Previous Article | Next Article 
Journal of Clinical Microbiology, August 1999, p. 2533-2537, Vol. 37, No. 8
0095-1137/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Performance of the Affymetrix GeneChip HIV PRT 440 Platform for Antiretroviral Drug Resistance Genotyping of Human
Immunodeficiency Virus Type 1 Clades and Viral Isolates with
Length Polymorphisms
Maryanne
Vahey,1,*
Martin E.
Nau,2
Sandra
Barrick,2
John D.
Cooley,2
Robert
Sawyer,2
Alex A.
Sleeker,2
Peter
Vickerman,2
Stuart
Bloor,3
Brendan
Larder,3
Nelson L.
Michael,1 and
Scott A.
Wegner1
Division of Retrovirology, Walter Reed Army
Institute of Research,1 and The Henry M. Jackson Foundation for the Advancement of Military
Medicine,2 Rockville, Maryland, and
Virco UK, Cambridge, United Kingdom3
Received 30 November 1998/Returned for modification 2 February
1999/Accepted 10 May 1999
The performance of a silica chip-based resequencing method, the
Affymetrix HIV PRT 440 assay (hereafter referred to as the Affymetrix
assay), was evaluated on a panel of well-characterized nonclade B viral
isolates and on isolates exhibiting length polymorphisms. Sequencing of
human immunodeficiency virus type 1 (HIV-1) pol cDNAs from
clades A, C, D, E, and F resulted in clade-specific regions of
base-calling ambiguities in regions not known to be associated with
resistance polymorphisms, as well as a small number of spurious
resistance polymorphisms. The Affymetrix assay failed to detect the
presence of additional serine codons distal to reverse transcriptase
(RT) codon 68 that are associated with multinucleoside RT inhibitor
resistance. The increasing prevalence of non-clade B HIV-1 strains in
the United States and Europe and the identification of clinically
relevant pol gene length polymorphisms will impact the
generalizability of the Affymetrix assay, emphasizing the need to
accommodate this expanding pool of pol genotypes in future assay versions.
*
Corresponding author. Mailing address: Division of
Retrovirology, Walter Reed Army Institute of Research, 1600 E. Gude
Dr., Rockville, MD 20850. Phone: (301) 294-1887, ext. 1044. Fax: (301) 762-7460. E-mail: mvahey{at}pasteur.hjf.org.
Journal of Clinical Microbiology, August 1999, p. 2533-2537, Vol. 37, No. 8
0095-1137/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
This article has been cited by other articles:
-
Miller, M. B., Tang, Y.-W.
(2009). Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology. Clin. Microbiol. Rev.
22: 611-633
[Abstract]
[Full Text]
-
Tao, Q., Wang, X., Bao, H., Wu, J., Shi, L., Li, Y., Qiao, C., Yakovlevich, S. A., Mikhaylovna, P. N., Chen, H.
(2009). Detection and differentiation of four poultry diseases using asymmetric reverse transcription polymerase chain reaction in combination with oligonucleotide microarrays. jvdi
21: 623-632
[Abstract]
[Full Text]
-
Wang, C., Mitsuya, Y., Gharizadeh, B., Ronaghi, M., Shafer, R. W.
(2007). Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance. Genome Res
17: 1195-1201
[Abstract]
[Full Text]
-
Sulaiman, I. M., Tang, K., Osborne, J., Sammons, S., Wohlhueter, R. M.
(2007). GeneChip Resequencing of the Smallpox Virus Genome Can Identify Novel Strains: a Biodefense Application. J. Clin. Microbiol.
45: 358-363
[Abstract]
[Full Text]
-
Sulaiman, I. M., Liu, X., Frace, M., Sulaiman, N., Olsen-Rasmussen, M., Neuhaus, E., Rota, P. A., Wohlhueter, R. M.
(2006). Evaluation of Affymetrix Severe Acute Respiratory Syndrome Resequencing GeneChips in Characterization of the Genomes of Two Strains of Coronavirus Infecting Humans. Appl. Environ. Microbiol.
72: 207-211
[Abstract]
[Full Text]
-
Nissley, D. V., Halvas, E. K., Hoppman, N. L., Garfinkel, D. J., Mellors, J. W., Strathern, J. N.
(2005). Sensitive Phenotypic Detection of Minor Drug-Resistant Human Immunodeficiency Virus Type 1 Reverse Transcriptase Variants. J. Clin. Microbiol.
43: 5696-5704
[Abstract]
[Full Text]
-
Roudinskii, N. I., Sukhanova, A. L., Kazennova, E. V., Weber, J. N., Pokrovsky, V. V., Mikhailovich, V. M., Bobkov, A. F.
