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. 2012 Sep;13(5):513-23.
doi: 10.1093/bib/bbs008. Epub 2012 Mar 6.

Adjusting confounders in ranking biomarkers: a model-based ROC approach

Tao Yu  1 , Jialiang Li, Shuangge Ma
Affiliations

Adjusting confounders in ranking biomarkers: a model-based ROC approach

Tao Yu et al. Brief Bioinform. 2012 Sep.

Abstract

High-throughput studies have been extensively conducted in the research of complex human diseases. As a representative example, consider gene-expression studies where thousands of genes are profiled at the same time. An important objective of such studies is to rank the diagnostic accuracy of biomarkers (e.g. gene expressions) for predicting outcome variables while properly adjusting for confounding effects from low-dimensional clinical risk factors and environmental exposures. Existing approaches are often fully based on parametric or semi-parametric models and target evaluating estimation significance as opposed to diagnostic accuracy. Receiver operating characteristic (ROC) approaches can be employed to tackle this problem. However, existing ROC ranking methods focus on biomarkers only and ignore effects of confounders. In this article, we propose a model-based approach which ranks the diagnostic accuracy of biomarkers using ROC measures with a proper adjustment of confounding effects. To this end, three different methods for constructing the underlying regression models are investigated. Simulation study shows that the proposed methods can accurately identify biomarkers with additional diagnostic power beyond confounders. Analysis of two cancer gene-expression studies demonstrates that adjusting for confounders can lead to substantially different rankings of genes.

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Figures

Figure 1:
Figure 1:
Simulation study with binary response. Upper four panels: AUC of X41 vs. X54. Lower four panels: AUC of X41 vs. X598. Solid green line: 45° reference line.
See this image and copyright information in PMC

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