原创力文档a variational bayes algorithm for fast and accurate multiple locus genome-wide association analysis变分贝叶斯算法快速、准确多个轨迹全基因组关联分析.pdfVIP
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a variational bayes algorithm for fast and accurate multiple locus genome-wide association analysis变分贝叶斯算法快速、准确多个轨迹全基因组关联分析
Logsdon et al. BMC Bioinformatics 2010, 11:58
/1471-2105/11/58
METHODOLOGY ARTICLE Open Access
A variational Bayes algorithm for fast and
accurate multiple locus genome-wide association
analysis
1 1 1,2*
Benjamin A Logsdon , Gabriel E Hoffman , Jason G Mezey
Abstract
Background: The success achieved by genome-wide association (GWA) studies in the identification of candidate
loci for complex diseases has been accompanied by an inability to explain the bulk of heritability. Here, we
describe the algorithm V-Bay, a variational Bayes algorithm for multiple locus GWA analysis, which is designed to
identify weaker associations that may contribute to this missing heritability.
Results: V-Bay provides a novel solution to the computational scaling constraints of most multiple locus methods
and can complete a simultaneous analysis of a million genetic markers in a few hours, when using a desktop.
Using a range of simulated genetic and GWA experimental scenarios, we demonstrate that V-Bay is highly
accurate, and reliably identifies associations that are too weak to be discovered by single-marker testing
approaches. V-Bay can also outperform a multiple locus analysis method based on the lasso, which has similar
scaling properties for large numbers of genetic markers. For demonstration purposes, we also use V-Bay to confirm
associations with gene expression in cell lines derived from the Phase II individuals of HapMap.
Conclusions: V-Bay is a versatile, fast, and accurate multiple locus GWA analysis tool for the practitioner interested
in identifying weaker associations without high false positive rates.
Background with weaker associations may contribute to a portion of
Genome-wide association (GWA) stud
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