DNAseq of OPSCC tumors
DNA that passed our quality control standards was submitted to the University of Michigan Advanced Genomics Core for targeted capture sequencing using the DNA ThruPLEX kit (Takara Biosciences). Using a custom designed probe panel from Nextera, targeted capture was performed with high density probes covering the HPV16 genome and coding exons of 226 genes. Following library preparation and capture, samples were sequenced on an Illumina HiSEQ4000 with paired end 150nt reads