Challenges and directions: an analysis of Genetic Analysis Workshop 17 data by collapsing rare variants within family data

Table 2 Comparison of family data with collapsing and family data without collapsing

Chromosome	Gene	Number of synonymous SNPs	Number of nonsynonymous SNPs	Total number of SNPs	Number of risk SNPs	Collapsing		Noncollapsing, power (%)
						Power (All) (%)^a	Power (nonsynonymous) (%)^b
6	VEGFA	2	2	4	1	100.0	100.0	100.0
4	VEGFC	0	1	1	1	100.0	100.0	100.0
10	SIRT1	9	14	23	9	19.0	47	99
9	VLDLR	8	15	23	8	10.0	3.50	58.50
17	SREBF1	5	16	21	10	18.5	36	22.50
1	PIK3R3	3	2	5	1	11.0	1	0
8	PLAT	14	11	25	8	8.0	34	0
5	FLT4	3	5	8	2	6.0	12.50	0

Power is calculated based on the threshold P < 0.05. Because of limited space, only those genes whose power is greater than 10% are shown.
^a All rare SNPs were collapsed.
^b Only nonsynonymous rare SNPs were collapsed.

ISSN: 1753-6561