WES and RNAseq of CALGB40601 subset
First-strand cDNA was synthesized from total RNA without mRNA purification or fragmentation, followed by strand-specific second-strand synthesis using dUTP incorporation. The cDNA was processed for Illumina paired-end sequencing with QC, adapter ligation, and enzymatic treatments, including Uracil-DNA Glycosylase digestion to preserve coding strand information. The 10 libraries were pooled, hybridized to the HGSC VCRome 2.1 (42Mb, NimbleGen) design with minor revisions. Seventy samples were sequenced in one lane of the NovaSeq 6000 S4 flow cell to generate paired end reads.