Allele-specific copy number analysis of a breast-cancer primary tumor and metastasis. (A,B) Patchwork analysis of (A) chromosome 16 of a breast-cancer primary tumor, and (B) of the same chromosome of a patient-matched metastasis. Top panels: Patchwork plot for genomic segments; middle panels: total and minor copy number for chromosome 16; bottom panel: normalized coverage for chromosome 16. With a few short deviations, the entire chromosome 16 displays heterozygous copy number 3 in the primary tumor sample. The copy number profile is nearly identical for the metastasis sample, except that most of the q-arm has yet another copy of the amplified chromosome.