Figure 3. Comparison of array CN calls to sequence-based calls in MCF-7.

a) a log₂ plot of copy number alterations found in the MCF-7 breast cancer cell line. Sequence based copy number calls made with the readDepth package (bottom) reveal the same gross morphology seen by an assay done with a 100 k SNP array (top) b) an absolute copy number plot of MCF-7 chromosome 20, showing high level amplifications and fine-scale copy number changes not detectible with array-based methods.