Table 2.

Power for 250–1000 trios/subjects and 900,000 markers in a completely ascertained sample

N trios/	Effect			Equal weights	FBAT up-weighted		Wald up-weighted
pairs	Size	FBAT	Wald	Liptak(1:1)	Liptak(2:1)	Liptak(3:1)	Liptak(1:2)	Liptak(1:3)
250	1.25	0.004	0.008	0.009	0.013	0.014	0.007	0.005
	1.375	0.104	0.116	0.121	0.177	0.196	0.075	0.050
	1.5	0.446	0.462	0.470	0.586	0.623	0.304	0.217
	1.625	0.804	0.796	0.803	0.889	0.910	0.623	0.486
	1.75	0.957	0.949	0.949	0.983	0.991	0.850	0.734
500	1.25	0.128	0.128	0.147	0.208	0.227	0.086	0.054
	1.375	0.749	0.705	0.756	0.851	0.875	0.570	0.431
	1.5	0.990	0.974	0.984	0.997	0.998	0.935	0.859
	1.625	>0.999	>0.999	>0.999	>0.999	>0.999	0.997	0.984
	1.75	>0.999	>0.999	>0.999	>0.999	>0.999	>0.999	0.999
1000	1.25	0.776	0.696	0.773	0.869	0.891	0.594	0.450
	1.375	>0.999	0.997	0.999	1.000	>0.999	0.992	0.972
	1.5	>0.999	>0.999	>0.999	>0.999	>0.999	>0.999	>0.999
	1.625	>0.999	>0.999	>0.999	>0.999	>0.999	>0.999	>0.999
	1.75	>0.999	>0.999	>0.999	>0.999	>0.999	>0.999	>0.999

The number of trios reflects the number of trios included in either the FBAT or in the family-based component of the FBAT-Liptak tests. The number of subjects reflects the total number of subjects used (including both the offspring from the trios and unselected controls) used in the Wald or in the population-based component of the Wald-Liptak test. The standard FBAT test is denoted as “FBAT,” the population-based test is denoted as “Wald”, and our new integrated approach using both the population and family based information is denoted as “FBAT-Liptak. The numbers in parentheses, reflect the weighting of the FBAT component of the Liptak-CNV test relative to the Wald component of the Liptak-CNV, (e.g., (2:1) indicates that the FBAT component has twice the weight of the Wald component). The power reflects the proportion of replicates were the association p-value< 5.56×10⁻⁸.