title: Model for assessment of proficiency of human immunodeficiency virus type 1 sequencing-based genotypic antiretroviral assays.
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.
authors.affiliation: Department of Immunology/Microbiology, Rush Medical College, 1653 W. Congress Parkway, Chicago, IL 60612, USA. diana_huang@rush.edu
authors.forename: Diana D
authors.initials: DD
authors.lastname: Huang
authors.forename: James W
authors.initials: JW
authors.lastname: Bremer
authors.forename: Donald J
authors.initials: DJ
authors.lastname: Brambilla
authors.forename: Paul E
authors.initials: PE
authors.lastname: Palumbo
authors.forename: Grace
authors.initials: G
authors.lastname: Aldrovandi
authors.forename: Susan
authors.initials: S
authors.lastname: Eshleman
authors.forename: Clark
authors.initials: C
authors.lastname: Brown
authors.forename: Susan
authors.initials: S
authors.lastname: Fiscus
authors.forename: Lisa
authors.initials: L
authors.lastname: Frenkel
authors.forename: Hasnah
authors.initials: H
authors.lastname: Hamdan
authors.forename: Stephen
authors.initials: S
authors.lastname: Hart
authors.forename: Andrea
authors.initials: A
authors.lastname: Kovacs
authors.forename: Paul
authors.initials: P
authors.lastname: Krogstad
authors.forename: Phillip
authors.initials: P
authors.lastname: LaRussa
authors.forename: John
authors.initials: J
authors.lastname: Sullivan
authors.forename: Adriana
authors.initials: A
authors.lastname: Weinberg
authors.forename: Yu Qi
authors.initials: YQ
authors.lastname: Zhao
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology*; D003062:Codon; D024882:Drug Resistance, Viral; D005838:Genotype; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics*; D009154:Mutation; D017422:Sequence Analysis, DNA; D013698:Templates, Genetic
chemical_list: D019380:Anti-HIV Agents; D003062:Codon