Details of the sequencing of BriTROC-1 samples are given elsewhere (10 (link)). For new samples, DNA was extracted from 10 × 10 μm sections using QIAmp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer's protocol. 50 to 200 ng was sheared with a Covaris LE220 focused-ultrasonicator (Covaris) to produce 100 to 200bp fragments. Libraries were generated using SureSelect XT standard protocol (Agilent Technologies) for low-input and FFPE samples. Analysis of PTEN, KRAS, RB1, BRCA2, RAD51B, FANCM, PALB2, RAD51D, TP53, RAD51C, BRIP1, CDK12, NF1, BRCA1, BARD1, and PIK3CA was performed using a custom Ampliseq panel on a HiSeq4000 system (Illumina), using paired-end 125 bp protocols. The mean coverage was >7,000×. Nine samples were used as a panel of normal controls, five of them adjacent normal tissue and four samples whole blood. sWGS was performed on a HiSeq4000 system (Illumina), using paired-end 150 bp protocols, with 250 to 300 ng input DNA according to the manufacturer's instructions. The minimum number of reads per sample was set at 5 to 10 million (mean coverage of 0.1×). Using our previous calculations (https://gmacintyre.shinyapps.io/sWGS_power/), 10 million reads with a bin size of 30kb had 80% power (a = 0.01) to detect CN change ± 2 at 30% purity assuming ploidy of 2.