Li Jiang, Sham Pak Chung, Song Youqiang, Li Miaoxin
Department of Biochemistry, the University of Hong Kong, Pokfulam, Hong Kong.
Department of Psychiatry, the University of Hong Kong, Pokfulam, Hong Kong.
Genet Epidemiol. 2015 Jul;39(5):395-7. doi: 10.1002/gepi.21898. Epub 2015 May 21.
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/.
基于集合的关联测试，即将一组单核苷酸多态性组合成一个统一的测试，已成为识别复杂疾病弱效应或低频风险位点的重要方法。然而，目前尚无用于研究设计的全面且用户友好的工具来估计基于集合测试的效能。我们开发了一种模拟工具来估计多种代表性基于集合测试（SPS）的统计效能。SPS具有图形界面，便于参数设置和结果可视化。高级功能包括加载真实基因型以定义遗传结构、对有或无异质性的风险位点进行基于集合的荟萃分析以及并行模拟。在原理验证示例中，SPS在常规设置下平均不超过3秒即可估计效能。SPS已作为一个独立的功能模块集成到一个用户友好的软件工具（KGG）中，可从http://statgenpro.psychiatry.hku.hk/limx/kgg/免费获取。
