Resequencing microarray technology for genotyping human papillomavirus in cervical smears

PLoS One. 2014 Nov 10;9(11):e109301. doi: 10.1371/journal.pone.0109301. eCollection 2014.

Abstract

There are more than 40 human papillomaviruses (HPVs) belonging to the alpha genus that cause sexually transmitted infections; these infections are among the most frequent and can lead to condylomas and anogenital intra-epithelial neoplasia. At least 18 of these viruses are causative agents of anogenital carcinomas. We evaluated the performance of a resequencing microarray for the detection and genotyping of alpha HPV of clinical significance using cloned HPV DNA. To reduce the number of HPV genotypes tiled on microarray, we used reconstructed ancestral sequences (RASs) as they are more closely related to the various genotypes than the current genotypes are among themselves. The performance of this approach was tested by genotyping with a set of 40 cervical smears already genotyped using the commercial PapilloCheck kit. The results of the two tests were concordant for 70% (28/40) of the samples and compatible for 30% (12/40). Our findings indicate that RASs were able to detect and identify one or several HPV in clinical samples. Associating RASs with homonym sequences improved the genotyping of HPV present in cases of multiple infection. In conclusion, we demonstrate the diagnostic potential of resequencing technology for genotyping of HPV, and illustrate its value both for epidemiological studies and for monitoring the distribution of HPV in the post-vaccination era.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alphapapillomavirus / genetics*
  • Base Sequence
  • Cluster Analysis
  • DNA Primers / genetics
  • DNA, Viral / genetics*
  • Female
  • Genotype
  • Humans
  • Molecular Sequence Data
  • Oligonucleotide Array Sequence Analysis / methods*
  • Phylogeny*
  • Real-Time Polymerase Chain Reaction
  • Sequence Analysis, DNA
  • Vaginal Smears / methods*

Substances

  • DNA Primers
  • DNA, Viral

Grant support

This program was supported by the Programme Transversal de Recherche DEVA No. 246 financed by the Institut Pasteur (Paris, France), sponsored by the Fondation Total-Institut Pasteur and the Elisabeth Taub award from the Académie Nationale de Médécine. This study was funded by the French Institut National du Cancer (Canceropole 2011-1VADS 03-IP1). The funders had no role in study design, data analysis or preparation of the manuscript.