Incorporating predicted functions of nonsynonymous variants into gene-based analysis of exome sequencing data: a comparative study

Table 1 Top ten genes ranked by SIFT-based VT test p-value

Gene	SIFT	PolyPhen-2	Binary	Unweighted	Number of SNPs	Number of nonsynonymous SNPs
FAM13A1	0.0002	0.0001	0.0007	0.0003	34	23
DGKZ	0.0002	0.0005	0.0002	0.0004	22	15
TRIM42	0.0003	0.0002	0.0009	0.0032	39	30
ADAM15	0.0003	0.0003	0.0016	0.0004	30	20
FLT1	0.0003	0.0007	0.0002	0.0002	35	20
GRIA4	0.0004	0.0003	0.0004	0.0066	18	6
IRF6	0.0005	0.0005	0.0021	0.0119	15	7
HDAC4	0.0007	0.0144	0.0011	0.0010	36	16
GDF15	0.0009	0.0006	0.0040	0.0006	10	6
SUSD2	0.0009	0.0008	0.0015	0.0005	45	29

All genes had tied rank 1 by the mixture model combining both SIFT-based and PolyPhen-2-based VT test p-values. P-values were obtained from 10,000 permutations.

ISSN: 1753-6561