Figure 1.

Illustration of SNP array analysis by example of matched neuroblastoma samples using the dChip software [25,26]. Normal (N) and tumor (T) DNA of five selected patients were hybridized to 10K Affymetrix SNP arrays (data kindly provided by R George [22]). (a) Copy numbers are shown as shades of red. Sample 1, 2 and 3 show a copy-number loss on 11q, whereas samples 4 and 5 are normal. (b) The inferred comparison of the genotype (loss of heterozygosity (LOH) analysis) results in a single lane per case, in which regions of LOH are depicted in blue and heterozygous regions are in yellow. Besides classical LOH with copy-number loss (11q region of samples 1-3), a region of UPD, identified by copy-neutral LOH, is identified in sample 3 on 11p. (c) The actual genotype calls for the UPD region and part of the adjacent region of sample 3 are shown in expanded form. The region of UPD shows only red (A) or blue (B) SNP calls, whereas other regions have the expected numbers of retained heterozygous alleles resulting in an AB call (yellow).