The WTCCC consortium provided a complete panel of imputed and directly genotyped allelic frequencies of individuals accessed by diseases of interest and control individuals. The hypertension and diabetes datasets were downloaded and organized locally http://www.wtccc.org.uk/. Initially, we determined the complete set of markers that were both genotyped and imputed in each dataset. A Perl script was developed to generate a meta-population for each marker respecting the observed and imputed allelic frequencies for selected cases and controls. This script can be obtained by author request. Data were exported and analyzed by the specialized R package SnpAssoc [14], which determined for each SNP its association statistic under dominant, recessive, codominant and log-addictive models of genetic inheritance. This procedure was conducted, independently, by two co-authors (MAAA and TVP) and results were concordant. The complete set of association statistics was collected and organized locally and is available upon request.
