The WTCCC data-set comprised 469 557 single nucleotide polymorphisms (SNPs) distributed across the genome. For the current analysis we selected autosomal SNPs for analysis that had a minor allele frequency of at least 5% in our total sample and met stringent levels of genotyping quality. The large number of genotypes scored in a study such as this requires the use of generic approaches to quality control, allowing SNPs to be excluded where the quality of genotyping is in question. We used the following quality filter for inclusion of SNPs:
