Targeted deep sequencing of HIV-1 using the IonTorrentPGM platform.

ABSTRACT: The characterization of mixed HIV-1 populations is a key question in clinical and basic research settings. This can be achieved through targeted deep sequencing (TDS), where next-generation sequencing is used to examine in depth a sub-genomic region of interest. This study explores the suitability of IonTorrent PGM(LifeTechnologies) for the TDS-based analysis of HIV-1 evolution. Using laboratory reagents and primary specimens sampled at pre-peak viremia the error rates from misincorporation and in vitro recombination were <0.5%. The sequencing error rate was 2- to 3-fold higher in/around homopolymeric tracts, and could be discerned from true polymorphism using bidirectional sequencing. The limit of detection of complex variants was further lowered by using haplotyping. The application of t

SUBMITTER: Kijak GH 

PROVIDER: S-EPMC4219931 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature