title: Cetuximab and Nivolumab in Recurrent/Metastatic Head and Neck Cancer
design: Whole exome sequencing of DNA was performed at the Genomics Platform of the Broad 4 Institute of Harvard and MIT as previously described (1, 2). DNA was extracted using the 5 Qiagen AllPrep DNA/RNA Mini Kit from FFPE tumor specimens, cell-free DNA, and 6 matched normal whole blood. Libraries were generated from a single aliquot of 150–7 500 ng input DNA in 100 μl TE buffer. Libraries were prepared using the Kapa HyperPrep 8 kit and quantified using PicoGreen. Adapters were ligated using the TruSeq DNA exome 9 kit from Illumina per manufacturer instructions. Pooled libraries were sequenced using a 10 HiSeq2500 with 76 bp paired-end reads. The mean target coverages for tumor and 11 normal samples were 150x and 80x respectively.Raw reads were aligned to the hg19 reference using BWA-MEM through Picard and the 15 Genome Analysis Toolkit (GATK) developed by the Broad Institute.