Terada Aika, Yamada Ryo, Tsuda Koji, Sese Jun
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.
Bioinformatics. 2016 Nov 15;32(22):3513-3515. doi: 10.1093/bioinformatics/btw418. Epub 2016 Jul 13.
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.
全基因组关联研究中的一个主要问题是解决遗传力缺失问题。虽然考虑多个单核苷酸多态性（SNP）之间的上位性相互作用可能有助于解决这个问题，但现有软件无法检测到具有统计学意义的高阶相互作用。我们提出了名为LAMPLINK的软件，它采用一种前沿方法从全基因组病例对照数据中枚举具有统计学意义的SNP组合。LAMPLINK作为PLINK的一组附加功能来实现，因此现有的PLINK程序可以适用。应用于千人基因组计划数据时，LAMPLINK检测到在日本人群中具有统计学显著聚集性的五个SNP的组合。
LAMPLINK可在http://a-terada.github.io/lamplink/获取 联系方式：terada@cbms.k.u-tokyo.ac.jp或sese.jun@aist.go.jp 补充信息：补充数据可在《生物信息学》在线获取。
