Journal
HEREDITY
Volume 103, Issue 3, Pages 223-237Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/hdy.2009.56
Keywords
Bayes; cQTL; multilocus association analysis; SNP; gene expression; family structure
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Funding
- Academy of Finland [202324]
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For small pedigrees, the issue of correcting for known or estimated relatedness structure in population-based Bayesian multilocus association analysis is considered. Two such relatedness corrections: [1] a random term arising from the infinite polygenic model and [2] a fixed covariate following the class D model of Bonney, are compared with the case of no correction using both simulated and real marker and gene-expression data from lymphoblastoid cell lines from four CEPH families. This comparison is performed with clinical quantitative trait locus (cQTL) models-multilocus association models where marker data and expression levels of gene transcripts as well as possible genotype x expression interaction terms are jointly used to explain quantitative trait variation. We found out that regardless of having a correction term in the model, the cQTL-models fit a few extra small-effect components (similar to finite polygenic models) which itself serves as a relatedness correction. For small data and small heritability one may use the covariate model, which clearly outperforms the infinite polygenic model in small data examples. Heredity (2009) 103, 223-237; doi: 10.1038/hdy.2009.56; published online 20 May 2009
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