Whole Genome Sequencing of Tumour and Normal Samples

The germline and tumour DNA were tested using Illumina Infinium arrays (Illumina, San Diego, CA, USA) according to manufacturer’s instructions. DNA from tumour and matched normal underwent whole-genome paired-end sequencing using an Illumina X-Ten. Sequence reads were trimmed using Cutadapt (version 1.11)²⁸ and aligned to GRCh37 using BWA-MEM (version 0.7.12)²⁹ . Duplicate alignments were marked with Picard (version 1.129, http://picard.sourceforge.net) and BAM files were coordinated-sorted using Samtools (version 1.3)^{30 (link)}. Mean coverage was determined using samtools and the following command: samtools depth -a bam_file | awk ‘{sum + =$3} END { print “Average = “,sum/NR}’ > output_coverage. Tumours were sequenced to an average read depth of ~70 × (range of 55X–104X) and normal to ~36 × (range of 28X–44X). The WGS data have been deposited in the European Genome-phenome Archive (EGA) repository under the accession code EGAS0000100330³¹ .