Genomic DNAs from flash-frozen tissue samples were extracted using the Gentra Puregene Tissue Kit (Qiagen) according to the manufacturer’s protocols. Deep-targeted exome sequencing of 263 genes (T200) was used to evaluate genomic alterations in 54 samples as described(14 (link)). Since matched normal tissue was not available, we used a common normal control sample to identify single nucleotide variants by MuTect and small insertions and deletions by Pindel (15 (link),16 (link)). To reduce false positives, outputs generated by MuTect and Pindel were filtered by the following approaches: (1) removal of novel mutations with VAF>0.4 and documented mutations from COSMIC with VAF>0.6, (2) removal of known SNP and exon variants as well as polymorphic genes with VAF<0.4, and (3) sequencing depth of at least 100 reads for documented mutations and 300 reads for novel mutations. The filtering criterion for VAF was chosen after manual curation of mutations selected with different VAF thresholds. Hits found across many samples were manually curated to reduce the rate of false positive mutations.