|Title||TEAM: efficient two-locus epistasis tests in human genome-wide association study.|
|Publication Type||Journal Article|
|Year of Publication||2010|
|Authors||Zhang, Xiang, Shunping Huang, Fei Zou, and Wei Wang|
|Date Published||2010 Jun 15|
|Keywords||Algorithms, Epistasis, Genetic, Genome, Human, Genome-Wide Association Study, Genomics, Humans, Population Groups, Software|
As a promising tool for identifying genetic markers underlying phenotypic differences, genome-wide association study (GWAS) has been extensively investigated in recent years. In GWAS, detecting epistasis (or gene-gene interaction) is preferable over single locus study since many diseases are known to be complex traits. A brute force search is infeasible for epistasis detection in the genome-wide scale because of the intensive computational burden. Existing epistasis detection algorithms are designed for dataset consisting of homozygous markers and small sample size. In human study, however, the genotype may be heterozygous, and number of individuals can be up to thousands. Thus, existing methods are not readily applicable to human datasets. In this article, we propose an efficient algorithm, TEAM, which significantly speeds up epistasis detection for human GWAS. Our algorithm is exhaustive, i.e. it does not ignore any epistatic interaction. Utilizing the minimum spanning tree structure, the algorithm incrementally updates the contingency tables for epistatic tests without scanning all individuals. Our algorithm has broader applicability and is more efficient than existing methods for large sample study. It supports any statistical test that is based on contingency tables, and enables both family-wise error rate and false discovery rate controlling. Extensive experiments show that our algorithm only needs to examine a small portion of the individuals to update the contingency tables, and it achieves at least an order of magnitude speed up over the brute force approach.
|Original Publication||TEAM: Efficient two-locus epistasis tests in human genome-wide association study.|
|PubMed Central ID||PMC2881371|
|Grant List||P01 CA142538 / CA / NCI NIH HHS / United States |
P30 ES010126 / ES / NIEHS NIH HHS / United States
TEAM: efficient two-locus epistasis tests in human genome-wide association study.