The allelic and genotypic association of SNPs with CA was determined using the Chi-square test in the software package PLINK v1.07 [23]. For each SNP, deviation from Hardy–Weinberg was assessed in the total population and also in cases and controls individually. A sex specific analysis in cases and controls was done separately using Chi-squared tests for allelic and genotypic association. The program QVALUE 1.0 was used [25–27] to correct for multiple testing on all reported p-values. This includes allelic and genotypic p-values for the total population, males and females separately across both ethnicities (experiment-wise correction). A q-value <0.05 was considered statistically significant.
