Somatic rearrangements. (A) Heatmap representing the average logR ratio of tumor/germline coverage depth observed on all amplicons of a given gene (rows) in the sequenced samples (columns). Red, gains; blue, losses. Black frames indicate significant changes (P <5.6 × 10–6). (B) The logR ratios of tumor/germline coverage depth of the Her2 gene correlate with the results of immunohistochemistry. (C), (D) Scatterplot representing the allelic fraction of the germline variants in the germline DNA (x axis) and tumor DNA (y-axis) for tumors showing a low (C) or high (D) level of chromosomal instability. The standard deviation of heterozygotes (SDH) score, calculated from the standard deviation of the allelic fraction of heterozygous single nucleotide polymorphisms in the tumor, is indicated. (E) Distribution of SDH scores in the sequenced cohort as a function of histological grade (x axis). Invasive lobular carcinoma (ILC; red) and invasive ductal carcinoma (IDC) showing lobular features (orange) are indicated. (F) Cumulative fraction of tumors with high SDH score (y axis), at increasing tumor cellularity (x axis). IHC, immunohistochemistry.