Tumor genomic DNA was purified from the same sample using the AllPrep DNA/RNA/miRNA kit (QIAGEN) with disruption on a Tissuelyser II (QIAGEN).  Custom target capture libraries were constructed from 100 ng to 1 µg of DNA from tumor and normal tissue after sample shearing, end repair, and phosphorylation and ligation to barcoded sequencing adaptors. Ligated DNA was size selected for lengths between 200 and 350 bp and subjected to hybrid capture using NimbleGen Oncoseq-v4 custom target capture baits (Roche).