Table 1.

Power for 500–2000 trios and 900,000 markers for a quantitative trait.

N	Effect			Equal weights	FBAT up-weighted		Wald up-weighted
trios	Size	FBAT	Wald	Liptak(1:1)	Liptak(2:1)	Liptak(3:1)	Liptak(1:2)	Liptak(1:3)
500	0.1	0.000	0.004	0.003	0.001	0.002	0.002	0.001
	0.125	0.000	0.026	0.016	0.013	0.012	0.011	0.009
	0.15	0.004	0.095	0.061	0.060	0.062	0.042	0.036
	0.175	0.024	0.259	0.176	0.182	0.183	0.133	0.108
	0.2	0.075	0.504	0.376	0.396	0.392	0.309	0.251
1000	0.1	0.008	0.058	0.041	0.054	0.049	0.033	0.024
	0.125	0.043	0.265	0.210	0.242	0.231	0.172	0.136
	0.15	0.172	0.637	0.547	0.587	0.577	0.467	0.402
	0.175	0.417	0.906	0.853	0.879	0.869	0.786	0.721
	0.2	0.712	0.987	0.972	0.983	0.980	0.948	0.917
2000	0.1	0.144	0.519	0.458	0.488	0.478	0.378	0.297
	0.125	0.511	0.922	0.891	0.907	0.895	0.823	0.753
	0.15	0.867	0.997	0.994	0.996	0.995	0.985	0.972
	0.175	0.987	>0.999	>0.999	>0.999	>0.999	>0.999	>0.999
	0.2	0.999	>0.999	>0.999	>0.999	>0.999	>0.999	>0.999

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.