Integrative Bayesian tensor regression for imaging genetics applications

• Authors: Yajie Liu, The University of Texas, Houston; Nilanjana Chakraborty, University of Pennsylvania; Zhaohui Qin, Emory University; Suprateek Kundu, The University if Texas, Houston
• Journal Title: Frontiers in Neuroscience
• Volume: Volume 17
• Publisher: Frontiers | 2023-08-23, Pages 1212218-None
• Type of Work: Article | Final Publisher PDF
• Publisher DOI: http://doi.org/10.3389/fnins.2023.1212218
• Subjects: Biology, Biostatistics; Health Sciences, General
• Keywords: alzheimer's disease; Bayesian tensor regression models; collinearity; imaging genetics analysis; transcriptomics

Abstract

Identifying biomarkers for Alzheimer's disease with a goal of early detection is a fundamental problem in clinical research. Both medical imaging and genetics have contributed informative biomarkers in literature. To further improve the performance, recently, there is an increasing interest in developing analytic approaches that combine data across modalities such as imaging and genetics. However, there are limited methods in literature that are able to systematically combine high-dimensional voxel-level imaging and genetic data for accurate prediction of clinical outcomes of interest. Existing prediction models that integrate imaging and genetic features often use region level imaging summaries, and they typically do not consider the spatial configurations of the voxels in the image or incorporate the dependence between genes that may compromise prediction ability. We propose a novel integrative Bayesian scalar-on-image regression model for predicting cognitive outcomes based on high-dimensional spatially distributed voxel-level imaging data, along with correlated transcriptomic features. We account for the spatial dependencies in the imaging voxels via a tensor approach that also enables massive dimension reduction to address the curse of dimensionality, and models the dependencies between the transcriptomic features via a Graph-Laplacian prior. We implement this approach via an efficient Markov chain Monte Carlo (MCMC) computation strategy. We apply the proposed method to the analysis of longitudinal ADNI data for predicting cognitive scores at different visits by integrating voxel-level cortical thickness measurements derived from T1w-MRI scans and transcriptomics data. We illustrate that the proposed imaging transcriptomics approach has significant improvements in prediction compared to prediction using a subset of features from only one modality (imaging or genetics), as well as when using imaging and transcriptomics features but ignoring the inherent dependencies between the features. Our analysis is one of the first to conclusively demonstrate the advantages of prediction based on combining voxel-level cortical thickness measurements along with transcriptomics features, while accounting for inherent structural information.