ArticleJournal of clinical microbiology2003
Evaluation of the editing process in human immunodeficiency virus type 1 genotyping.
Article in Journal of clinical microbiology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Low nucleotide diversity of the Plasmodium falciparum AP2-EXP2 gene among clinical samples from Ghana.Parasites & vectors · 2024Article
- Review
- Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing.Viruses · 2020Article
- HIV-1 Protease, Reverse Transcriptase, and Integrase Variation.Journal of virology · 2016Article
- Japanese external quality assessment program to standardize HIV-1 drug-resistance testing (JEQS2010 program) using in vitro transcribed RNA as reference material.AIDS research and human retroviruses · 2015Article
- LETTER TO THE EDITOR Performance of the ViroSeq® HIV-1 Genotyping System v2.0 in Central Africa.The open AIDS journal · 2015Article
- Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba.PloS one · 2015Article
- A comparison of two measures of HIV diversity in multi-assay algorithms for HIV incidence estimation.PloS one · 2014Article
- Capacity building and predictors of success for HIV-1 drug resistance testing in the Asia-Pacific region and Africa.Journal of the International AIDS Society · 2013Article
- Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase.AIDS research and human retroviruses · 2012Article
- Automating HIV drug resistance genotyping with RECall, a freely accessible sequence analysis tool.Journal of clinical microbiology · 2012Article
- Evaluation of in-house genotyping assay performance using dried blood spot specimens in the Global World Health Organization laboratory network.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2012Article
- Genotyping external quality assurance in the World Health Organization HIV drug resistance laboratory network during 2007-2010.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2012Article
- The Brazilian network for HIV-1 genotyping external quality control assurance programme.Journal of the International AIDS Society · 2011Article
- High failure rate of the ViroSeq HIV-1 genotyping system for drug resistance testing in Cameroon, a country with broad HIV-1 genetic diversity.Journal of clinical microbiology · 2011Article
- Comparative evaluation of the ViroSeq™ HIV-1 genotyping system and an in-house method for analysis of HIV-1 drug-resistance mutations in China.Molecular diagnosis & therapy · 2011Article
- Development and evaluation of a national reference panel of HIV-1 protease and reverse transcriptase drug-resistance mutations for HIV-1 genotypic resistance assays in China.Molecular diagnosis & therapy · 2010Article
- TREAT Asia Quality Assessment Scheme (TAQAS) to standardize the outcome of HIV genotypic resistance testing in a group of Asian laboratories.Journal of virological methods · 2009Article
- Sensitivity of the ViroSeq HIV-1 genotyping system for detection of the K103N resistance mutation in HIV-1 subtypes A, C, and D.The Journal of molecular diagnostics : JMD · 2006Article
- Model for assessment of proficiency of human immunodeficiency virus type 1 sequencing-based genotypic antiretroviral assays.Journal of clinical microbiology · 2005Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
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.
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