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Journal of Clinical Microbiology, August 2005, p. 3963-3970, Vol. 43, No. 8
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.8.3963-3970.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Model for Assessment of Proficiency of Human Immunodeficiency Virus Type 1 Sequencing-Based Genotypic Antiretroviral Assays

Diana D. Huang,1* James W. Bremer,1 Donald J. Brambilla,2 Paul E. Palumbo,3 and for the Pediatric ACTG Sequencing Working Group

Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois,1 New England Research Institute, Inc. Watertown, Massachusetts,2 Pediatrics, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey3

Received 16 September 2004/ Returned for modification 7 November 2004/ Accepted 7 May 2005

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 ≥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.

* Corresponding author. Mailing address: Department of Immunology/Microbiology, Rush Medical College, 1653 W. Congress Parkway, Chicago, IL 60612. Phone: (312) 942-8737. Fax: (312) 942-2808. E-mail: diana_huang{at}rush.edu.

Journal of Clinical Microbiology, August 2005, p. 3963-3970, Vol. 43, No. 8
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.8.3963-3970.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.





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