Evaluation of the editing process in human immunodeficiency virus type 1 genotyping.
Sequencing-based human immunodeficiency virus type 1 (HIV-1) genotyping assays require subjective interpretation (editing) of sequence data from multiple primers to form consensus sequences and identify antiretroviral drug resistance mutations. We assessed interlaboratory variations in editing and their impact on the recognition of resistance mutations. Six samples were analyzed in a central laboratory by using a research-use-only HIV-1 genotyping system previously produced by Applied Biosystems. The electronic files of individual primer sequences from the samples were sent to 10 laboratories to compare sequence editing strategies. Each sequence data set included sequences from seven primers spanning protease codons 1 to 99 and reverse transcriptase codons 1 to 320. Each laboratory generated a consensus sequence for each sample and completed a questionnaire about editing strategy. The amount of editing performed, the concordance of consensus sequences among the laboratories, and the identification of resistance mutations were evaluated. Sequence agreement was high among the laboratories despite wide variations in editing strategies. All laboratories identified 66 (88%) of 75 resistance mutations in the samples. Nonconcordant identifications were made for 9 (12%) of the 75 mutations, all of which required editing for identification. These results indicate a need for standardized editing guidelines in genotyping assays. Proficiency in editing should be assessed in training and included in quality control programs for HIV-1 genotyping.
Huang
Diana D
DD
Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612, USA. diana_huang@rush.edu
Eshleman
Susan H
SH
Brambilla
Donald J
DJ
Palumbo
Paul E
PE
Bremer
James W
JW
D019380:Anti-HIV Agents / Q000494:pharmacology; D001483:Base Sequence; D016384:Consensus Sequence; D003627:Data Interpretation, Statistical; D024882:Drug Resistance, Viral / Q000235:genetics*; D005838:Genotype; D016333:HIV Protease / Q000235:genetics*; D054303:HIV Reverse Transcriptase / Q000235:genetics*; D015497:HIV-1 / Q000145:classification* / Q000187:drug effects / Q000235:genetics; D006801:Humans; D007753:Laboratories / Q000592:standards; D008826:Microbial Sensitivity Tests / Q000592:standards; D009154:Mutation; D015588:Observer Variation; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods / Q000592:standards*; D011795:Surveys and Questionnaires
D019380:Anti-HIV Agents; D054303:HIV Reverse Transcriptase; D016333:HIV Protease