Figure 5

Analysis of chromosome 8 in sample PD4115a. (A) Virtual SNP array data from this sample show few distinct clusters (compared with the 188× sample in Figure 3A), with amplification of chromosome 8 (green) being the most prominent. (B) Read depth ratios for chromosome 8 organized by genomic coordinate. (C) Histograms of read depth ratios for chromosome 8 corrected for 24% normal admixture, indicating regions of copy numbers 2, 3 and 4 (cyan, orange and pink), with the latter two being clonal amplifications. (D) Variant allele frequencies for chromosome 8. The region with copy number 4 (pink) has variant allele frequencies clustered around 0.5, suggesting duplication of both chromosomal homologs, while the telomeric region with copy number 2 (cyan) has a loss of heterozygosity, suggesting a copy neutral LOH event. LOH: loss of heterozygosity