Evans et al considered prediction for the seven diseases of the WTCCC [19]. Approximately 2000 cases were available for each disease, with a common set of 1480 controls, and a marker panel of all SNPs on the Affymetrix 500K chip after quality control and exclusion of previously known loci. As this is the same chip used in the ISC study, it is assumed here that the panel is equivalent to 74062 independent SNPs. Logistic regression and allele score estimators were both used to construct scores, and a series of P-value thresholds from 10−5 to 0.8 were considered.
