Scatter plots of spouses for PC1 and PC2, by generational cohort.

<p><b>Scatter plots of spouse-pair male versus female:</b> Top left: Fig 4a, PC1 in the original cohort. Top right: Fig 4b, PC2 in the original cohort. Bottom left: Fig 4c, PC1 in the offspring cohort. Bottom right: Fig 4d, PC2 in the offspring cohort.</p

Probability density functions of spouse kinship estimates comparing results from GCTA (unadjusted for genetic ancestry) to those from PC-Relate (adjusted for genetic ancestry) in the FHS original cohort and offspring cohort.

<p>Probability density functions of spouse kinship estimates comparing results from GCTA (unadjusted for genetic ancestry) to those from PC-Relate (adjusted for genetic ancestry) in the FHS original cohort and offspring cohort.</p

Principal components analyses on FHS participants.

<p>Principal components analysis on FHS participants with: Top left: Fig 3a, FHS and HGDP participants projected. Top right: Fig 3b, original cohort participants projected. Bottom left: Fig 3c, offspring cohort participants projected. Bottom right: Fig 3d, third generation cohort participants projected.</p

Comparison of kinship estimates without ancestry adjustment (using GCTA) versus with ancestry adjustment (using PC-Relate).

<p>(a) Original cohort. Blue color represents Ashkenazi spouse pairs; red color represents Northwestern European spouse pairs; green color represents Southern European spouse pairs; black color represents spouse pairs of different ancestry. (b) Offspring cohort. Blue color represents Ashkenazi spouse pairs; red color represents Northwestern European spouse pairs; green color represents Southern European spouse pairs; black color represents spouse pairs of different ancestry.</p

Regression of Hardy–Weinberg disequilibrium parameter F on squared SNP PC Loadings.

<p>Regression of Hardy–Weinberg disequilibrium parameter F on squared SNP PC Loadings.</p

Flow diagram illustrating SNP selection for each analysis.

<p>Black box—SNPs used to characterize global genetic ancestry and identify continentally admixed and non-white individuals; SNPs used in GCTA analysis; SNPs used for regression analysis using F; SNPs used to calculate spousal genetic correlations. Blue box—SNPs used to characterize European/West Asian ancestry. Red box—SNPs used for regression analysis using D.</p

Regression analysis of linkage disequilibrium parameter, D on the product of the PC loadings for unlinked SNPs.

<p>Regression analysis of linkage disequilibrium parameter, D on the product of the PC loadings for unlinked SNPs.</p

Spouse Correlations in the FHS cohorts.

<p>Spouse Correlations in the FHS cohorts.</p

Additional file 2: Figure S2. of A longitudinal genome-wide association study of anti-tumor necrosis factor response among Japanese patients with rheumatoid arthritis

Regions showing moderate evidence of association (p < 1x10−5) with anti-TNF response (GEE models). (PDF 324 kb

Additional file 1: Figure S1. of A longitudinal genome-wide association study of anti-tumor necrosis factor response among Japanese patients with rheumatoid arthritis

Regional plots showing association results from GEE models at 6q15, 6q27 and 10q25.3, when the analyses were restricted to patients with moderate or severe disease activity at baseline (n = 413). (PDF 350 kb