title: SPS: A Simulation Tool for Calculating Power of Set-Based Genetic Association Tests.
abstract: Set-based association tests, combining a set of single-nucleotide polymorphisms into a unified test, have become important approaches to identify weak-effect or low-frequency risk loci of complex diseases. However, there is no comprehensive and user-friendly tool to estimate power of set-based tests for study design. We developed a simulation tool to estimate statistical power of multiple representative set-based tests (SPS). SPS has a graphic interface to facilitate parameter settings and result visualization. Advanced functions include loading real genotypes to define genetic architecture, set-based meta-analysis for risk loci with or without heterogeneity, and parallel simulations. In proof-of-principle examples, SPS took no more than 3 sec on average to estimate the power in a conventional setting. The SPS has been integrated into a user-friendly software tool (KGG) as an independent functional module and it is freely available at http://statgenpro.psychiatry.hku.hk/limx/kgg/.
authors.affiliation: Department of Biochemistry, the University of Hong Kong, Pokfulam, Hong Kong.
authors.forename: Jiang
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Psychiatry, the University of Hong Kong, Pokfulam, Hong Kong.|The Centre for Genomic Sciences, the University of Hong Kong, Pokfulam, Hong Kong.|State Key Laboratory for Cognitive and Brain Sciences, the University of Hong Kong, Pokfulam, Hong Kong.|The Centre for Reproduction, Development and Growth, the University of Hong Kong, Pokfulam, Hong Kong.
authors.forename: Pak Chung
authors.initials: PC
authors.lastname: Sham
authors.affiliation: Department of Biochemistry, the University of Hong Kong, Pokfulam, Hong Kong.|The Centre for Genomic Sciences, the University of Hong Kong, Pokfulam, Hong Kong.|The Centre for Reproduction, Development and Growth, the University of Hong Kong, Pokfulam, Hong Kong.
authors.forename: Youqiang
authors.initials: Y
authors.lastname: Song
authors.affiliation: Department of Psychiatry, the University of Hong Kong, Pokfulam, Hong Kong.|The Centre for Genomic Sciences, the University of Hong Kong, Pokfulam, Hong Kong.|State Key Laboratory for Cognitive and Brain Sciences, the University of Hong Kong, Pokfulam, Hong Kong.|The Centre for Reproduction, Development and Growth, the University of Hong Kong, Pokfulam, Hong Kong.
authors.forename: Miaoxin
authors.initials: M
authors.lastname: Li
mesh_terms: D000465:Algorithms; D000704:Analysis of Variance; D003198:Computer Simulation; D056726:Genetic Association Studies / Q000379:methods*; D005838:Genotype; D006801:Humans; D008957:Models, Genetic; D009010:Monte Carlo Method; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012984:Software
keywords: complex disease; meta-analysis; power; set-based association test; simulation