Table 2.

The power for single-variant association analysis. We compared the power of single allelic analysis and joint multi-allelic analysis for detecting associations with each alternative allele. The power was evaluated under the threshold of $\alpha =5\times {10}^{-8}$, adjusting for the increased multiple testing burden for analyzing multiple alleles.

Sample Size	Genetic Effects	Single Allelic Analysis	Multi-Allelic Analysis
Type I Error/Power for the Analysis of the Primary (i.e., more frequent) Alt Alleles
10,000	0	4.7 × 10−8	4.2 × 10−8
	0.1	0.24	0.25
	0.25	0.57	0.57
	0.5	0.75	0.76
20,000	0	4.6 × 10−8	4.2 × 10−8
	0.1	0.36	0.37
	0.25	0.67	0.68
	0.5	0.82	0.82
Type I Error/Power for the Analysis of Secondary (i.e., less frequency) Alt Alleles
10,000	0	4.1 × 10−8	4.8 × 10−8
	0.1	0.037	0.056
	0.25	0.24	0.3
	0.5	0.48	0.55
20,000	0	4.9 × 10−8	4.3 × 10−8
	0.1	0.087	0.12
	0.25	0.36	0.43
	0.5	0.6	0.66