Rational genomic optimization of DNA detection for human papillomavirus type 16 in head and neck squamous cell carcinoma

Background We aimed to use genomic data for optimizing polymerase chain reaction (PCR) primer/probe sets for detection of human papillomavirus (HPV)‐16 in body fluids of patients with HPV‐related head and neck squamous cell carcinoma (HPV‐HNSCC). Methods We used genomic HPV‐HNSCC sequencing data from a single institutional and a TCGA cohort. Optimized primer/probe sets were designed and tested for analytical performance in CaSki HPV‐16 genome and confirmed in salivary rinse samples from patients with HPV‐HNSCC. Results The highest read density was observed between E5 and L2 regions. The E1 region contained a region that was universally present. Among candidate PCR primer/probe sets created, six reliably detected 30 HPV‐16 copy number. In a CLIA certified laboratory setting, the combination of two novel primer/probe with E7 sets improved performance in salivary rinse samples with a sensitivity of 96% and specificity of 100%. Conclusions PCR‐based detection of HPV‐16 DNA in HPV‐HNSCC can be improved using rational genomic design.