(2004). Diversity of Human Immunodeficiency Virus Type 1 Subtype A and CRF03_AB Protease in Eastern Europe: Selection of the V77I Variant and Its Rapid Spread in Injecting Drug User Populations. J. Virol.
78: 11276-11287
[Abstract]
[Full Text]
-
Gonzalez, R., Masquelier, B., Fleury, H., Lacroix, B., Troesch, A., Vernet, G., Telles, J. N.
(2004). Detection of Human Immunodeficiency Virus Type 1 Antiretroviral Resistance Mutations by High-Density DNA Probe Arrays. J. Clin. Microbiol.
42: 2907-2912
[Abstract]
[Full Text]
-
Morley, S., MacDonald, G., Kirn, D., Kaye, S., Brown, R., Soutar, D.
(2004). The dl1520 Virus Is Found Preferentially in Tumor Tissue after Direct Intratumoral Injection in Oral Carcinoma. Clin. Cancer Res.
10: 4357-4362
[Abstract]
[Full Text]
-
Kessler, N., Ferraris, O., Palmer, K., Marsh, W., Steel, A.
(2004). Use of the DNA Flow-Thru Chip, a Three-Dimensional Biochip, for Typing and Subtyping of Influenza Viruses. J. Clin. Microbiol.
42: 2173-2185
[Abstract]
[Full Text]
-
Wong, C. W., Albert, T. J., Vega, V. B., Norton, J. E., Cutler, D. J., Richmond, T. A., Stanton, L. W., Liu, E. T., Miller, L. D.
(2004). Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays. Genome Res
14: 398-405
[Abstract]
[Full Text]
-
Kawaguchi, K., Kaneko, S., Honda, M., Kawai, H. F., Shirota, Y., Kobayashi, K.
(2003). Detection of Hepatitis B Virus DNA in Sera from Patients with Chronic Hepatitis B Virus Infection by DNA Microarray Method. J. Clin. Microbiol.
41: 1701-1704
[Abstract]
[Full Text]
-
Jagodzinski, L. L., Cooley, J. D., Weber, M., Michael, N. L.
(2003). Performance Characteristics of Human Immunodeficiency Virus Type 1 (HIV-1) Genotyping Systems in Sequence-Based Analysis of Subtypes Other than HIV-1 Subtype B. J. Clin. Microbiol.
41: 998-1003
[Abstract]
[Full Text]
-
Shafer, R. W.
(2002). Genotypic Testing for Human Immunodeficiency Virus Type 1 Drug Resistance. Clin. Microbiol. Rev.
15: 247-277
[Abstract]
[Full Text]
-
Cunningham, S., Ank, B., Lewis, D., Lu, W., Wantman, M., Dileanis, J., Jackson, J. B., Palumbo, P., Krogstad, P., Eshleman, S. H.
(2001). Performance of the Applied Biosystems ViroSeq Human Immunodeficiency Virus Type 1 (HIV-1) Genotyping System for Sequence-Based Analysis of HIV-1 in Pediatric Plasma Samples. J. Clin. Microbiol.
39: 1254-1257
[Abstract]
[Full Text]
-
Hanna, G. J., Johnson, V. A., Kuritzkes, D. R., Richman, D. D., Martinez-Picado, J., Sutton, L., Hazelwood, J. D., D'Aquila, R. T.
(2000). Comparison of Sequencing by Hybridization and Cycle Sequencing for Genotyping of Human Immunodeficiency Virus Type 1 Reverse Transcriptase. J. Clin. Microbiol.
38: 2715-2721
[Abstract]
[Full Text]
-
Keim, P., Price, L. B., Klevytska, A. M., Smith, K. L., Schupp, J. M., Okinaka, R., Jackson, P. J., Hugh-Jones, M. E.
(2000). Multiple-Locus Variable-Number Tandem Repeat Analysis Reveals Genetic Relationships within Bacillus anthracis. J. Bacteriol.
182: 2928-2936
[Abstract]
[Full Text]
-
Larder, B. A., Bloor, S., Kemp, S. D., Hertogs, K., Desmet, R. L., Miller, V., Sturmer, M., Staszewski, S., Ren, J., Stammers, D. K., Stuart, D. I., Pauwels, R.
(1999). A Family of Insertion Mutations between Codons 67 and 70 of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Confer Multinucleoside Analog Resistance. Antimicrob. Agents Chemother.
43: 1961-1967
[Abstract]
[Full Text]