Research Article: Collaborative update of a rule-based expert system for HIV-1 genotypic resistance test interpretation

Date Published: July 28, 2017

Publisher: Public Library of Science

Author(s): Roger Paredes, Philip L. Tzou, Gert van Zyl, Geoff Barrow, Ricardo Camacho, Sergio Carmona, Philip M. Grant, Ravindra K. Gupta, Raph L. Hamers, P. Richard Harrigan, Michael R. Jordan, Rami Kantor, David A. Katzenstein, Daniel R. Kuritzkes, Frank Maldarelli, Dan Otelea, Carole L. Wallis, Jonathan M. Schapiro, Robert W. Shafer, Cecilio López-Galíndez.

http://doi.org/10.1371/journal.pone.0181357

Abstract

HIV-1 genotypic resistance test (GRT) interpretation systems (IS) require updates as new studies on HIV-1 drug resistance are published and as treatment guidelines evolve.

An expert panel was created to provide recommendations for the update of the Stanford HIV Drug Resistance Database (HIVDB) GRT-IS. The panel was polled on the ARVs to be included in a GRT report, and the drug-resistance interpretations associated with 160 drug-resistance mutation (DRM) pattern-ARV combinations. The DRM pattern-ARV combinations included 52 nucleoside RT inhibitor (NRTI) DRM pattern-ARV combinations (13 patterns x 4 NRTIs), 27 nonnucleoside RT inhibitor (NNRTI) DRM pattern-ARV combinations (9 patterns x 3 NNRTIs), 39 protease inhibitor (PI) DRM pattern-ARV combinations (13 patterns x 3 PIs) and 42 integrase strand transfer inhibitor (INSTI) DRM pattern-ARV combinations (14 patterns x 3 INSTIs).

There was universal agreement that a GRT report should include the NRTIs lamivudine, abacavir, zidovudine, emtricitabine, and tenofovir disoproxil fumarate; the NNRTIs efavirenz, etravirine, nevirapine, and rilpivirine; the PIs atazanavir/r, darunavir/r, and lopinavir/r (with “/r” indicating pharmacological boosting with ritonavir or cobicistat); and the INSTIs dolutegravir, elvitegravir, and raltegravir. There was a range of opinion as to whether the NRTIs stavudine and didanosine and the PIs nelfinavir, indinavir/r, saquinavir/r, fosamprenavir/r, and tipranavir/r should be included. The expert panel members provided highly concordant DRM pattern-ARV interpretations with only 6% of NRTI, 6% of NNRTI, 5% of PI, and 3% of INSTI individual expert interpretations differing from the expert panel median by more than one resistance level. The expert panel median differed from the HIVDB 7.0 GRT-IS for 20 (12.5%) of the 160 DRM pattern-ARV combinations including 12 NRTI, two NNRTI, and six INSTI pattern-ARV combinations. Eighteen of these differences were updated in HIVDB 8.1 GRT-IS to reflect the expert panel median. Additionally, HIVDB users are now provided with the option to exclude those ARVs not considered to be universally required.

The HIVDB GRT-IS was updated through a collaborative process to reflect changes in HIV drug resistance knowledge, treatment guidelines, and expert opinion. Such a process broadens consensus among experts and identifies areas requiring further study.

Partial Text

HIV-1 drug resistance is one of the main obstacles to the long-term effectiveness of antiretroviral (ARV) therapy. In upper-income countries, genotypic resistance testing (GRT) is performed routinely at diagnosis, treatment initiation, and at the time of virological failure (VF). In lower- and middle-income countries, it is performed in the public health sectors for ad hoc drug resistance surveillance and, increasingly, for managing patients with VF. Interpreting GRT results is one of the most difficult challenges facing HIV care providers because there are many drug-resistance mutations (DRMs) associated with each of the ARV classes. These DRMs have variable effects on in vitro ARV susceptibility and occur in many different combinations.

Decision support systems have become increasingly important for the interpretation of genetic sequences for clinical purposes. Such systems comprise rule-based systems designed to emulate consultation with a subject-matter expert and machine-learning systems that use an algorithm to arrive at an optimized result through the analysis of a large dataset. Machine-learning systems are useful for scenarios in which sufficient amounts of appropriate raw data are available for algorithm training and validation. Rule-based systems are useful for scenarios that require knowledge for which the raw data are either not available or are too heterogeneous to combine in a manner amenable to machine learning. Compared with machine-learning systems, rule-based systems have the advantage of being transparent and educational but the disadvantage of being subjective.

 

Source:

http://doi.org/10.1371/journal.pone.0181357

 

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