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Open Access Methodology article

A novel approach for biomarker selection and the integration of repeated measures experiments from two assays

Benoit Liquet125*, Kim-Anh Lê Cao3, Hakim Hocini45 and Rodolphe Thiébaut125

Author Affiliations

1 Univ. Bordeaux, ISPED, centre INSERM U-897-Epidémiologie-Biostatistique, Bordeaux, F-33000, FRANCE

2 INSERM, ISPED, centre INSERM U-897-Epidémiologie-Biostatistique, Bordeaux, F-33000, FRANCE

3 Queensland Facility for Advanced Bioinformatics and the institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia

4 INSERM U955 Eq 16, UPEC Université, Créteil, FRANCE

5 Vaccine Research Institute ANRS, Paris, France

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BMC Bioinformatics 2012, 13:325  doi:10.1186/1471-2105-13-325

Published: 6 December 2012

Abstract

Background

High throughput ’omics’ experiments are usually designed to compare changes observed between different conditions (or interventions) and to identify biomarkers capable of characterizing each condition. We consider the complex structure of repeated measurements from different assays where different conditions are applied on the same subjects.

Results

We propose a two-step analysis combining a multilevel approach and a multivariate approach to reveal separately the effects of conditions within subjects from the biological variation between subjects. The approach is extended to two-factor designs and to the integration of two matched data sets. It allows internal variable selection to highlight genes able to discriminate the net condition effect within subjects. A simulation study was performed to demonstrate the good performance of the multilevel multivariate approach compared to a classical multivariate method. The multilevel multivariate approach outperformed the classical multivariate approach with respect to the classification error rate and the selection of relevant genes. The approach was applied to an HIV-vaccine trial evaluating the response with gene expression and cytokine secretion. The discriminant multilevel analysis selected a relevant subset of genes while the integrative multilevel analysis highlighted clusters of genes and cytokines that were highly correlated across the samples.

Conclusions

Our combined multilevel multivariate approach may help in finding signatures of vaccine effect and allows for a better understanding of immunological mechanisms activated by the intervention. The integrative analysis revealed clusters of genes, that were associated with cytokine secretion. These clusters can be seen as gene signatures to predict future cytokine response. The approach is implemented in the R package mixOmics (http://cran.r-project.org/ webcite) with associated tutorials to perform the analysisa.