Old lessons learned anew: family-based methods for detecting genes responsible for quantitative and qualitative traits in the Genetic Analysis Workshop 17 mini-exome sequence data

Table 2 Linkage and association analyses in all 200 replicates

Gene	Causal SV	MAF	β ^a	Merlin-VC	ROMP	ASSOC
Q1
FLT1	c13s431	0.0172	0.7414		1 (0.5%)	32 (16%)
FLT1	c13s523	0.0667	0.6500		7 (3.5%)	75 (37.5%)
FLT1	CSV^b					1 (0.5%)
KDR	c4s1878	0.1650	0.1357		18 (9%)	10 (5%)
KDR	c4s1884	0.0208	0.2956		2 (1%)
VEGFC	c4s4935	0.0007	1.3573	13 (6.5%)	200 (100%)	200 (100%)
VEGFA	c6s2981	0.0022	1.2065	50 (25%)	200 (100%)	200 (100%)
Q2
LPL	c8s442	0.01578	0.49459		11 (5.5%)	15 (7.5%)
SIRT1	c10s3109	0.00072	0.51421		4 (2%)
SREBF1	c17s1043	0.0043	0.49941		2 (1%)	4 (2%)
VLDLR	CSV^b				4 (2%)	1 (0.5%)
VNN1	c6s5380	0.17073	0.24437		4 (2%)	10 (5%)
VNN3	c6s5441	0.09828	0.27053		1 (0.5%)	3 (1.5%)

Number (%) of replicates are shown where the test achieved genome-wide significance. ASSOC and ROMP results are presented for collapsing definition 2 (MAF < 1% and nonsynonymous SV).
^a Effect size of SV on quantitative trait [1].
^b Multiple causal variants exist in this gene’s collapsed sequence variant.

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