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The benefits of selecting phenotype-specific variants for applications of mixed models in genomics

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Item Type:Article
Title:The benefits of selecting phenotype-specific variants for applications of mixed models in genomics
Creators Name:Lippert, C., Quon, G., Kang, E.Y., Kadie, C.M., Listgarten, J. and Heckerman, D.
Abstract:Applications of linear mixed models (LMMs) to problems in genomics include phenotype prediction, correction for confounding in genome-wide association studies, estimation of narrow sense heritability, and testing sets of variants (e.g., rare variants) for association. In each of these applications, the LMM uses a genetic similarity matrix, which encodes the pairwise similarity between every two individuals in a cohort. Although ideally these similarities would be estimated using strictly variants relevant to the given phenotype, the identity of such variants is typically unknown. Consequently, relevant variants are excluded and irrelevant variants are included, both having deleterious effects. For each application of the LMM, we review known effects and describe new effects showing how variable selection can be used to mitigate them.
Keywords:Genetic Selection, Genetic Variation, Genome-Wide Association Study, Genomics, Heritable Quantitative Trait, Phenotype, Theoretical Models
Source:Scientific Reports
ISSN:2045-2322
Publisher:Nature Publishing Group
Volume:3
Page Range:1815
Date:9 May 2013
Official Publication:https://doi.org/10.1038/srep01815
PubMed:View item in PubMed

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