Enriching rare variants using family-specific linkage information

BMC Proceedings

Table 2 Results of selecting one family using the family-specific LOD score for Q1 and Q2

Gene	LOD	LOD_max	Expected	Observed	p-value
Q1
ARNT	0.07	0.09	0.375	0.390	0.33
ELAVL4*	0.09	0.10	0.125	0.070	0.99
FLT1	0.12	0.18	0.625	0.850	2.47 × 10⁻¹¹
FLT4	0.24	0.24	0	0	NA
HIF1A*	0.03	0.04	0.125	0.090	0.93
HIF3A*	0.65	0.75	0.125	0.010	1.00
KDR	0.71	0.76	0.75	0.965	1.09 × 10⁻¹²
VEGFA*	3.32	2.40	0.375	1.000	<10⁻¹²
VEGFC*	3.87	4.44	0.125	1.000	<10⁻¹²
Q2
BCHE	0.12	0.13	0.5	0.555	0.06
GCKR*	0.08	0.09	0.125	0.100	0.86
INSIG1	0.09	0.11	0	0	NA
LPL	0.16	0.15	0.875	0.925	0.02
PDGFD*	0.12	0.12	0.125	0.205	3.12 × 10⁻⁴
PLAT	0.23	0.20	0.375	0.395	0.28
RARB	0.09	0.11	0	0	NA
SIRT1	0.15	0.15	0.375	0.485	6.56 × 10⁻⁴
SREBF1	0.28	0.27	0.75	0.875	2.23 × 10⁻⁵
VLDLR	0.12	0.13	0.375	0.480	1.08 × 10⁻³
VNN1	0.28	0.23	0.875	0.785	1.00
VNN3	0.28	0.23	0.75	0.795	0.07
VWF	0.09	0.10	0.125	0.105	0.80

Asterisks indicate a single nonmonomorphic causal variant in the gene. LOD is the average LOD score of linkage analysis in 200 replications. LOD_max is the average maximum family-specific LOD score in 200 replications. “Expected” is the chance of selecting a family carrying rare alleles from random selection; “Observed” is the frequency of selecting a family carrying rare alleles by selecting the family with the LOD_max score.

ISSN: 1753-6561