Biomarker discovery using targeted maximum‐likelihood estimation: Application to the treatment of antiretroviral‐resistant HIV infection

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Abstract
Researchers in clinical science and bioinformatics frequently aim to learn which of a set of candidate biomarkers is important in determining a given outcome, and to rank the contributions of the candidates accordingly. This article introduces a new approach to research questions of this type, based on targeted maximum‐likelihood estimation of variable importance measures. The methodology is illustrated using an example drawn from the treatment of HIV infection. Specifically, given a list of candidate mutations in the protease enzyme of HIV, we aim to discover mutations that reduce clinical virologic response to antiretroviral regimens containing the protease inhibitor lopinavir. In the context of this data example, the article reviews the motivation for covariate adjustment in the biomarker discovery process. A standard maximum‐likelihood approach to this adjustment is compared with the targeted approach introduced here. Implementation of targeted maximum‐likelihood estimation in the context of biomarker discovery is discussed, and the advantages of this approach are highlighted. Results of applying targeted maximum‐likelihood estimation to identify lopinavir resistance mutations are presented and compared with results based on unadjusted mutation–outcome associations as well as results of a standard maximum‐likelihood approach to adjustment. The subset of mutations identified by targeted maximum likelihood as significant contributors to lopinavir resistance is found to be in better agreement with the current understanding of HIV antiretroviral resistance than the corresponding subsets identified by the other two approaches. This finding suggests that targeted estimation of variable importance represents a promising approach to biomarker discovery. Copyright © 2008 John Wiley & Sons, Ltd.