Abstract:
BACKGROUND:Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. RESULTS:A non-parametric Bayesian approach in the form of a Bayesian neural network is proposed for use in analyzing genetic association studies. Demonstrations on synthetic and real data reveal they are able to efficiently and accurately determine which variants are involved in determining case-control status. By using graphics processing units (GPUs) the time needed to build these models is decreased by several orders of magnitude. In comparison with commonly used approaches for detecting interactions, Bayesian neural networks perform very well across a broad spectrum of possible genetic relationships. CONCLUSIONS:The proposed framework is shown to be a powerful method for detecting causal SNPs while being computationally efficient enough to handle large datasets.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Beam AL,Motsinger-Reif A,Doyle Jdoi
10.1186/s12859-014-0368-0subject
Has Abstractpub_date
2014-11-21 00:00:00pages
368issn
1471-2105pii
s12859-014-0368-0journal_volume
15pub_type
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