After clustering of genotyping data using the internal Illumina BeadStudio cluster files, values for logR ratio (LRR) and B allele frequency (BAF) were exported from each project and normalised: Effects of %GC content on LRR were removed by regressing on GC and GC2, while wave effects31 were removed by fitting a loess function. Normalised data for probes within 2.5Mb of the 16p11.2 deletion were analysed using cnvHap, and CNV calls intersecting the single-copy sequences within the deletion (chr16:29514353-30107356, build hg18) were extracted. 16p11.2 deletions were identified by a minimum 90% of probes within the deleted region being called as having reduced copy number.
