Detection and identification of human papillomavirus using a PCR-restriction fragment mass polymorphism assay

Abstract

A polymerase chain reaction-restriction fragment mass polymorphism (PCR-RFMP) assay protocol using PGMY09/11 primers for the detection and identification of human papillomavirus (HPV) has recently been developed. The present study evaluated the analytical sensitivity and clinical utility of HPV genotyping employing PCR-RFMP as compared to direct sequencing. Serial dilutions of cloned HPV DNA were analyzed in order to assess the limit of detection (LOD) and three sets of HPV clone mixtures (types 16+18, 16+11 and 18+11) were used to assess the accuracy of the genotyping assays. For 423 cervical specimens that were cytologically categorized as normal or cancer, the concordance between the two assays was evaluated. Clinical sensitivity was calculated by evaluating 101 histologically confirmed cases. The PCR-RFMP HPV assay had a lower LOD and 100% accuracy when detecting double HPV infection. Agreement between the two assays upon 423 clinical specimens was 91.0% with a κ-value of 0.86. The incidence of multiple HPV infections among HPV-positive patients was 19.0% by PCR-RFMP and 5.4% by sequencing. The clinical sensitivity of PCR-RFMP and sequencing was 92% and 84%, respectively. In conclusion, the PCR-RFMP assay for HPV genotyping correlated well with direct sequencing, provides high analytical and clinical sensitivity, and is advantageous in the detection of multiple HPV infections.