title: Sequence imputation of HPV16 genomes for genetic association studies.
abstract: BACKGROUND
  Human Papillomavirus type 16 (HPV16) causes over half of all cervical cancer and some HPV16 variants are more oncogenic than others. The genetic basis for the extraordinary oncogenic properties of HPV16 compared to other HPVs is unknown. In addition, we neither know which nucleotides vary across and within HPV types and lineages, nor which of the single nucleotide polymorphisms (SNPs) determine oncogenicity.
  
  
  METHODS
  A reference set of 62 HPV16 complete genome sequences was established and used to examine patterns of evolutionary relatedness amongst variants using a pairwise identity heatmap and HPV16 phylogeny. A BLAST-based algorithm was developed to impute complete genome data from partial sequence information using the reference database. To interrogate the oncogenic risk of determined and imputed HPV16 SNPs, odds-ratios for each SNP were calculated in a case-control viral genome-wide association study (VWAS) using biopsy confirmed high-grade cervix neoplasia and self-limited HPV16 infections from Guanacaste, Costa Rica.
  
  
  RESULTS
  HPV16 variants display evolutionarily stable lineages that contain conserved diagnostic SNPs. The imputation algorithm indicated that an average of 97.5±1.03% of SNPs could be accurately imputed. The VWAS revealed specific HPV16 viral SNPs associated with variant lineages and elevated odds ratios; however, individual causal SNPs could not be distinguished with certainty due to the nature of HPV evolution.
  
  
  CONCLUSIONS
  Conserved and lineage-specific SNPs can be imputed with a high degree of accuracy from limited viral polymorphic data due to the lack of recombination and the stochastic mechanism of variation accumulation in the HPV genome. However, to determine the role of novel variants or non-lineage-specific SNPs by VWAS will require direct sequence analysis. The investigation of patterns of genetic variation and the identification of diagnostic SNPs for lineages of HPV16 variants provides a valuable resource for future studies of HPV16 pathogenicity.
authors: Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors: Benjamin
authors: B
authors: Smith
authors: Zigui
authors: Z
authors: Chen
authors: Laura
authors: L
authors: Reimers
authors: Koenraad
authors: K
authors: van Doorslaer
authors: Mark
authors: M
authors: Schiffman
authors: Rob
authors: R
authors: Desalle
authors: Rolando
authors: R
authors: Herrero
authors: Kai
authors: K
authors: Yu
authors: Sholom
authors: S
authors: Wacholder
authors: Tao
authors: T
authors: Wang
authors: Robert D
authors: RD
authors: Burk
mesh_terms: D001483:Base Sequence; D016022:Case-Control Studies; D005260:Female; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics*; D055106:Genome-Wide Association Study; D052162:Human papillomavirus 16 / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012015:Reference Standards; D017422:Sequence Analysis, DNA / Q000379:methods*