Discovering Genetic Factors for psoriasis through exhaustively searching for significant second order SNP-SNP interactions.

ABSTRACT: In this paper, we aim at discovering genetic factors of psoriasis through searching for statistically significant SNP-SNP interactions exhaustively from two real psoriasis genome-wide association study datasets (phs000019.v1.p1 and phs000982.v1.p1) downloaded from the database of Genotypes and Phenotypes. To deal with the enormous search space, our search algorithm is accelerated with eight biological plausible interaction patterns and a pre-computed look-up table. After our search, we have discovered several SNPs having a stronger association to psoriasis when they are in combination with another SNP and these combinations may be non-linear interactions. Among the top 20 SNP-SNP interactions being found in terms of pairwise p-value and improvement metric value, we have discovered 27 novel

SUBMITTER: Lee KY 

PROVIDER: S-EPMC6185942 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature