LAMPLINK: detection of statistically significant SNP combinations from GWAS data

Bioinformatics. 2016 Nov 15;32(22):3513-3515. doi: 10.1093/bioinformatics/btw418. Epub 2016 Jul 13.

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.

MeSH terms

  • Animals
  • Genome
  • Genome-Wide Association Study*
  • Humans
  • Polymorphism, Single Nucleotide*
  • Software*