title: DNA whole exome sequencing of human: melanoma: Sample 331A
design: 250-500ng of extracted DNA, using Qiagen AllPrep DNA/RNA Mini Kit (cat# 80204), was used as input for library preparation. Sample were barcoded using unique 8 base molecular barcodes followed by a library enrichment process, and all libraries above 40ng/µl were considered acceptable for solution-phase hybrid selection and sequencing. Libraries preparation was carried out using the SureSelect Target Enrichment System Sequencing Platform Library Prep v2 (Agilent Technologies, G3360-90000), according to manufacturer's specifications, followed by quantification and normalization using PicoGreen to ensure equal concentration. Libraries were then quantified using qPCR (KAPA Biosystems, KK4832), denturated with 0.2M NaOH and diluted to 20pM using hybridization buffer (Illumina). Cluster amplification was performed according to the manufacturer's protocol (Illumina), HiSeq 2500 v4 cluster chemistry and flowcells, as well as Illumina's Multiplexing Sequencing Primer Kit. Libraries were sequenced using the HiSeq 2500 v4 Sequencing-by-Synthesis method (paired end 76bp reads) followed by analysis with RTA v.1.12.4.2. The minimum depth of coverage was 150X and 80X for tumor and normal samples respectively. All procedures were done at the Genomics Platform of the Broad Institute of Harvard and MIT.