WES and RNAseq of CALGB40601 subset
The barcoded libraries were constructed with the HGSC custom protocol using the NEBNext End Repair Module ( Cat E6050L) 3'-adenylation of fragments NEBNext dA-Tailing Module (Cat E6053L), and ligation of the Illumina dual indexed barcoded adaptors (Illumina Cat#20022370), LM-PCR for 6 cycles using KAPA HiFi DNA Polymerase (Kapa Biosystems, Inc., Cat # KK2612). The 10 libraries were pooled for hybridization to the HGSC VCRome 2.1 design (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.