Molecular profiling of head and neck squamous cell carcinomas
This study performed targeted DNA sequencing of key NF-_B signaling pathway regulatory genes in matched tumor and normal tissues from patients with HPV-associated head and neck squamous cell carcinoma (HNSCC). A custom Ion Torrent AmpliSeq panel was designed to interrogate ten genes whose products regulate NF-_B activity and are frequently altered in the NF-_B-active subtype of HPV+ HNSCC: TRAF3, CYLD, TRAF2, NFKBIA, TNFAIP3, TRAF6, BIRC2, BIRC3, MYD88, and MAP3K14. The panel comprised 250 overlapping amplicons in a 2-primer pool format, achieving 93.65% coverage across the 24.86 kb target region. Genomic DNA was isolated from formalin-fixed paraffin-embedded (FFPE) macro-dissected tumor and matched normal tissues at the UNC Lineberger Comprehensive Cancer Center Translational Genomics... (for more see dbGaP study page.)