DNA was prepared from blood [13], [55], [56]. Genotyping and primary assessments of genotyping were performed by investigators blinded to clinical diagnoses. DNAs from groups of 20 individuals of the same ethnicity and phenotype were carefully quantitated and combined. This number of individuals/pool was selected since we have extensively validated use of pools of this size [13]–[17], [37], [38] with respect to statistical power as well as the advantages and disadvantages of pooling noted above. Hybridization probes were prepared as described (Affymetrix assay 6.0, [15]). For each pool 150 ng of pooled DNA was processed, labeled and hybridized to Affymetrix 6.0 arrays according to the instructions of the manufacturer (Affymetrix, Santa Clara CA) and [13]–[15]. Quality controls for assays were performed as recommended (Affymetrix, Santa Clara CA) and (Fig. S2). Features of this portion of methods are depicted in Fig. S1.
