title: Promises and pitfalls of Illumina sequencing for HIV resistance genotyping.
abstract: Genetic sequencing ("genotyping") plays a critical role in the modern clinical management of HIV infection. This virus evolves rapidly within patients because of its error-prone reverse transcriptase and short generation time. Consequently, HIV variants with mutations that confer resistance to one or more antiretroviral drugs can emerge during sub-optimal treatment. There are now multiple HIV drug resistance interpretation algorithms that take the region of the HIV genome encoding the major drug targets as inputs; expert use of these algorithms can significantly improve to clinical outcomes in HIV treatment. Next-generation sequencing has the potential to revolutionize HIV resistance genotyping by lowering the threshold that rare but clinically significant HIV variants can be detected reproducibly, and by conferring improved cost-effectiveness in high-throughput scenarios. In this review, we discuss the relative merits and challenges of deploying the Illumina MiSeq instrument for clinical HIV genotyping.
authors.affiliation: BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.
authors.forename: Chanson J
authors.initials: CJ
authors.lastname: Brumme
authors.affiliation: Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada. Electronic address: apoon42@uwo.ca.
authors.forename: Art F Y
authors.initials: AFY
authors.lastname: Poon
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology / Q000627:therapeutic use; D024882:Drug Resistance, Viral; D005838:Genotype; D060005:Genotyping Techniques / Q000191:economics / Q000379:methods / Q000592:standards; D006678:HIV / Q000145:classification* / Q000235:genetics*; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods / Q000592:standards; D006801:Humans; D009154:Mutation
chemical_list: D019380:Anti-HIV Agents
keywords: HIV drug resistance; Human immunodeficiency virus; Next-generation sequencing; Resistance genotyping; Sequence bioinformatics