Download or read book Genome Wide Association Studies and Genomic Prediction written by Cedric Gondro and published by Humana Press. This book was released on 2017-04-30 with total page 566 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Genome wide association studies and genomic selection for crop improvement in the era of big data written by Nunzio D’Agostino and published by Frontiers Media SA. This book was released on 2023-05-05 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Multi Layered Genome Wide Association Prediction in Animals written by Ruidong Xiang and published by Frontiers Media SA. This book was released on 2022-04-29 with total page 116 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Genome Wide Association Studies written by Tatsuhiko Tsunoda and published by Springer Nature. This book was released on 2019-10-31 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Statistical Methods Computing and Resources for Genome Wide Association Studies written by Riyan Cheng and published by Frontiers Media SA. This book was released on 2021-08-24 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Machine Learning in Genome Wide Association Studies written by Ting Hu and published by Frontiers Media SA. This book was released on 2020-12-15 with total page 74 pages. Available in PDF, EPUB and Kindle. Book excerpt: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Download or read book Genome Wide Association Studies written by Krishnarao Appasani and published by Cambridge University Press. This book was released on 2016-01-14 with total page 449 pages. Available in PDF, EPUB and Kindle. Book excerpt: Experts from academia and industry highlight the potential of genome-wide association studies from basic science to clinical and biotechnological/pharmaceutical applications.
Download or read book Genetics Genomics and Breeding of Conifers written by Christophe Plomion and published by CRC Press. This book was released on 2011-08-10 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt: With contributions by internationally reputed researchers in the field, this book presents the implications of the genomic revolution for conifers—promoting a better understanding of the evolution of these organisms as well as new knowledge about the molecular basis of quantitative trait variation. Both of these discoveries play important roles in their domestication. Topics include cytogenetics, patterns of nucleotide diversity, genetic mapping, integration of molecular markers in breeding, transcriptomics, advances in proteomics and metabolomics in gymnosperms, and economic importance.
Download or read book Genomic Selection for Crop Improvement written by Rajeev K. Varshney and published by Springer. This book was released on 2017-12-05 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic Selection for Crop Improvement serves as handbook for users by providing basic as well as advanced understandings of genomic selection. This useful review explains germplasm use, phenotyping evaluation, marker genotyping methods, and statistical models involved in genomic selection. It also includes examples of ongoing activities of genomic selection for crop improvement and efforts initiated to deploy the genomic selection in some important crops. In order to understand the potential of GS breeding, it is high time to bring complete information in the form of a book that can serve as a ready reference for geneticist and plant breeders.
Download or read book Primer to Analysis of Genomic Data Using R written by Cedric Gondro and published by Springer. This book was released on 2015-05-18 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Through this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for graduate and undergraduate courses in bioinformatics and genomic analysis or for use in lab sessions. How to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R is also taught. A wide range of R packages useful for working with genomic data are illustrated with practical examples. The key topics covered are association studies, genomic prediction, estimation of population genetic parameters and diversity, gene expression analysis, functional annotation of results using publically available databases and how to work efficiently in R with large genomic datasets. Important principles are demonstrated and illustrated through engaging examples which invite the reader to work with the provided datasets. Some methods that are discussed in this volume include: signatures of selection, population parameters (LD, FST, FIS, etc); use of a genomic relationship matrix for population diversity studies; use of SNP data for parentage testing; snpBLUP and gBLUP for genomic prediction. Step-by-step, all the R code required for a genome-wide association study is shown: starting from raw SNP data, how to build databases to handle and manage the data, quality control and filtering measures, association testing and evaluation of results, through to identification and functional annotation of candidate genes. Similarly, gene expression analyses are shown using microarray and RNAseq data. At a time when genomic data is decidedly big, the skills from this book are critical. In recent years R has become the de facto tool for analysis of gene expression data, in addition to its prominent role in analysis of genomic data. Benefits to using R include the integrated development environment for analysis, flexibility and control of the analytic workflow. Included topics are core components of advanced undergraduate and graduate classes in bioinformatics, genomics and statistical genetics. This book is also designed to be used by students in computer science and statistics who want to learn the practical aspects of genomic analysis without delving into algorithmic details. The datasets used throughout the book may be downloaded from the publisher’s website.
