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. 2007 Aug 28:8:58.
doi: 10.1186/1471-2156-8-58.

Power analysis for genome-wide association studies

Robert J Klein  1
Affiliations

Power analysis for genome-wide association studies

Robert J Klein. BMC Genet. .

Abstract

Background: Genome-wide association studies are a promising new tool for deciphering the genetics of complex diseases. To choose the proper sample size and genotyping platform for such studies, power calculations that take into account genetic model, tag SNP selection, and the population of interest are required.

Results: The power of genome-wide association studies can be computed using a set of tag SNPs and a large number of genotyped SNPs in a representative population, such as available through the HapMap project. As expected, power increases with increasing sample size and effect size. Power also depends on the tag SNPs selected. In some cases, more power is obtained by genotyping more individuals at fewer SNPs than fewer individuals at more SNPs.

Conclusion: Genome-wide association studies should be designed thoughtfully, with the choice of genotyping platform and sample size being determined from careful power calculations.

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Figures

Figure 1
Figure 1
Power for the test of genotypic association as a function of sample size at different genotype relative risks (GRR). All panels are for the CEU HapMap population when the number of cases equals the number of controls and a multiplicative model is used. (A) Power for the Affymetrix 100 K system. (B) Power for the Illumina 300 K system. (C) Power for the Affymetrix 500 K system. (D) Power for the Illumina 550 K system.
Figure 2
Figure 2
Power for genotypic and allelic tests. Data is shown for a GRR of 1.5 under a multiplicative model, the CEU HapMap population, and the specified genotyping system.
Figure 3
Figure 3
Coverage of tag SNPs. Fraction of non-tag SNPs in LD with a tag SNP with r2 above specified threshold for the ENCODE and non-ENCODE regions of the HapMap project for the CEU and YRI populations. Results are shown for the Illumina 550 K (A) and Affymetrix 500 K (B) chips. The JPT+CHB population was not included because the curves generally overlap with the CEU curves and would make the graph harder to read. Results for the JPT+CHB population and for the other chips are qualitatively similar to the curves shown here.
Figure 4
Figure 4
Total individuals required for 80% power. The computations assume the number of cases equals the number of controls and a GRR of 1.75. CEU, JPT+CHB, and YRI are the HapMap populations. Affy 250 K Nsp and Affy 250 K Sty represent the two chips that make up the Affymetrix 500 K genotyping system.
Figure 5
Figure 5
Power as a function of number of chips needed for the Affymetrix 500 K system and its two components. Calculations are done for a GRR of (A) 1.5 and (B) 2.0.
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