Copy number analyses via single nucleotide polymorphism microarray. Whole-genome SNP typing was performed using DNA from the patients indicated and the Illumina HumanHap 550 Bead Chip array. The figure shows SNPs from 3 patients on chromosome 16. For each patient, the top panel represents the intensity ratio, and the bottom panel represents the allele ratio. Intensity ratio is a measure of patient SNP log signal intensity compared with reference sample SNP intensity; 2 copies = intensity ratio of 0; 1 copy = intensity ratio of −1. Most values are centered around zero, indicating diploid copy number. Allele ratio is the ratio of the signal for one of 2 genotypes over the total signal. Homozygous SNPs localize to 0 or 1; heterozygous SNPs localize to 0.5. In Family A homozygote III-15, genotyping data in the 16q24.2-16qter candidate region demonstrate an extended block of homozygosity extending to the telomeric end of chromosome 16 (red bar). Note that the intensity ratio in this region is unchanged, indicating the homozygosity is not caused by a large deletion. The bottom panel shows, from top to bottom, (+) strand genes, cytogenetic bands, chromosome position, and (−) strand genes.