Subject characteristics of the ESCC cases and controls.

<p>Subject characteristics of the ESCC cases and controls.</p

Association of PC1 from Paschou and GWAS PCAs on site and disease status.

<p>The intercept corresponds to the MAYO site.</p

Association of PCs 1, 3 and 4 from GWAS PCA to site.

<p>The intercept corresponds to the MAYO site.</p

Comparison of effect on the inflation factor λ of controlling for ancestry.

<p>The first 10 PCs obtained through Paschou PCA, GWAS control PCA, GWAS PCA and GWAS LD PCA are used as covariates in testing genome-wide association to ovarian cancer. Note that the Paschou panel was designed to capture only one significant PC.</p

Inflation factors in genomewide ovarian cancer association testing before (uncorrected) and after controlling for cumulative PCs from GWAS PCA, Paschou PCA, GWAS control PCA and GWAS LD PCA.

<p>Inflation factors in genomewide ovarian cancer association testing before (uncorrected) and after controlling for cumulative PCs from GWAS PCA, Paschou PCA, GWAS control PCA and GWAS LD PCA.</p

Comparison of Paschou and GWAS PCAs.

<p>Blue, green and red points represent individuals with the highest estimates of north-western, south-eastern and Ashkenazi Jewish ancestry respectively taken from MLE analysis with Price et al. AIMs panel.</p

Top hits for ovarian cancer association.

<p>Negative log p-values of top hits for ovarian cancer association after controlling for ancestry using first 4 PCs of GWAS control PCA compared to not controlling for ancestry (left panel) and controlling for ancestry using first 4 PCs of GWAS PCA (right panel).</p

Six-way Venn diagram showing polymorphic putative functional variants shared by reported ethnicities.

<p>Numbers of shared variants are shown at intersections. The total numbers of polymorphic variants by ethnicity are listed in the upper-left hand corner.</p

Manhattan plots for the endometrial cancer association analysis.

<p>Results of single variant analyses (−log₁₀p) are plotted against chromosome position (NCBI build 37) for association over all ethnicities (A) and for associations within Caucasians (B). Suggestive variants are labeled above. Results were adjusted for age at diagnosis, BMI, study site, plate, and the first four principal components.</p

Cases and Controls by Reported Ethnicity and Study.

<p>Cases and Controls by Reported Ethnicity and Study.</p