OncoPanel Gene Sequencing

Targeted exome sequencing was performed for Patients 1, 2 and 4 on a panel of 300 genes (see Supplementary Methods) using a customized next-generation cancer sequencing platform, the OncoPanel, developed at Brigham and Women's Hospital Dana-Farber Cancer Institute, as described (25). Somatic DNA mutations, copy number variations, and gene rearrangements can be detected from formalin-fixed paraffin embedded tumor sections. DNA was isolated from tissue containing at least 20% tumor nuclei and analyzed by massively parallel sequencing using a solution-phase Agilent SureSelect hybrid capture kit and an Illumina HiSeq 2500 sequencer. Exonic sequences of 300 genes and sequences of 113 introns across 35 genes were included (see Supplementary Methods).