Email updates

Keep up to date with the latest news and content from BMC Genetics and BioMed Central.

Open Access Highly Accessed Software

GWAPower: a statistical power calculation software for genome-wide association studies with quantitative traits

Sheng Feng1*, Shengchu Wang1, Chia-Cheng Chen2 and Lan Lan1

Author Affiliations

1 Deaprtment of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina 27710, USA

2 Department of Statistics, North Carolina State University, Raleigh, North Carolina 27695, USA

For all author emails, please log on.

BMC Genetics 2011, 12:12  doi:10.1186/1471-2156-12-12

Published: 21 January 2011

Abstract

Background

In designing genome-wide association (GWA) studies it is important to calculate statistical power. General statistical power calculation procedures for quantitative measures often require information concerning summary statistics of distributions such as mean and variance. However, with genetic studies, the effect size of quantitative traits is traditionally expressed as heritability, a quantity defined as the amount of phenotypic variation in the population that can be ascribed to the genetic variants among individuals. Heritability is hard to transform into summary statistics. Therefore, general power calculation procedures cannot be used directly in GWA studies. The development of appropriate statistical methods and a user-friendly software package to address this problem would be welcomed.

Results

This paper presents GWAPower, a statistical software package of power calculation designed for GWA studies with quantitative traits, where genetic effect is defined as heritability. Based on several popular one-degree-of-freedom genetic models, this method avoids the need to specify the non-centrality parameter of the F-distribution under the alternative hypothesis. Therefore, it can use heritability information directly without approximation. In GWAPower, the power calculation can be easily adjusted for adding covariates and linkage disequilibrium information. An example is provided to illustrate GWAPower, followed by discussions.

Conclusions

GWAPower is a user-friendly free software package for calculating statistical power based on heritability in GWA studies with quantitative traits. The software is freely available at: http://dl.dropbox.com/u/10502931/GWAPower.zip webcite