BMC Genetics (May 2008)

PGA: power calculator for case-control genetic association analyses

  • Chen Bingshu E,
  • Rosenberg Philip S,
  • Menashe Idan

DOI
https://doi.org/10.1186/1471-2156-9-36
Journal volume & issue
Vol. 9, no. 1
p. 36

Abstract

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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