Genomic Profiling and Protein Network Analysis

Genomic DNA was extracted as previously described and Illumina sequencing libraries were made with the NEB Ultra II FS kit^{31 (link)}. Libraries were sequenced on an Illumina NextSeq 500 with paired end 2 x 36 bp read chemistry, generating ~16 million reads per sample. Single nucleotide variant analysis, ploidy levels and chromosome coverage maps were generated as previously described^{31 (link)}. To construct the String interaction network, we filtered out genes with synonymous mutations and used the remaining list of mutant genes as input queries. The interaction network was constructed using functional and physical protein associations and the resulting network was clustered by MCL clustering with the inflation parameter set to 2. Breakpoint analysis of coverage data was done by thorough inspection in IGV genome browser.