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Open Access Highly Accessed Software

PGA: power calculator for case-control genetic association analyses

Idan Menashe1*, Philip S Rosenberg1 and Bingshu E Chen12

Author Affiliations

1 Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Department of Health and Human Services, Rockville, MD, USA

2 Department of Mathematics and Statistics, Concordia University, Montréal, Québec, Canada

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BMC Genetics 2008, 9:36  doi:10.1186/1471-2156-9-36

Published: 13 May 2008

Abstract

Background

Statistical power calculations inform the design and interpretation of genetic association studies, but few programs are tailored to case-control studies of single nucleotide polymorphisms (SNPs) in unrelated subjects.

Results

We have developed the "Power for Genetic Association analyses" (PGA) package which comprises algorithms and graphical user interfaces for sample size and minimum detectable risk calculations using SNP or haplotype effects under different genetic models and study constrains. The software accounts for linkage disequilibrium and statistical multiple comparisons. The results are presented in graphs or tables and can be printed or exported in standard file formats.

Conclusion

PGA is user friendly software that can facilitate decision making for association studies of candidate genes, fine-mapping studies, and whole-genome scans. Stand-alone executable files and a Matlab toolbox are available for download at: http://dceg.cancer.gov/bb/tools/pga webcite