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

ABSTRACT:

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 se

SUBMITTER: Saito Y 

PROVIDER: S-EPMC7699136 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature