title: Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing.
abstract: Deep sequencing is a powerful and cost-effective tool to characterize the genetic diversity and evolution of virus populations. While modern sequencing instruments readily cover viral genomes many thousand fold and very rare variants can in principle be detected, sequencing errors, amplification biases, and other artifacts can limit sensitivity and complicate data interpretation. For this reason, the number of studies using whole genome deep sequencing to characterize viral quasi-species in clinical samples is still limited. We have previously undertaken a large scale whole genome deep sequencing study of HIV-1 populations. Here we discuss the challenges, error profiles, control experiments, and computational test we developed to quantify the accuracy of variant frequency estimation.
authors.affiliation: Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Fabio
authors.initials: F
authors.lastname: Zanini
authors.affiliation: Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.
authors.forename: Johanna
authors.initials: J
authors.lastname: Brodin
authors.affiliation: Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.
authors.forename: Jan
authors.initials: J
authors.lastname: Albert
authors.affiliation: Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Neher
mesh_terms: D019295:Computational Biology / Q000379:methods; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D054643:INDEL Mutation; D016133:Polymerase Chain Reaction / Q000379:methods / Q000592:standards; D011995:Recombination, Genetic; D015203:Reproducibility of Results
keywords: Amplification bias; Indel errors; Population sequencing