcomes Using Penalization
  • Author: Liu, Jin ; Huang, Jian ; Ma, Shuangge
  • Subjects: Connecticut ; Muridae ; Iowa City Iowa ; Laboratories ; Multivariate Analysis ; Mammals ; Markers ; Mice ; Gene Expression ; Bioinformatics ; Studies ; Genomes ; Genetics ; Generalized Linear Models ; Mice ; Immunology ; Fines & Penalties ; Public Health ; Variables
  • Is Part Of: PLoS One, Dec 2012, Vol.7(12), p.e51198
  • Description: Genome-wide association studies have been extensively conducted, searching for markers for biologically meaningful outcomes and phenotypes. Penalization methods have been adopted in the analysis of the joint effects of a large number of SNPs (single nucleotide polymorphisms) and marker identification. This study is partly motivated by the analysis of heterogeneous stock mice dataset, in which multiple correlated phenotypes and a large number of SNPs are available. Existing penalization methods designed to analyze a single response variable cannot accommodate the correlation among multiple response variables. With multiple response variables sharing the same set of markers, joint modeling is first employed to accommodate the correlation. The group Lasso approach is adopted to select markers associated with all the outcome variables. An efficient computational algorithm is developed. Simulation study and analysis of the heterogeneous stock mice dataset show that the proposed method can outperform...
  • Language: English
  • Identifier: E-ISSN: 19326203 ; DOI: 10.1371/journal.pone.0051198

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