Fig. 4: Somatic mutational landscape of 54 breast cancers enriched for HRD.

The 54 tumors that were whole genome sequenced are depicted in this figure. A Clinical and histological parameters for each tumor: HRD status per test, bi-allelic BRCA status (≥class 2 VUSes are included in this figure), estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), tumor morphology (ductal or lobular), histological grade and whether the tumor was a primary or metastatic tumor. B The relative contributions of different types of indels. Insertions: all insertions. Repeats: indels in repeat regions were defined as the presence of ≥1 copy of the indel sequence downstream (i.e., in the 3′ direction) from the breakpoint, where sequence length must be <50 basepairs. Microhomology: indels with flanking microhomology were defined as the presence of the following sequence features up or downstream from the breakpoint: (i) ≥1 copy of the indel sequence if the indel sequence length is ≥50 bp; (ii) ≥2 bp sequence identity to the indel sequence; or (iii) ≥1 bp sequence identity if the indel sequence length is ≥3 bp. For (ii) and (iii) the number of up or downstream bases searched was equal to the length of the indel. None: other deletions [10]. C The relative contributions of twelve substitution signatures [28]. D The relative contributions of six rearrangement signatures [28]. E Number of somatic single nucleotide variants (SNVs). F Number of somatic insertions and deletions (indels). G Number and type of somatic structural rearrangements.