Assessing the impact of global versus local ancestry in association studies

BMC Proceedings

Table 2 p-Values for the three most significant SNPs located within the lactase gene, by varying ancestry adjustment methods

			p-Value local adjusted^b
Chr	SNP^a	p-Value unadjusted	All SNPs	Every other SNP	SNPs r² < 0.5	p-Value global adjusted	p-Value local^c and global adjusted
2	RS2322660	0.00008	0.99	0.80	0.31	0.25	0.81
2	RS2322659	0.00043	0.80	0.70	0.30	0.21	0.56
2	RS2015532	0.00411	0.81	0.91	0.47	0.35	0.83

^aSNPs: RS1042712, RS3769013, RS3769012, RS872151, RS2304371, RS4954445 were all significant at p < 0.05 in unadjusted models and adjustment for ancestry by any method resulted in all p > 0.35. SNP RS11884924 within the lactase gene was not significant p > 0.45 for all association tests.
^bLocal PCs are estimated for different combinations of SNPs: 1) all local SNPs (n = 2773); 2) every other SNP (n = 1386) or 3) SNPs with r² < 0.5 (n = 969).
^cLocal PC is estimated from all SNPs in a region.

ISSN: 1753-6561