Outcome-guided Bayesian Clustering for Disease Subtype Discovery Using High-dimensional Transcriptomic Data

TL;DR

This paper introduces a Bayesian clustering method that integrates clinical and high-dimensional transcriptomic data to discover disease subtypes that are clinically meaningful, with improved accuracy demonstrated on breast cancer data.

Contribution

The novel GuidedBayesianClustering method fully combines clinical outcomes and omics data for disease subtype discovery, feature selection, and outcome-guided clustering within a Bayesian framework.

Findings

Outperforms existing methods in simulations and breast cancer data analysis.

Effectively identifies clinically relevant disease subtypes.

Selects disease-related genes with controlled false discovery rate.

Abstract

The discovery of disease subtypes is an essential step for developing precision medicine, and disease subtyping via omics data has become a popular approach. While promising, subtypes obtained from conventional approaches may not be necessarily associated with clinical outcomes. The collection of rich clinical data along with omics data has provided an unprecedented opportunity to facilitate the disease subtyping process and to discovery clinically meaningful disease subtypes. Thus, we developed an outcome-guided Bayesian clustering (GuidedBayesianClustering) method to fully integrate the clinical data and the high-dimensional omics data. A Gaussian mixed model framework was applied to perform sample clustering; a spike-and-slab prior was utilized to perform gene selection; a mixture model prior was employed to incorporate the guidance from a clinical outcome variable; and a decision framework was adopted to infer the false discovery rate of the selected genes. We deployed conjugate priors to facilitate efficient Gibbs sampling. Our proposed full Bayesian method is capable of simultaneously (i) obtaining sample clustering (disease subtype discovery); (ii) performing feature selection (select genes related to the disease subtype); and (iii) utilizing clinical outcome variable to guide the disease subtype discovery. The superior performance of the GuidedBayesianClustering was demonstrated through simulations and applications of breast cancer expression data.