Genome-Wide Association Studies and Genomic Prediction

by Cedric Gondro

Author	: Cedric Gondro
Publisher	: Humana Press
Total Pages	: 0
Release	: 2013-06-12
Genre	: Science
ISBN	: 9781627034463

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With the detailed genomic information that is now becoming available, we have a plethora of data that allows researchers to address questions in a variety of areas. Genome-wide association studies (GWAS) have become a vital approach to identify candidate regions associated with complex diseases in human medicine, production traits in agriculture, and variation in wild populations. Genomic prediction goes a step further, attempting to predict phenotypic variation in these traits from genomic information. Genome-Wide Association Studies and Genomic Prediction pulls together expert contributions to address this important area of study. The volume begins with a section covering the phenotypes of interest as well as design issues for GWAS, then moves on to discuss efficient computational methods to store and handle large datasets, quality control measures, phasing, haplotype inference, and imputation. Later chapters deal with statistical approaches to data analysis where the experimental objective is either to confirm the biology by identifying genomic regions associated to a trait or to use the data to make genomic predictions about a future phenotypic outcome (e.g. predict onset of disease). As part of the Methods in Molecular Biology series, chapters provide helpful, real-world implementation advice.

Genome-Wide Association Studies

by Krishnarao Appasani

Author	: Krishnarao Appasani
Publisher	: Cambridge University Press
Total Pages	: 449
Release	: 2016-01-14
Genre	: Medical
ISBN	: 1107042763

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Experts from academia and industry highlight the potential of genome-wide association studies from basic science to clinical and biotechnological/pharmaceutical applications.

Genome-Wide Association Studies

by Tatsuhiko Tsunoda

Author	: Tatsuhiko Tsunoda
Publisher	: Springer Nature
Total Pages	: 216
Release	: 2019-10-31
Genre	: Medical
ISBN	: 9811381771

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This book examines the utility of genome-wide association studies (GWAS) in the era of next-generation sequencing and big data, identifies limitations and potential means of overcoming them, and looks to the future of GWAS and what may lay beyond. GWAS are among the most powerful tools for elucidating the genetic aspects of human and disease diversity. In Genome-Wide Association Studies, experts in the field explore in depth the impacts of GWAS on genomic research into a variety of common diseases, including cardiovascular, autoimmune, diabetic, cancer, and infectious diseases. The book will equip readers with a sound understanding both of the types of disease and phenotypes that are suited for GWAS and of the ways in which a road map resulting from GWAS can lead to the realization of personalized/precision medicine: functional analysis, drug seeds, pathway analysis, disease mechanism, risk prediction, and diagnosis.

Genetic Dissection of Complex Traits

by D.C. Rao

Author	: D.C. Rao
Publisher	: Academic Press
Total Pages	: 788
Release	: 2008-04-23
Genre	: Medical
ISBN	: 0080569110

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The field of genetics is rapidly evolving and new medical breakthroughs are occuring as a result of advances in knowledge of genetics. This series continually publishes important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines. Five sections on the latest advances in complex traits Methods for testing with ethical, legal, and social implications Hot topics include discussions on systems biology approach to drug discovery; using comparative genomics for detecting human disease genes; computationally intensive challenges, and more

Design, Analysis, and Interpretation of Genome-Wide Association Scans

by Daniel O. Stram

Author	: Daniel O. Stram
Publisher	: Springer Science & Business Media
Total Pages	: 344
Release	: 2013-11-23
Genre	: Medical
ISBN	: 1461494435

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This book presents the statistical aspects of designing, analyzing and interpreting the results of genome-wide association scans (GWAS studies) for genetic causes of disease using unrelated subjects. Particular detail is given to the practical aspects of employing the bioinformatics and data handling methods necessary to prepare data for statistical analysis. The goal in writing this book is to give statisticians, epidemiologists, and students in these fields the tools to design a powerful genome-wide study based on current technology. The other part of this is showing readers how to conduct analysis of the created study. Design and Analysis of Genome-Wide Association Studies provides a compendium of well-established statistical methods based upon single SNP associations. It also provides an introduction to more advanced statistical methods and issues. Knowing that technology, for instance large scale SNP arrays, is quickly changing, this text has significant lessons for future use with sequencing data. Emphasis on statistical concepts that apply to the problem of finding disease associations irrespective of the technology ensures its future applications. The author includes current bioinformatics tools while outlining the tools that will be required for use with extensive databases from future large scale sequencing projects. The author includes current bioinformatics tools while outlining additional issues and needs arising from the extensive databases from future large scale sequencing projects.

