Model for assessment of proficiency of human immunodeficiency virus type 1 sequencing-based genotypic antiretroviral assays.

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  • Additional Information
    • Corporate Authors:
      Pediatric ACTG Sequencing Working Group
    • Source:
      Publisher: American Society for Microbiology Country of Publication: United States NLM ID: 7505564 Publication Model: Print Cited Medium: Print ISSN: 0095-1137 (Print) Linking ISSN: 00951137 NLM ISO Abbreviation: J Clin Microbiol Subsets: MEDLINE
    • Publication Information:
      Original Publication: Washington, American Society for Microbiology.
    • Subject Terms:
      Anti-HIV Agents/*pharmacology ; HIV-1/*genetics; Codon ; Drug Resistance, Viral ; Genotype ; HIV-1/drug effects ; Mutation ; Sequence Analysis, DNA ; Templates, Genetic
    • Abstract:
      Use of sequencing-based genotyping as a diagnostic assay for human immunodeficiency virus (HIV) antiretroviral resistance is increasing. Periodic evaluation of the proficiency of laboratories performing this assay should be established. It is important to identify components of the assay that influence the generation of reliable sequencing data and that should and can be monitored. A model was developed to determine what parameters were reasonable and feasible for assessing the performance of genotyping assays. Ten laboratories using the genotyping platform, HIV-1 Genotyping System (HGS) v. 1 and software versions 1.1 or 2.0, participated in two rounds of testing. For each round, each group was sent a panel consisting of three clinical samples to sequence in real time. Six months later, seven laboratories using the TRUGENE HIV-1 Genotyping Kit participated in a separate round, working with both panels at the same time. Analysis of the data showed that one main indicator of genotyping proficiency was achievement of > or =98% sequence homology of a sample tested to a group consensus sequence for that sample. A second was concordant identification of codons at sites identified with resistance mutations in the sample, although scoring of these criteria is still undetermined from this study. These criteria are applicable to all sequence-based genotyping platforms and have been used as a baseline for assessing the performance of genotyping for the determination of antiretroviral resistance in our ongoing proficiency program.
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    • Grant Information:
      N01AI85354 United States AI NIAID NIH HHS; N01-AI-85354 United States AI NIAID NIH HHS
    • Accession Number:
      0 (Anti-HIV Agents)
      0 (Codon)
    • Publication Date:
      Date Created: 20050806 Date Completed: 20050915 Latest Revision: 20181113
    • Publication Date:
      20221213
    • Accession Number:
      PMC1233968
    • Accession Number:
      10.1128/JCM.43.8.3963-3970.2005
    • Accession Number:
      16081937