title: Predicting response to antiretroviral treatment by machine learning: the EuResist project.
abstract: For a long time, the clinical management of antiretroviral drug resistance was based on sequence analysis of the HIV genome followed by estimating drug susceptibility from the mutational pattern that was detected. The large number of anti-HIV drugs and HIV drug resistance mutations has prompted the development of computer-aided genotype interpretation systems, typically comprising rules handcrafted by experts via careful examination of in vitro and in vivo resistance data. More recently, machine learning approaches have been applied to establish data-driven engines able to indicate the most effective treatments for any patient and virus combination. Systems of this kind, currently including the Resistance Response Database Initiative and the EuResist engine, must learn from the large data sets of patient histories and can provide an objective and accurate estimate of the virological response to different antiretroviral regimens. The EuResist engine was developed by a European consortium of HIV and bioinformatics experts and compares favorably with the most commonly used genotype interpretation systems and HIV drug resistance experts. Next-generation treatment response prediction engines may valuably assist the HIV specialist in the challenging task of establishing effective regimens for patients harboring drug-resistant virus strains. The extensive collection and accurate processing of increasingly large patient data sets are eagerly awaited to further train and translate these systems from prototype engines into real-life treatment decision support tools.
authors.affiliation: Department of Biotechnology, University of Siena, Siena, Italy. zazzi@unisi.it
authors.forename: Maurizio
authors.initials: M
authors.lastname: Zazzi
authors.forename: Francesca
authors.initials: F
authors.lastname: Incardona
authors.forename: Michal
authors.initials: M
authors.lastname: Rosen-Zvi
authors.forename: Mattia
authors.initials: M
authors.lastname: Prosperi
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer
authors.forename: Andre
authors.initials: A
authors.lastname: Altmann
authors.forename: Anders
authors.initials: A
authors.lastname: Sonnerborg
authors.forename: Tamar
authors.initials: T
authors.lastname: Lavee
authors.forename: Eugen
authors.initials: E
authors.lastname: Schülter
authors.forename: Rolf
authors.initials: R
authors.lastname: Kaiser
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology / Q000627:therapeutic use; D001185:Artificial Intelligence; D024882:Drug Resistance, Viral; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology*; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008826:Microbial Sensitivity Tests / Q000379:methods*
chemical_list: D019380:Anti-HIV Agents