can survival prediction be improved by merging gene expression data sets生存预测可以提高融合基因表达数据集.pdfVIP

Can Survival Prediction Be Improved By Merging Gene Expression Data Sets? 1,2 2 2 1,2 Haleh Yasrebi *, Peter Sperisen , Viviane Praz , Philipp Bucher 1 Swiss Institute for Experimental Cancer Research (ISREC), Swiss Federal Institute of Technology (EPFL), School of Life Sciences, EPFL SV ISREC, Lausanne, Switzerland, 2 Swiss Institute of Bioinformatics, EPFL SV ISREC, Lausanne, Switzerland Abstract Background: High-throughput gene expression profiling technologies generating a wealth of data, are increasingly used for characterization of tumor biopsies for clinical trials. By applying machine learning algorithms to such clinically documented data sets, one hopes to improve tumor diagnosis, prognosis, as well as prediction of treatment response. However, the limited number of patients enrolled in a single trial study limits the power of machine learning approaches due to over- fitting. One could partially overcome this limitation by merging data from different studies. Nevertheless, such data sets differ from each other with regard to technical biases, patient selection criteria and follow-up treatment. It is therefore not clear at all whether the advantage of increased sample size outweighs the disadvantage of higher heterogeneity of merged data sets. Here, we present a systematic study to answer this question specifically for breast cancer data sets. We use survival prediction based on Cox regression as an assay to measure the added value of merged data sets. Results: Using time-dependent Receiver Operating Characteristic-Area Under the Curve (ROC-AUC) and hazard ratio as performance measures, we see in overall no significant improvement or deterioration of survival prediction with merged data sets as compared to individual data sets