title: BGB006246 Pre-treatment tumor WES
design: Genomic DNA concentration was determined via a PicoGreen assay that is based on use of Quant-iT‚Ñ¢ PicoGreen¬Æ dsDNA reagent. The DNA sample (250-500 ug) was fragmented by sonication on the Covaris E-220 instrument. The paired-end pre-capture library preparation was performed on the Beckman Biomek FXp liquid handler. This process includes DNA end repair, 3‚Äô-adenylation of fragments, ligation to Illumina-specified ‚Äòmultiplexing PE adapters‚Äô, pre-capture ligation-mediated PCR (LM-PCR) utilizing Kapa High-Fidelity DNA polymerase. All processes are automated and include multiple SPRI-bead purification steps after each enzyme reaction. For exome sequencing, a set of ~96 unique dual indexed barcoded adaptors (Illumina cat # 20022370) was used to multiplex samples for capture hybridization and sequencing. Illumina NovaSeq 6000 instrumentation with S4 flowcell Xp worflow was utilized to generate WES 150 bp paired-end reads for samples in a format of multiplexed dual indexed pools. The libraries were loaded at an average concentration of 250-280 pM.  Real-time analysis (RTA) software (RTA v3.3.3) was used to monitor run performance, assessing cluster density, signal intensity and phasing/pre-phasing data.
library_name: BGB006246_Pre_tumor_dna
identifiers.namespace: NCI-phs004049
identifiers.id: BGB006246_Pre_tumor_dna