Characterizing the Relationship Between HIV-1 Genotype and Phenotype: Prediction-Based Classification

This paper establishes a framework for understanding the complex relationships between HIV-1 genotypic markers of resistance to antiretroviral drugs and clinical measures of disease progression. A new classification scheme based on the probabilities of how new patients will respond to antiretroviral therapy given the available data is proposed as a method for distinguishing among groups of viral sequences. This approach draws from existing cluster analysis, discriminant analysis, and recursive partitioning techniques and requires a model relating genotypic characteristics to phenotypic response. A data set of 2746 sequences and the corresponding Indinavir 50% inhibitory concentrations are described and used for illustrative purposes.