- Saito, Yuki;
- Favorov, Alexander V;
- Forman, Michael;
- Ren, Shuling;
- Sakai, Akihiro;
- Fukusumi, Takahito;
- Liu, Chao;
- Sadat, Sayed;
- Ando, Mizuo;
- Xu, Guorong;
- Khan, Zubair;
- Pang, John;
- Valsamakis, Alex;
- Fisch, Kathleen M;
- Califano, Joseph A
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.