Human papillomavirus genotyping by multiplex pyrosequencing in cervical cancer patients from India

Cervical cancer is a leading cause of cancer-related deaths among women in India. Human papillomavirus (HPV) infection is the causative agent of cervical cancer; and infection with the high-risk genotypes, predominantly HPV 16 and 18, is the biggest risk factor. Vaccines targeting HPV16 and 18 have been found to confer protection in large-scale clinical trials. HPV genotyping has traditionally been carried out to screen the population "at risk" using indirect methods based on polymerase chain reaction (PCR) using consensus primers combined with various DNA hybridization techniques, and often followed by the sequencing of candidate products. Recently, a high-throughput and direct method based on DNA sequencing has been described for HPV genotyping using multiplex pyrosequencing. We present a pilot study on HPV genotyping of cervical cancer and non-malignant cervical samples using multiplex pyrosequencing. Using genomic DNA from cell lines, cervical biopsies, surgical tissues or formalin-fixed, paraffin-embedded tissue samples, we could successfully resolve 6 different HPV types out of the 7 tested, with their prevalence found to be in agreement with earlier reports. We also resolved coinfections with two different HPV types in several samples. An HPV 16 genotype with a specific and recurrent sequence variation was observed in 8 cancer samples and one non-malignant sample. We find this technique eminently suited for high-throughput applications, which can be easily extended to large sample cohorts to determine a robust benchmark for HPV genotypes prevalent in India.