All called 16p11.2 deletions were validated by direct analysis of LRR. Data for each probe were normalised by first subtracting the median value across all samples (so that the distribution of LRR for each probes was centred on zero), and then dividing by the variance across all samples (to correct for variation in the sensitivity of different probes to copy number variation). The normalised data were then smoothed by application of a 9-point moving average and visualised graphically (see Supplementary Figure S6); putative deletions were checked by subsequent manual confirmation of loss-of-heterozygosity across the entire region. Equally, all deletions called by this method were confirmed by cnvHap.
