Added predictive value of omics data: specific issues related to validation illustrated by two case studies

BACKGROUND In the last years, the importance of independent validation of the prediction ability of a new gene signature has been largely recognized. Recently, with the development of gene signatures which integrate rather than replace the clinical predictors in the prediction rule, the focus has been moved to the validation of the added predictive value of a gene signature, i.e. to the verification that the inclusion of the new gene signature in a prediction model is able to improve its prediction ability. METHODS The high-dimensional nature of the data from which a new signature is derived raises challenging issues and necessitates the modification of classical methods to adapt them to this framework. Here we show how to validate the added predictive value of a signature derived from high-dimensional data and critically discuss the impact of the choice of methods on the results. RESULTS The analysis of the added predictive value of two gene signatures developed in two recent studies on the survival of leukemia patients allows us to illustrate and empirically compare different validation techniques in the high-dimensional framework. CONCLUSIONS The issues related to the high-dimensional nature of the omics predictors space affect the validation process. An analysis procedure based on repeated cross-validation is suggested.