*3.1. Whole Genome Sequencing (WGS)*

DNA from tumour and matched blood underwent 2 × 150 bp sequencing on an Illumina HiSeq X Ten instrument (Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research) averaging over 80× and 40× coverage, respectively. Read adapters were trimmed using Illumina's Bcl2fastq Conversion software (Illumina) and filtered to remove low quality bases (<Q15), short reads (<70 bp) and missing read pairs using cutadapt v1.9 [103]. Remaining reads were aligned to GRCh38 reference using bwa-mem v0.7.15 [104], with the ALT-aware mode. Alignment statistics were calculated using QualiMap v2.1.3 [105] and stromal contamination was calculated using Sequenza [106]. Sequencing statistics are summarized in Table S2. The sequencing data for the tumor and blood samples are available in the NCBI BioSample database under the following range of accessions: SAMN14209964–SAMN14209992.
