Principal-component-based population structure adjustment in the North American Rheumatoid Arthritis Consortium data: impact of single-nucleotide polymorphism set and analysis method

Table 1 Summary of PCA with six SNP subsets

SNP Subset for PCA	No. SNPs	PCs significantly associated with RA (α = 0.05)	λ^a
S1. Filtered SNPs	459,422	1, 2, 3, 5, 6, 8, 9	1.023
S2. Removing the MHC region	457,776	1, 2, 3, 5	1.027
S3. Removing MHC and inversion on chr 8	456,846	1, 2, 3, 4	1.028
S4. Removing chr 6 and inversion on chr 8	427,806	1, 2, 3, 4	1.030
S5. Removing LD between SNPs with r² > 0.4	164,418	1, 2, 3, 4	1.022
S6. Removing LD between SNPs with r² > 0.2	81,240	1, 2, 3, 4, 5	1.023

^aInflation factor for genome-wide SNP association test statistics adjusting for PCs significantly associated with RA at (α = 0.05) as linear covariates

ISSN: 1753-6561