Patient and patient-derived xenograft samples used in this study were described previously [13 (link),21 (link),22 (link)]. Site specific DNA methylation analyses of the YAP1 locus were performed as described previously [21 (link),23 (link)]. In brief, DNA samples were digested with AluI and HhaI (New England Biolabs, Ipswich, MA, USA) and methylated DNA fragments were enriched using recombinant MBD2-MBD (Clontech, Mountain View, CA, USA) immobilized on magnetic Talon beads (Clontech). Precipitated DNA containing methylated DNA fragments were eluted and subjected to quantitative real-time PCR using the IQ SYBR Green Supermix (BioRad, Hercules, CA, USA) using YAP1-F: GGACTCGGAGACCGACCT and YAP1-R: GTCTTGGGGTTCATGACG primers. Male white blood cell (WBC) genomic DNA was treated in vitro with M.SssI (New England Biolabs) to obtain a fully methylated positive control. Untreated male WBC DNA served as a negative control. For quantitative assessment of locus specific methylation levels, Ct-values of the samples of interest were normalized to Ct-values of the positive control (SssI) and calculated methylation indices (ranging from 0.0 to 1.0) were used to derive methylation heatmaps.