title: 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.
  
  
  
  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.
authors.affiliation: PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan.|Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan.|Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan.
authors.forename: Aika
authors.initials: A
authors.lastname: Terada
authors.affiliation: Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507 Japan.
authors.forename: Ryo
authors.initials: R
authors.lastname: Yamada
authors.affiliation: Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan.|Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan.|Center for Materials Research by Information Integration, NIMS, Ibaraki, 305-0047 Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Tsuda
authors.affiliation: Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan.|Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Sese
mesh_terms: D000818:Animals; D016678:Genome; D055106:Genome-Wide Association Study; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012984:Software