BiGen: Integrative Clinical and Brain-Imaging Genetics Analysis Using Structural Equation Model

The identification of genetic variants associated with complex brain diseases has evolved in the past decades. Studies in the field have taken different approaches and study designs including genome-wide association studies. Neuroimaging and connectomics have also improved our understanding of the structural connectivity of the human brain and produced reliable measurements. Combining both neuroimaging and genetic characteristics significantly contributes to understand their complex relationship in affecting behaviour and cognition. Throughout this thesis we proposed analysis pipeline to study the association between imaging and genetics of two different types of brain disease, which is, Alzheimers disease and glioblastoma. We observe the need for a unified model to study the complex interplay between genetic, environmental and clinical, neuroimaging and phenotype features. In this chapter, we developed BiGen, a mathematical model to measure the inter-correlation structure through the integration of genetic, environmental, neuroimaging and disease measurements. We utilised the structural equation model and used a path construct of latent variables to study the hidden association between genes and brain-related diseases, mediated by connectivity characteristics. We applied BiGen to simulated data and to a dataset from the Alzheimers Disease Neuroimaging Initiative.