Assessing the impact of global versus local ancestry in association studies

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BMC Proc. 2009; 3(Suppl 7): S107.

Published online 2009 December 15.

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Table 1

Mean rank correlations between Wald test statistics after adjusting for 10 global PCs (global), 10 local PCs (local), or both global and local PCs (both)

Wald test Statistic^a

1	2	SNPs	Mean rank correlation (SD)^b	Minimum	Maximum
Global	Local	all SNPs	0.72 (0.04)	0.50	0.81
Global	Local	p < 0.05	0.60 (0.07)	0.35	0.72
Global	Both	all SNPs	0.82 (0.05)	0.58	0.92
Global	Both	p < 0.05	0.71 (0.09)	0.35	0.87
Local	Both	all SNPs	0.81(0.02)	0.75	0.88
Local	Both	p < 0.05	0.68 (0.05)	0.53	0.80

^aThe Wald test statistic is calculated as the β coefficient/standard error for the relationship between the test SNP and height, after adjusting for the PCs as indicated in the column.

^bThe rank correlation is calculated between the two Wald test statistics in each local region and then averaged using all SNPs in the dataset or only the SNPs with p < 0.05 for either the first or second Wald test statistics.

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