Patient 23
Genomic DNA was automatically extracted from FFPE tumors using Maxwell RSC DNA FFPE Kit (Promega Maxwell RSC). DNA quantification was performed with a Qubit dsDNA broad-range assay kit and the Qubit 4.0 fluorometer (Life Technologies, Carlsbad, CA). Extracted DNA (250 ng) was sheared in the Covaris E220 Focused ultrasonicator (Covaris, LLC) to a fragment size of 250 bp. Fragmented DNA was processed for library preparation using a custom hybridization-based capture panel (VHIO-iCCA, panel size: 458,253 bp) performed with Agilent SureSelectXT Low Input Target Enrichment System (Agilent Technologies, Inc) following the manufacturers instructions