Netboost: Boosting-supported network analysis improves high-dimensional omics prediction in acute myeloid leukemia and Huntington's disease

TL;DR

Netboost is a novel three-step network-based dimension reduction method that enhances high-dimensional omics data analysis, improving prediction accuracy in diseases like AML and Huntington's disease.

Contribution

Netboost introduces a boosting-supported network analysis technique that effectively identifies relevant features and modules in high-dimensional omics datasets, outperforming traditional methods.

Findings

Improves survival prediction in AML using DNA methylation and gene expression data.

Enhances disease classification accuracy in Huntington's disease mouse models.

Replicates key signatures in independent AML datasets.

Abstract

Background: State-of-the art selection methods fail to identify weak but cumulative effects of features found in many high-dimensional omics datasets. Nevertheless, these features play an important role in certain diseases. Results: We present Netboost, a three-step dimension reduction technique. First, a boosting-based filter is combined with the topological overlap measure to identify the essential edges of the network. Second, sparse hierarchical clustering is applied on the selected edges to identify modules and finally module information is aggregated by the first principal components. The primary analysis is than carried out on these summary measures instead of the original data. We demonstrate the application of the newly developed Netboost in combination with CoxBoost for survival prediction of DNA methylation and gene expression data from 180 acute myeloid leukemia (AML) patients and show, based on cross-validated prediction error curve estimates, its prediction superiority over variable selection on the full dataset as well as over an alternative clustering approach. The identified signature related to chromatin modifying enzymes was replicated in an independent dataset of AML patients in the phase II AMLSG 12-09 study. In a second application we combine Netboost with Random Forest classification and improve the disease classification error in RNA-sequencing data of Huntington's disease mice. Conclusion: Netboost improves definition of predictive variables for survival analysis and classification. It is a freely available Bioconductor R package for dimension reduction and hypothesis generation in high-dimensional omics applications.