PDX-LX104 xenograft sample library
Snap frozen EBUS and PDX samples were used to generate purified DNA using the Qiagen DNeasy kit (#69504) with the Qiagen RNAse A treatment option (#19101) according to the manufacturer’s instructions. DNA was assayed and quality controlled using the Qubit 2.0  Fluorometer (Invitrogen #Q32866) according to the manufacturer’s instructions.  Targeted re-sequencing was performed using the Ion AmpliSeq ™ comprehensive cancer panel v2 (Life Technologies # 4477685), which targets exons of 409 tumor suppressor genes and oncogenes (Supplementary data sheet 1). Library construction was performed using the Ion AmpliSeq™ Library Kit 2.0 (Life Technologies, # 4478379) and library templates were prepared and barcoded for sequencing using the Ion OneTouch™ System as per manufacturer’s instructions. Four barcoded samples were multiplexed per Ion 316™ chip (Life Technologies, # 4466616) and sequenced on the Ion Proton Personal Genome Machine (PGM™) sequencer (Life Technologies, Foster City, CA)