Principal components ancestry adjustment for Genetic Analysis Workshop 17 data

BMC Proceedings

Table 1 Distribution of minor allele frequencies of SNPs in the genes studied

Genes	SNPs	MAF < 0.005		0.005 < MAF < 0.01		0.01 < MAF < 0.05		0.05 < MAF < 0.5		Total
		Q1	Q2	Q1	Q2	Q1	Q2	Q1	Q2	Q1	Q2
Causal	Noncausal	60	100	5	9	12	15	9	15	86	139
	Causal	32	61	0	5	5	4	2	2	39	72
Noncausal	Noncausal	1,422	532	189	57	295	90	288	80	2,194	759

The Q1 causal genes are ARNT, ELAVL4, FLT1, FLT4, HIF1A, HIF3A, KDR, VEGFA, and VEGFC. The Q2 causal genes are BCHE, GCKR, INSIG1, LPL, PDGFD, PLAT, RARB, SIRT1, SREBF1, VLDLR, VNN1, VNN3, and VWF. The noncausal genes are all genes on chromosomes 12, 21, and 22 for Q1 and all genes on chromosomes 21 and 22 for Q2.

ISSN: 1753-6561