Analysis approach and type of lesions detected by SNP-A. (A) Normal male (left portion) and abnormal female karyotype with multiple lesions, including del(5q) (right portion). Whole genome scan is shown (top panel); each color represents copy number of a different chromosome (chromosome Y is not included on the array). Chromosome 5 is presented (middle panel) for both patients. Red dots depict single SNP signal intensity, while blue lines present an average value of SNP signal intensity. Green vertical bars represent heterozygous SNP loci, while blue bars show areas of LOH. In comparison to the normal chromosome 5 (left portion), the deletion 5q can be easily observed as a reduction in copy number and area of homozygous SNP loci (right portion). Idiogram of chromosome X is shown (bottom panel) demonstrating the haploid copy number with homozygous SNP loci (male DNA, left portion) and diploid DNA copy number with characteristic distribution of heterozygous SNP loci (female DNA, right portion). MC-detected chromosomal abnormalities (karyograms included) confirmed by SNP-A (B). (C) SNP-A–detected microdeletion of chromosome 21 and microduplication of chromosome 3. Copy number confirmation using Taq-Man Real-Time PCR shown as blue bars and compared with normal T cells (CD3+) obtained from the same patient. Microsatellite ID marker is displayed above the bars. Y axis (2^−ΔΔCt) presents the relative quantification scale, where 1 equals diploid DNA copy number. Examples of deleted and duplicated genes are included. Error bars represent SD.