UC Berkeley

Statistical and computational methods are seeing a growing role in genetic epidemiology and pharmacogenomics. Genetic epidemiology is the study of the interplay between genetic and environmental factors on human health and disease in populations. Pharmacogenomics is the study of how genes affect response to drugs. Chapter 2 illustrates an admixture mapping study of multiple sclerosis from local ancestry estimates provided by a linear-chain random conditional field. Chapter 3 shows the application of regression-based methods and causal inference principles to study the relationship between genotype and DNA methylation of human labial salivary glands in Sjogren's syndrome. Chapter 4 applies variational autoencoder to perform dimensionality reduction on DNA methylation data for discovery of clinically-relevant disease subtypes in Sjogren's syndrome. Chapter 5 applies sparse canonical correlation analysis to summarize gene expression-drug sensitivity associations and introduces a nuclear norm-based dissimilarity measure to compare associations from different cell line groups in pharmacogenomic studies. Finally, Chapter 6 presents a 1D convolutional neural network model for imputing human leukocyte antigen alleles from phased genotype data.