Genotype To Phenotype

This timely text presents a comprehensive guide to genetic association, a new and rapidly expanding field that aims to elucidate how our genetic code (genotypes) influences the traits we possess (phenotypes). The book provides a detailed review of methods of gene mapping used in association with experimental crosses, as well as genome-wide association studies. Emphasis is placed on model selection procedures for analyzing data from large-scale genome scans based on specifically designed modifications of the Bayesian information criterion. Features: presents a thorough introduction to the theoretical background to studies of genetic association (both genetic and statistical); reviews the latest advances in the field; illustrates the properties of methods for mapping quantitative trait loci using computer simulations and the analysis of real data; discusses open challenges; includes an extensive statistical appendix as a reference for those who are not totally familiar with the fundamentals of statistics.

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.

This new edition builds on the success of the first by reviewing the increased understanding of the mechanisms of gene action in humans, focusing particularly on those derived from the study of genetic diseases. It deals mainly with the fundamental aspects of gene arrangement and expression rather than mutation. As well as updating and revising material from the first edition, it covers methods of exploring gene function and contains a range of chapters on specific systems which raise issues of special interest such as imprinting or homologous genes within clusters.

Illuminating the processes and patterns that link genotype to phenotype, epigenetics seeks to explain features, characters, and developmental mechanisms that can only be understood in terms of interactions that arise above the level of the gene. With chapters written by leading authorities, this volume offers a broad integrative survey of epigenetics. Approaching this complex subject from a variety of perspectives, it presents a broad, historically grounded view that demonstrates the utility of this approach for understanding complex biological systems in development, disease, and evolution. Chapters cover such topics as morphogenesis and organ formation, conceptual foundations, and cell differentiation, and together demonstrate that the integration of epigenetics into mainstream developmental biology is essential for answering fundamental questions about how phenotypic traits are produced.

A Probabilistic Model of the Genotype/Phenotype Relationship provides a new hypothesis on the relationship between genotype and phenotype. The main idea of the book is that this relationship is probabilistic, in other words, the genotype does not fully explain the phenotype. This idea is developed and discussed using the current knowledge on complex genetic diseases, phenotypic plasticity, canalization and others.

This new edition builds on the success of the first by reviewing the increased understanding of the mechanisms of gene action in humans, focusing particularly on those derived from the study of genetic diseases. It deals mainly with the fundamental aspects of gene arrangement and expression rather than mutation. As well as updating and revising material from the first edition, it covers methods of exploring gene function and contains a range of chapters on specific systems which raise issues of special interest such as imprinting or homologous genes within clusters.

In The Selfish Gene, Richard Dawkins crystallized the gene's eye view of evolution developed by W.D. Hamilton and others. The book provoked widespread and heated debate. Written in part as a response, The Extended Phenotype gave a deeper clarification of the central concept of the gene as the unit of selection; but it did much more besides. In it, Dawkins extended the gene's eye view to argue that the genes that sit within an organism have an influence that reaches out beyond the visible traits in that body - the phenotype - to the wider environment, which can include other individuals. So, for instance, the genes of the beaver drive it to gather twigs to produce the substantial physical structure of a dam; and the genes of the cuckoo chick produce effects that manipulate the behaviour of the host bird, making it nurture the intruder as one of its own. This notion of the extended phenotype has proved to be highly influential in the way we understand evolution and the natural world. It represents a key scientific contribution to evolutionary biology, and it continues to play an important role in research in the life sciences. The Extended Phenotype is a conceptually deep book that forms important reading for biologists and students. But Dawkins' clear exposition is accessible to all who are prepared to put in a little effort. Oxford Landmark Science books are 'must-read' classics of modern science writing which have crystallized big ideas, and shaped the way we think.

Scientific Frontiers in Developmental Toxicology and Risk Assessment reviews advances made during the last 10-15 years in fields such as developmental biology, molecular biology, and genetics. It describes a novel approach for how these advances might be used in combination with existing methodologies to further the understanding of mechanisms of developmental toxicity, to improve the assessment of chemicals for their ability to cause developmental toxicity, and to improve risk assessment for developmental defects. For example, based on the recent advances, even the smallest, simplest laboratory animals such as the fruit fly, roundworm, and zebrafish might be able to serve as developmental toxicological models for human biological systems. Use of such organisms might allow for rapid and inexpensive testing of large numbers of chemicals for their potential to cause developmental toxicity; presently, there are little or no developmental toxicity data available for the majority of natural and manufactured chemicals in use. This new approach to developmental toxicology and risk assessment will require simultaneous research on several fronts by experts from multiple scientific disciplines, including developmental toxicologists, developmental biologists, geneticists, epidemiologists, and biostatisticians.