A comparison of genomic profiles of complex diseases under different models

Background: Various approaches are being used to predict individual risk to polygenic diseases from data provided by genome-wide association studies. As there are substantial differences between the diseases investigated, the data sets used and the way they are tested, it is difficult to assess which models are more suitable for this task. Results: We compared different approaches for seven complex diseases provided by the Wellcome Trust Case Control Consortium (WTCCC) under a within-study validation approach. Risk models were inferred using a variety of learning machines and assumptions about the underlying genetic model, including a haplotype-based approach with different haplotype lengths and different thresholds in association levels to choose loci as part of the predictive model. In accordance with previous work, our results generally showed low accuracy considering disease heritability and population prevalence. However, the boosting algorithm returned a predictive area under the ROC curve (AUC) of 0.8805 for Type 1 diabetes (T1D) and 0.8087 for rheumatoid arthritis, both clearly over the AUC obtained by other approaches and over 0.75, which is the minimum required for a disease to be successfully tested on a sample at risk, which means that boosting is a promising approach. Its good performance seems to be related to its robustness to redundant data, as in the case of genome-wide data sets due to linkage disequilibrium. Conclusions: In view of our results, the boosting approach may be suitable for modeling individual predisposition to Type 1 diabetes and rheumatoid arthritis based on genome-wide data and should be considered for more in-depth research.This work was supported by the Spanish Secretary of Research, Development and Innovation [TIN2010-20900-C04-1]; the Spanish Health Institute Carlos III [PI13/02714]and [PI13/01527] and the Andalusian Research Program under project P08-TIC-03717 with the help of the European Regional Development Fund (ERDF). The authors are very grateful to the reviewers, as they believe that their comments have helped to substantially improve the quality of the paper