PGA: power calculator for case-control genetic association analyses.
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.


CONCLUSIONS
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.
Menashe
Idan
I
Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Department of Health and Human Services, Rockville, MD, USA. menashei@mail.nih.gov
Rosenberg
Philip S
PS
Chen
Bingshu E
BE
D016022:Case-Control Studies; D019295:Computational Biology / Q000706:statistics & numerical data*; D003196:Computer Graphics; D020022:Genetic Predisposition to Disease; D020641:Polymorphism, Single Nucleotide; D014584:User-Computer Interface