Exome Capture of Tumor and Blood Samples

DNA from both tumor and peripheral blood samples were used in the exome capture protocol as previously described.^{34 (link)} Briefly, 200 ng DNA was fragmented on a Covaris E-Series using the settings suggested in the Sureselect^XT Target Enrichment System for Illumina Paired-End Sequencing Library protocol (version 1.5). DNA was end-repaired, A-tailed and adaptors ligated using the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Hitchin, UK). Adaptor-ligated DNA was amplified using the NEBNext High-fidelity PCR master mix (New England Biolabs) using 7 PCR cycles and 750 ng DNA hybridized against RNA baits overnight (SureSelect Human All Exon V5, Agilent Technologies). The RNA baits were designed against the human exome with the addition of custom baits that tiled the IGH, IGK, IGL and MYC loci in order to detect the major translocations in myeloma. After hybridisation the captured DNA was indexed and amplified using Herculase II fusion DNA polymerase (Agilent Technologies) for 8 PCR cycles. Four exome samples were pooled and run on one lane of a HiSeq 2000 (Illumina, Hinxton, UK) using 76-bp paired end reads.