The Framingham Heart Study 100K SNP genome-wide association study resource: overview of 17 phenotype working group reports

Table 4 Power of the population-based association approach (GEE test) for a SNP with MAF = 0.1

			Nominal Type I Error
SNP QTL Heritability	Effect Size (SD)*	Model	0.05	0.01	0.001	10^-4	10^-5	10^-6	10^-7	10^-8
100% phenotype available (n = 1345)
1%	0.24	GEE	0.977	0.919	0.78	0.60	0.43	0.27	0.17	0.10
2%	0.33	GEE	1	1.00	0.99	0.97	0.91	0.84	0.72	0.59
3%	0.41	GEE	1	1	1	0.998	0.992	0.985	0.957	0.918
4%	0.47	GEE	1	1	1	1	1	1	0.996	0.991
5%	0.53	GEE	1	1	1	1	1	1	1	1
~80% subjects have phenotype(~20% missing at random): Sample size = 1076
1%	0.24	GEE	0.934	0.836	0.631	0.427	0.261	0.149	0.074	0.041
2%	0.33	GEE	1.00	0.99	0.97	0.93	0.82	0.66	0.51	0.37
3%	0.41	GEE	1	1	0.998	0.993	0.976	0.938	0.85	0.753
4%	0.47	GEE	0.998	0.998	0.998	0.998	0.991	0.984	0.971	0.949
5%	0.53	GEE	1	1	1	1	1	1	1	0.99
~60% subjects have phenotype(~40% missing at random): Sample size = 783
1%	0.24	GEE	0.879	0.737	0.48	0.281	0.137	0.055	0.023	0.008
2%	0.33	GEE	0.992	0.96	0.88	0.744	0.591	0.433	0.293	0.186
3%	0.41	GEE	1	1	0.982	0.945	0.874	0.754	0.602	0.467
4%	0.47	GEE	1	1	1	0.998	0.981	0.95	0.884	0.797
5%	0.53	GEE	1	1	0.999	0.997	0.996	0.982	0.964	0.931

*SD: Standard Deviation. The effect size is expressed in unit of standard deviation of the phenotype.

ISSN: 1471-2350