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LAMPLINK: detection of statistically significant SNP combinations from GWAS data.

ABSTRACT: One of the major issues in genome-wide association studies is to solve the missing heritability problem. While considering epistatic interactions among multiple SNPs may contribute to solving this problem, existing software cannot detect statistically significant high-order interactions. We propose software named LAMPLINK, which employs a cutting-edge method to enumerate statistically significant SNP combinations from genome-wide case-control data. LAMPLINK is implemented as a set of additional functions to PLINK, and hence existing procedures with PLINK can be applicable. Applied to the 1000 Genomes Project data, LAMPLINK detected a combination of five SNPs that are statistically significantly accumulated in the Japanese population.

Availability and implementation

LAMPLINK is available at http://a-terada.github.io/lamplink/ CONTACT: terada@cbms.k.u-tokyo.ac.jp or sese.jun@aist.go.jpSupplementary information: Supplementary data are available at Bioinformatics online.

SUBMITTER: Terada A

PROVIDER: S-EPMC5181558 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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LAMPLINK: detection of statistically significant SNP combinations from GWAS data.

Terada Aika A Yamada Ryo R Tsuda Koji K Sese Jun J

Bioinformatics (Oxford, England) 20160713 22

One of the major issues in genome-wide association studies is to solve the missing heritability problem. While considering epistatic interactions among multiple SNPs may contribute to solving this problem, existing software cannot detect statistically significant high-order interactions. We propose software named LAMPLINK, which employs a cutting-edge method to enumerate statistically significant SNP combinations from genome-wide case-control data. LAMPLINK is implemented as a set of additional ...[more]

PMID: 27412093

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