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. 2012 Mar;22(3):568–576. doi: 10.1101/gr.129684.111

Figure 2.

Figure 2.

Detection of large-scale and focal copy number alterations by sequencing- and array-based approaches. (A) Deletions and focal amplifications of chromosome 4 in sample TCGA-24-1103. Copy number estimates from array (gray), WGS (light blue), and exome (dark blue) indicate two regions of deletion as well as a focal amplification (window). Red lines indicate segmented exome CBS calls. (Below) Variant allele frequencies in the normal (blue) and tumor (green) indicate regions of loss of heterozygosity (LOH) in deleted segments. (B) Intersection of large-scale copy number alterations detected by SNP array, whole-genome sequencing, and exome sequencing approaches for five HGS-OVCa cases. For details, see Supplemental Table 3. (C) Intersection of gene-level (focal) copy number alterations detected by SNP array, whole-genome sequencing, and exome sequencing approaches for five HGS-OVCa cases.