library_construction_protocol: Archival tissue specimens from the University of Pittsburgh tumor samples were processed via fixation in 10% neutral buffered formalin, dehydrated in ethanol and embedded with paraffin wax (FFPE). H&E slides were prepared, and areas with high tumor density (>75% tumor cells) were marked for extraction. Two-mm punch biopsies were taken from the FFPE tumor dense regions for downstream tumor RNA extraction. FFPE tissue was de-paraffinized with xylenes, washed in consecutive ethanol rinses (100% and 70%), and heated to remove formalin cross-linking. Tumor RNA was extracted using the Quick-RNA FFPE Miniprep extraction kit (Zymo Research, Irvine, CA). University of Pittsburgh sample libraries were manually prepared via standard protocols using the Illumina TruSeq RNA Exome Library Prep Kit (Illumina, San Diego, CA)