Whole Genome Sequencing Protocol

Whole genome low-coverage short insert size library preparation was performed using the NEBNext Ultra DNA Library Prep Kit (New England Biolabs) and long-range (4422 bp insert size) mate-pair library preparation was done using the Nextera Mate Pair Sample Prep Kit (Illumina Inc.), both according to the manufacturer's protocol. Sequencing was performed on Illumina HiSeq instruments to an average 3x spanning coverage for short insert size paired-end and 38x spanning coverage for mate-pair, with the raw length of the reads displaying a median of 101bp. Structural variants larger than 5,000 bp were detected using the DELLY tool [40 (link)], as previously described [41 (link)]. DNA copy number analysis was performed using qDNAseq [42 (link)]. The sequencing data has been made available through the European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena; dataset ID: PRJEB9176.)