Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time
Several decision support systems have been developed to interpret HIV-1 drug resistance genotyping results. This study compares the ability of the most commonly used systems (ANRS, Rega, and Stanford's HIVdb) to predict virological outcome at 12, 24, and 48 weeks. Methodology/Principal Findi...
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sg-ntu-dr.10356-962962022-02-16T16:30:14Z Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time Frentz, Dineke Assel, Matthias De Luca, Andrea Fabbiani, Massimiliano Incardona, Francesca Libin, Pieter Manca, Nino Müller, Viktor Paredes, Roger Quiros-Roldan, Eugenia Ruiz, Lidia Torti, Carlo Vandamme, Anne-Mieke Van Laethem, Kristel Zazzi, Maurizio Boucher, Charles A. B. Prosperi, Mattia C. F. Sloot, Peter M. A. van de Vijver, David A. M. C. Nuallain, Breanndan O. School of Computer Engineering DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences Several decision support systems have been developed to interpret HIV-1 drug resistance genotyping results. This study compares the ability of the most commonly used systems (ANRS, Rega, and Stanford's HIVdb) to predict virological outcome at 12, 24, and 48 weeks. Methodology/Principal Findings Included were 3763 treatment-change episodes (TCEs) for which a HIV-1 genotype was available at the time of changing treatment with at least one follow-up viral load measurement. Genotypic susceptibility scores for the active regimens were calculated using scores defined by each interpretation system. Using logistic regression, we determined the association between the genotypic susceptibility score and proportion of TCEs having an undetectable viral load (<50 copies/ml) at 12 (8–16) weeks (2152 TCEs), 24 (16–32) weeks (2570 TCEs), and 48 (44–52) weeks (1083 TCEs). The Area under the ROC curve was calculated using a 10-fold cross-validation to compare the different interpretation systems regarding the sensitivity and specificity for predicting undetectable viral load. The mean genotypic susceptibility score of the systems was slightly smaller for HIVdb, with 1.92±1.17, compared to Rega and ANRS, with 2.22±1.09 and 2.23±1.05, respectively. However, similar odds ratio's were found for the association between each-unit increase in genotypic susceptibility score and undetectable viral load at week 12; 1.6 [95% confidence interval 1.5–1.7] for HIVdb, 1.7 [1.5–1.8] for ANRS, and 1.7 [1.9–1.6] for Rega. Odds ratio's increased over time, but remained comparable (odds ratio's ranging between 1.9–2.1 at 24 weeks and 1.9–2.2 at 48 weeks). The Area under the curve of the ROC did not differ between the systems at all time points; p = 0.60 at week 12, p = 0.71 at week 24, and p = 0.97 at week 48. Conclusions/Significance Three commonly used HIV drug resistance interpretation systems ANRS, Rega and HIVdb predict virological response at 12, 24, and 48 weeks, after change of treatment to the same extent. Published version 2013-04-29T07:18:25Z 2019-12-06T19:28:21Z 2013-04-29T07:18:25Z 2019-12-06T19:28:21Z 2010 2010 Journal Article Frentz, D., Boucher, C. A. B., Assel, M., De Luca, A., Fabbiani, M., Incardona, F., et al. (2010). Comparison of HIV-1 Genotypic Resistance Test Interpretation Systems in Predicting Virological Outcomes Over Time. PLoS ONE, 5(7), e11505. 1932-6203 https://hdl.handle.net/10356/96296 http://hdl.handle.net/10220/9871 10.1371/journal.pone.0011505 20634893 en PLoS ONE © 2010 Frentz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. application/pdf |
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DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences Frentz, Dineke Assel, Matthias De Luca, Andrea Fabbiani, Massimiliano Incardona, Francesca Libin, Pieter Manca, Nino Müller, Viktor Paredes, Roger Quiros-Roldan, Eugenia Ruiz, Lidia Torti, Carlo Vandamme, Anne-Mieke Van Laethem, Kristel Zazzi, Maurizio Boucher, Charles A. B. Prosperi, Mattia C. F. Sloot, Peter M. A. van de Vijver, David A. M. C. Nuallain, Breanndan O. Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time |
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Several decision support systems have been developed to interpret HIV-1 drug resistance genotyping results. This study compares the ability of the most commonly used systems (ANRS, Rega, and Stanford's HIVdb) to predict virological outcome at 12, 24, and 48 weeks.
Methodology/Principal Findings
Included were 3763 treatment-change episodes (TCEs) for which a HIV-1 genotype was available at the time of changing treatment with at least one follow-up viral load measurement. Genotypic susceptibility scores for the active regimens were calculated using scores defined by each interpretation system. Using logistic regression, we determined the association between the genotypic susceptibility score and proportion of TCEs having an undetectable viral load (<50 copies/ml) at 12 (8–16) weeks (2152 TCEs), 24 (16–32) weeks (2570 TCEs), and 48 (44–52) weeks (1083 TCEs). The Area under the ROC curve was calculated using a 10-fold cross-validation to compare the different interpretation systems regarding the sensitivity and specificity for predicting undetectable viral load. The mean genotypic susceptibility score of the systems was slightly smaller for HIVdb, with 1.92±1.17, compared to Rega and ANRS, with 2.22±1.09 and 2.23±1.05, respectively. However, similar odds ratio's were found for the association between each-unit increase in genotypic susceptibility score and undetectable viral load at week 12; 1.6 [95% confidence interval 1.5–1.7] for HIVdb, 1.7 [1.5–1.8] for ANRS, and 1.7 [1.9–1.6] for Rega. Odds ratio's increased over time, but remained comparable (odds ratio's ranging between 1.9–2.1 at 24 weeks and 1.9–2.2 at 48 weeks). The Area under the curve of the ROC did not differ between the systems at all time points; p = 0.60 at week 12, p = 0.71 at week 24, and p = 0.97 at week 48.
Conclusions/Significance
Three commonly used HIV drug resistance interpretation systems ANRS, Rega and HIVdb predict virological response at 12, 24, and 48 weeks, after change of treatment to the same extent. |
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School of Computer Engineering |
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School of Computer Engineering Frentz, Dineke Assel, Matthias De Luca, Andrea Fabbiani, Massimiliano Incardona, Francesca Libin, Pieter Manca, Nino Müller, Viktor Paredes, Roger Quiros-Roldan, Eugenia Ruiz, Lidia Torti, Carlo Vandamme, Anne-Mieke Van Laethem, Kristel Zazzi, Maurizio Boucher, Charles A. B. Prosperi, Mattia C. F. Sloot, Peter M. A. van de Vijver, David A. M. C. Nuallain, Breanndan O. |
format |
Article |
author |
Frentz, Dineke Assel, Matthias De Luca, Andrea Fabbiani, Massimiliano Incardona, Francesca Libin, Pieter Manca, Nino Müller, Viktor Paredes, Roger Quiros-Roldan, Eugenia Ruiz, Lidia Torti, Carlo Vandamme, Anne-Mieke Van Laethem, Kristel Zazzi, Maurizio Boucher, Charles A. B. Prosperi, Mattia C. F. Sloot, Peter M. A. van de Vijver, David A. M. C. Nuallain, Breanndan O. |
author_sort |
Frentz, Dineke |
title |
Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time |
title_short |
Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time |
title_full |
Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time |
title_fullStr |
Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time |
title_full_unstemmed |
Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time |
title_sort |
comparison of hiv-1 genotypic resistance test interpretation systems in predicting virological outcomes over time |
publishDate |
2013 |
url |
https://hdl.handle.net/10356/96296 http://hdl.handle.net/10220/9871 |
_version_ |
1725985685828009984 |