Comparison of exemplary lesions detected by genomewide SNP-A 6.0. (A) Whole-genome view shows the complete diploid set of human chromosomes. A close-up view of chromosome 21 shows the presence of a deletion on its long arm, illustrated by a decrease in the copy number line (blue line and red dots) and LOH (paucity of green bars, indicating the frequency of heterozygous loci [red box]). A closer look at the region shows loci potentially involved in disease pathogenesis. (B) Illustration of the 3 exemplary characteristic lesions seen by 6.0 SNP-A: deletion, duplication, and aCN-LOH. For deletions, LOH as indicated by contraction of the AA and BB alleles (blue lines) and reduction of the copy number (top) marks the affected region. For duplications, the doubling of the heterozygous AB allele and an increase in copy number delineate the abnormality. For aCN-LOH, the loss of the AB allele without contraction of the AA and BB alleles and a normal copy number identify the lesion. In each example, the normal copy number and allele calls for CD3⁺ cells (green lines) shows the absence of a germline abnormality, thus confirming the somatic nature of the lesions. (C) An exemplary microdeletion in chromosome 7, seen as a drop in the diploid copy number line (blue line in red box) and the absence of this abnormality in the CD3⁺ lymphocytes, is shown.