Mutational signatures of mutational context for paired samples pre- and post-neaodjuvant chemotherapy. Illustrated are the numbers of shared and unique single-nucleotide variants (SNVs) and their breakdown into 30 known signatures from COSMIC. Since inference of signatures de novo is complicated by the nonindependence and small numbers of samples, we do not attempt to do so but rather infer the breakdown using quadratic programming methods (see Methods). For each patient, three rectangles are presented showing SNVs called prechemotherapy only (left), shared SNV calls (center), and SNVs called post-chemotherapy only (right). The size of the rectangle indicates the number of SNVs, and the proportion of color denotes the breakdown into signatures, as indicated in the key. Only eight signatures that make sizeable contributions are individually identified.