Characterizing classes of antiretroviral drugs by genotype

This paper develops methods for using HIV-1 genotypic information to group patients who are expected to have similar patterns of sensitivity or resistance to two or more drugs. The methods presented are an extension of prediction based classification to handle multiple drug responses. Here, the goal is to determine the probability that one antiretroviral therapy will be more favourable than another for an individual given the specific genotypic or other characteristics of the infecting viral population. This approach requires a model relating genotype to a vector of drug specific phenotypic responses. A comparison of Nelfinavir and Indinavir is provided using 2746 protease sequences and corresponding in vitro sensitivity assays provided to us by the Virco Group.