Whole Exome Sequencing of Adrenocortical Carcinoma

Fresh frozen samples were checked and selected with H&E stainings for high tumor cellularity. For DNA from fresh-frozen samples, library preparation was performed according to Agilent’s “SureSelectXT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library” kit, whereas for DNA from FFPE tissue the “SureSelect Automated Library Prep and Capture System SureSelectXT Automated Target Enrichment for Illumina Paired-End Multiplexed Sequencing” kit was used. Samples were run paired-end (125 bp) on a HiSeq 2000 v4. Alignment of data were processed by the following parameters: reference genome: hs37d5, alignment program: bwa-0.7.8 mem, alignment parameter: -T 0, duplication marking program: picard-1.125, default duplication marking program parameters were used (https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates). Alterations that are likely to be benign, so called FLAGS^{66 (link)} were excluded. Previously published WES studies of ACC^{13 (link), 14 (link)} were utilized as a comparison to the here generated WES results. MutSigCV was used to calculate significantly recurrent mutations^{67 (link)}.