We focus on clusters of nominally-positive autosomal SNPs that lie within 100 or 25 kb of each other, depending on the density of markers available; the latter figure is closer to the average “haplotype block” length in the samples studied here [11, 12, 33, 34, 36, 37]. To use a valuable technical control that is possible with Affymetrix 500k reagents, we require that SNPs in each cluster come from both Sty I and Nsp I array types where possible [12]. In assessment of the data from each sample set, these criteria thus provide some assurance that haplotypes do occur at differing frequencies in disease vs controls. These criteria provide significant technical controls, based on requirements that multiple nearby SNPs must display positive results and that these positive results must come from two array types.
