Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach

Abstract

Abstract Background One of the main current challenges in computational biology is to make sense of the huge amounts of multidimensional experimental data that are being produced. For instance, large cohorts of patients are often screened using different high-throughput technologies, effectively producing multiple patient-specific molecular profiles for hundreds or thousands of patients. Results We propose and implement a network-based method that integrates such patient omics data into Patient Similarity Networks. Topological features derived from these networks were then used to predict relevant clinical features. As part of the 2017 CAMDA challenge, we have successfully applied this strategy to a neuroblastoma dataset, consisting of genomic and transcriptomic data. In particular, we observe that models built on our network-based approach perform at least as well as state of the art models. We furthermore explore the effectiveness of various topological features and observe, for instance, that redundant centrality metrics can be combined to build more powerful models. Conclusion We demonstrate that the networks inferred from omics data contain clinically relevant information and that patient clinical outcomes can be predicted using only network topological data. Reviewers This article was reviewed by Yang-Yu Liu, Tomislav Smuc and Isabel Nepomuceno.

Keywords

• Biological networks
• Network-based methods
• Network topology