Detection of loss-of-heterozygosity in prostate cancer samples using single-nucleotide polymorphism (SNP) arrays and dChipSNP. SNP allele calls are automatically compared between cancer and paired normal samples. Regions in which heterozygous alleles become homozygous in the cancer are shaded in blue, while regions that retain heterozygosity are shaded in yellow. A summary loss-of-heterozygosity (LOH) score is calculated within a 6 Mb sliding window and is indicated as the blue curve on the right. The dark blue and yellow represent observed values while lighter ones are inferred using a nearest neighbor scheme. The P = 0.05 threshold for significance derived from permuted datasets is shown as a red line. SNP markers are shown along the right, while the ideogram and representative genes are shown on the left (as indicated). A statistically significant region of LOH in the 10q23 locus was detected by this analysis and is demarcated by dChipSNP by dashed black rectangle. The 5 prostate cancers (out of 50) harboring LOH in this region are shown in the left window. For details, see the article by Lieberfarb et al. on p. 4781 of this issue.