HPV-EM: an accurate HPV detection and genotyping EM algorithm

Academic Article

Abstract

  • Accurate HPV genotyping is crucial in facilitating epidemiology studies, vaccine trials, and HPV-related cancer research. Contemporary HPV genotyping assays only detect < 25% of all known HPV genotypes and are not accurate for low-risk or mixed HPV genotypes. Current genomic HPV genotyping algorithms use a simple read-alignment and filtering strategy that has difficulty handling repeats and homology sequences. Therefore, we have developed an optimized expectation–maximization algorithm, designated HPV-EM, to address the ambiguities caused by repetitive sequencing reads. HPV-EM achieved 97–100% accuracy when benchmarked using cell line data and TCGA cervical cancer data. We also validated HPV-EM using DNA tiling data on an institutional cervical cancer cohort (96.5% accuracy). Using HPV-EM, we demonstrated HPV genotypic differences in recurrence and patient outcomes in cervical and head and neck cancers.
  • Published In

  • Scientific Reports  Journal
  • Digital Object Identifier (doi)

    Pubmed Id

  • 14925342
  • Author List

  • Inkman MJ; Jayachandran K; Ellis TM; Ruiz F; McLellan MD; Miller CA; Wu Y; Ojesina AI; Schwarz JK; Zhang J
  • Volume

  • 10
  • Issue

  • 1