Download or read book Integrative Analysis of Genome Wide Association Studies and Single Cell Sequencing Studies written by Sheng Yang and published by Frontiers Media SA. This book was released on 2021-09-09 with total page 113 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Genome wide Association Studies written by Tatsuhiko Tsunoda and published by . This book was released on 2019 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Association Mapping in Plants written by Nnadozie C. Oraguzie and published by Springer Science & Business Media. This book was released on 2007-01-06 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides both basic and advanced understanding of association mapping and an awareness of population genomics tools to facilitate mapping and identification of the underlying causes of quantitative trait variation in plants. It acts as a useful review of the marker technology, the statistical methodology, and the progress to date. It also offers guides to the use of single nucleotide polymorphisms (SNPs) in association studies.
Download or read book Methods in Statistical Genomics written by Philip Chester Cooley and published by RTI Press. This book was released on 2016-08-29 with total page 163 pages. Available in PDF, EPUB and Kindle. Book excerpt: The objective of this book is to describe procedures for analyzing genome-wide association studies (GWAS). Some of the material is unpublished and contains commentary and unpublished research; other chapters (Chapters 4 through 7) have been published in other journals. Each previously published chapter investigates a different genomics model, but all focus on identifying the strengths and limitations of various statistical procedures that have been applied to different GWAS scenarios.
Download or read book The Applications of New Multi Locus GWAS Methodologies in the Genetic Dissection of Complex Traits written by Yuan-Ming Zhang and published by Frontiers Media SA. This book was released on 2019-06-19 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Design Analysis and Interpretation of Genome Wide Association Scans written by Daniel O. Stram and published by Springer Science & Business Media. This book was released on 2013-11-23 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Genotyping by Sequencing for Crop Improvement written by Humira Sonah and published by John Wiley & Sons. This book was released on 2022-03-29 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: OGENOTYPING BY SEQUENCING FOR CROP IMPROVEMENT A thoroughly up-to-date exploration of genotyping-by-sequencing technologies and related methods in plant science In Genotyping by Sequencing for Crop Improvement, a team of distinguished researchers delivers an in-depth and current exploration of the latest advances in genotyping-by-sequencing (GBS) methods, the statistical approaches used to analyze GBS data, and its applications, including quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS) in crop improvement. This edited volume includes insightful contributions on a variety of relevant topics, like advanced molecular markers, high-throughput genotyping platforms, whole genome resequencing, QTL mapping with advanced mapping populations, analytical pipelines for GBS analysis, and more. The distinguished contributors explore traditional and advanced markers used in plant genotyping in extensive detail, and advanced genotyping platforms that cater to unique research purposes are discussed, as is the whole-genome resequencing (WGR) methodology. The included chapters also examine the applications of these technologies in several different crop categories, including cereals, pulses, oilseeds, and commercial crops. Genotyping by Sequencing for Crop Improvement also offers: A thorough introduction to molecular marker techniques and recent advancements in the technology Comprehensive explorations of the genotyping of seeds while preserving their viability, as well as advances in genomic selection Practical discussions of opportunities and challenges relating to high throughput genotyping in polyploid crops In-depth examinations of recent advances and applications of GBS, GWAS, and GS in cereals, pulses, oilseeds, millets, and commercial crops Perfect for practicing plant scientists with an interest in genotyping-by-sequencing technology, Genotyping by Sequencing for Crop Improvement will also earn a place in the libraries of researchers and students seeking a one-stop reference on the foundational aspects of – and recent advances in – genotyping-by-sequencing, genome-wide association studies, and genomic selection.
