Marker genotype quality control was performed in the control sample by using the exact test of deviation from the Hardy-Weinberg (DHW) proportions as implemented in the R package Genetics Base v1.6.0 (http://rgenetics.org/). This test estimates allelic correlations occurring at the locus level which may be caused by genotyping errors. The DHW test is not powerful enough to detect deviations caused by small error rates but can be used to detect gross genotyping errors which can cause large DHW. For this reason, a conservative p-value of 0.05/1114 = 0.000045 was used as a cut-off for declaring significant departures from HW proportions.
