Phenotypes and Genotypes Search for Influential Genes

This book presents the methodology of association mapping in experimental populations and genome-wide association studies (GWAS). The main emphasis is placed on methods based on modifications of the Bayesian information criterion, designed specifically to handle multiple testing problems in large-scale genome scans for trait loci (TL). The book is written at the level of a graduate course for bioinformatics students. The first chapter introduces the major concepts of quantitative trait loci (QTL) mapping. The second chapter discusses the methodology of QTL mapping in experimental populations, with the main emphasis on the related issues of model selection in linear models. The approach is then extended to TL via generalized linear models. Chapter three describes the methods for GWAS and related multiple testing and model selection problems. In both chapters two and three the properties of QTL mapping methods are illustrated with computer simulations and real data analysis.