Handbook of Statistical Genomics

by David J. Balding

Author	: David J. Balding
Publisher	: John Wiley & Sons
Total Pages	: 1740
Release	: 2019-07-09
Genre	: Science
ISBN	: 1119429250

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A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.

Analysis of Complex Disease Association Studies

by Eleftheria Zeggini

Author	: Eleftheria Zeggini
Publisher	: Academic Press
Total Pages	: 353
Release	: 2010-11-17
Genre	: Medical
ISBN	: 0123751438

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According to the National Institute of Health, a genome-wide association study is defined as any study of genetic variation across the entire human genome that is designed to identify genetic associations with observable traits (such as blood pressure or weight), or the presence or absence of a disease or condition. Whole genome information, when combined with clinical and other phenotype data, offers the potential for increased understanding of basic biological processes affecting human health, improvement in the prediction of disease and patient care, and ultimately the realization of the promise of personalized medicine. In addition, rapid advances in understanding the patterns of human genetic variation and maturing high-throughput, cost-effective methods for genotyping are providing powerful research tools for identifying genetic variants that contribute to health and disease. This burgeoning science merges the principles of statistics and genetics studies to make sense of the vast amounts of information available with the mapping of genomes. In order to make the most of the information available, statistical tools must be tailored and translated for the analytical issues which are original to large-scale association studies. Analysis of Complex Disease Association Studies will provide researchers with advanced biological knowledge who are entering the field of genome-wide association studies with the groundwork to apply statistical analysis tools appropriately and effectively. With the use of consistent examples throughout the work, chapters will provide readers with best practice for getting started (design), analyzing, and interpreting data according to their research interests. Frequently used tests will be highlighted and a critical analysis of the advantages and disadvantage complimented by case studies for each will provide readers with the information they need to make the right choice for their research. Additional tools including links to analysis tools, tutorials, and references will be available electronically to ensure the latest information is available. - Easy access to key information including advantages and disadvantage of tests for particular applications, identification of databases, languages and their capabilities, data management risks, frequently used tests - Extensive list of references including links to tutorial websites - Case studies and Tips and Tricks

Ecological Genomics

by Christian R. Landry

Author	: Christian R. Landry
Publisher	: Springer Science & Business Media
Total Pages	: 358
Release	: 2013-11-25
Genre	: Science
ISBN	: 9400773471

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Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. We provide an advanced-level book that covers this recent research and proposes future development for this field. A synthesis of the field of ecological genomics emerges from this volume. Ecological Genomics covers a wide array of organisms (microbes, plants and animals) in order to be able to identify central concepts that motivate and derive from recent investigations in different branches of the tree of life. Ecological Genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation.

The Applications of New Multi-Locus GWAS Methodologies in the Genetic Dissection of Complex Traits

by Yuan-Ming Zhang

Author	: Yuan-Ming Zhang
Publisher	: Frontiers Media SA
Total Pages	: 236
Release	: 2019-06-19
Genre	:
ISBN	: 2889458342

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Genome-Wide Association Studies (GWAS) are widely used in the genetic dissection of complex traits. Most existing methods are based on single-marker association in genome-wide scans with population structure and polygenic background controls. To control the false positive rate, the Bonferroni correction for multiple tests is frequently adopted. This stringent correction results in the exclusion of important loci, especially for GWAS in crop genetics. To address this issue, multi-locus GWAS methodologies have been recommended, i.e., FASTmrEMMA, ISIS EM-BLASSO, mrMLM, FASTmrMLM, pLARmEB, pKWmEB and FarmCPU. In this Research Topic, our purpose is to clarify some important issues in the application of multi-locus GWAS methods. Here we discuss the following subjects: First, we discuss the advantages of new multi-locus GWAS methods over the widely-used single-locus GWAS methods in the genetic dissection of complex traits, metabolites and gene expression levels. Secondly, large experiment error in the field measurement of phenotypic values for complex traits in crop genetics results in relatively large P-values in GWAS, indicating the existence of small number of significantly associated SNPs. To solve this issue, a less stringent P-value critical value is often adopted, i.e., 0.001, 0.0001 and 1/m (m is the number of markers). Although lowering the stringency with which an association is made could identify more hits, confidence in these hits would significantly drop. In this Research Topic we propose a new threshold of significant QTN (LOD=3.0 or P-value=2.0e-4) in multi-locus GWAS to balance high power and low false positive rate. Thirdly, heritability missing in GWAS is a common phenomenon, and a series of scientists have explained the reasons why the heritability is missing. In this Research Topic, we also add one additional reason and propose the joint use of several GWAS methodologies to capture more QTNs. Thus, overall estimated heritability would be increased. Finally, we discuss how to select and use these multi-locus GWAS methods.