SNP microarray analysis of samples from a single DS patient at two stages of disease, the TMD and the AMKL stage. SNP microarray analysis of AMKL4 (A) in comparison with TMD4 (B) for chromosome 5, with relative chromosomal position indicated by the ideogram (C). For each DNA, an allele difference plot (similar to B-allele frequency) is plotted in log2 scale for all SNP genotypes (top row), and a log2-ratio for the probe intensity of all probes (lower row). Red boxes indicate regions of SCNAs that are detected by differences in allele distribution and simultaneous loss of probe intensity, ie, lower log2-ratio. Here 2 deletions are detected on chromosome 5 (chr5:1.4-3.8Mbp and chr5:85.4-122.1Mbp).