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 Design and Analysis of Genome wide Association Studies written by Jeffrey Charles Barrett and published by . This book was released on 2008 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Genetic Analysis of Complex Disease written by William K. Scott and published by John Wiley & Sons. This book was released on 2021-12-06 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic Analysis of Complex Diseases An up-to-date and complete treatment of the strategies, designs and analysis methods for studying complex genetic disease in human beings In the newly revised Third Edition of Genetic Analysis of Complex Diseases, a team of distinguished geneticists delivers a comprehensive introduction to the most relevant strategies, designs and methods of analysis for the study of complex genetic disease in humans. The book focuses on concepts and designs, thereby offering readers a broad understanding of common problems and solutions in the field based on successful applications in the design and execution of genetic studies. This edited volume contains contributions from some of the leading voices in the area and presents new chapters on high-throughput genomic sequencing, copy-number variant analysis and epigenetic studies. Providing clear and easily referenced overviews of the considerations involved in genetic analysis of complex human genetic disease, including sampling, design, data collection, linkage and association studies and social, legal and ethical issues. Genetic Analysis of Complex Diseases also provides: A thorough introduction to study design for the identification of genes in complex traits Comprehensive explorations of basic concepts in genetics, disease phenotype definition and the determination of the genetic components of disease Practical discussions of modern bioinformatics tools for analysis of genetic data Reflecting on responsible conduct of research in genetic studies, as well as linkage analysis and data management New expanded chapter on complex genetic interactions This latest edition of Genetic Analysis of Complex Diseases is a must-read resource for molecular biologists, human geneticists, genetic epidemiologists and pharmaceutical researchers. It is also invaluable for graduate students taking courses in statistical genetics or genetic epidemiology.

Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1828 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

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 2013-06-12 with total page 0 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 Efficient Design and Analysis of Genome wide Association Studies written by Emrah Kostem and published by . This book was released on 2013 with total page 88 pages. Available in PDF, EPUB and Kindle. Book excerpt: The recent advances in genomic technologies, have made it possible to collect large-scale information on genetic variation across a diverse biological landscape. This has resulted in an exponential influx of genetic information and the field of genetics has become data-rich in a relatively short amount of time. These developments have opened new avenues to elucidate the genetic basis of complex diseases, where the traditional disease study approaches had little success. In recent years, the genome-wide association study (GWAS) approach has gained widespread popularity for its ease of use and effectiveness, and is now the standard approach to study complex diseases. In GWAS, information on millions of single-nucleotide polymorphisms (SNPs) is collected from case and control individuals. SNP genotyping is cost-effective and due to their abundance in the genome, SNPs are correlated to their neighboring genetic variation, which makes them tags for genomic regions. Typically, each SNP is statistically tested for association to disease, and the genomic regions tagged by the significant SNPs are believed to be harboring the functional variants contributing to disease. In order to reduce the cost of GWAS and the redundancy in the information collected, an informative subset of the SNPs, or tag SNPs, are genotyped. Typically, the genomic regions harboring the significantly associated tag SNPs may be large and contain many additional polymorphisms. At this stage of the study it may not be clear which specific genes or polymorphisms are in fact most strongly associated to disease. We present a novel framework for designing cost-effective follow-up association studies to further characterize such regions by genotyping additional SNPs to identify all the associated polymorphisms. This identification of all associated polymorphisms provides a catalog of all possible functional variants, and the values of the actual association statistics at these polymorphisms may provide information to identify causal variants. We present the utility of our method in identifying significant associations and causal variants using simulated and real GWAS datasets. Although GWAS have been widely used to study associations of SNPs to disease phenotypes, there has been growing interest in applying the GWAS approach to high-throughput biological phenotypes, such as gene expression. In these studies, the goal is to identify genomic regions that affect gene expression levels, known as expression quantitative trait loci (eQTL). A challenge in applying GWAS to eQTL studies is that there are tens of thousands of measurements, each representing the expression level of one gene, for each sample tested, as opposed to values for one or two clinical traits. This results in a tremendous computational burden when performing the analysis, requiring computation for billions of tests and demands substantial computational resources. We present a novel two-stage approach to efficiently identify all of the significant associations without testing all the SNPs. In the first-stage, a small number of informative SNPs across the genome are tested. Based on their observed associations, our approach locates the regions that may contain significant SNPs and only tests additional SNPs from those regions. We demonstrate that this method increases the computational speed of eQTL studies by a factor of ten, and can be applied to reduce the computational burden of a wide range of association statistics. Finally, we develop a novel approach to address a problem that has been of fundamental interest to geneticists for decades. The contribution of genetics to a trait, termed as heritability, is often measured by the amount of variation in the trait that is due to genetics. Heritability, quantifies the role of genetics in a trait and provides insight about disease etiology. Traditionally, heritabilities were estimated in studies of individuals with known relatedness such as classical twin studies. Recently, estimating the heritability of a trait from unrelated individuals using GWAS data, and further, partitioning the heritability into the contributions of genomic regions has received a lot of attention. Existing methods partition the heritability by jointly estimating the contributions of all regions. However, these methods are computationally intractable and may be inaccurate when the number of regions is large. In this work, we present an alternative approach that partitions the total heritability into the contributions of an arbitrary number of regions, while performing these computations in parallel. We demonstrate that our method is more accurate and computationally efficient than existing approaches.

Download or read book Analysis of Complex Disease Association Studies written by Eleftheria Zeggini and published by Academic Press. This book was released on 2010-11-17 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Genome Wide Association Studies written by Davoud Torkamaneh and published by Humana. This book was released on 2022-06-29 with total page 377 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed collection explores genome-wide association studies (GWAS), which have revolutionized the investigation of complex traits over the past decade and have unveiled numerous useful genotype–phenotype associations in plants. The book describes the key concepts and methods underlying GWAS, including the genetic architecture underlying variation for phenotypic traits, the structure of genetic variation in plants, technologies for capturing genetic information, study designs, and the statistical models and bioinformatics tools used for data analysis. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of invaluable implementation advice that leads to the most fruitful research results. Authoritative and practical, Genome-Wide Association Studies serves as an extremely valuable resource for the plant research community by rendering GWAS analysis less challenging and more accessible to a broader group of users.

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 Genetic Dissection of Complex Traits written by D.C. Rao and published by Academic Press. This book was released on 2008-04-23 with total page 788 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Biostatistical Genetics and Genetic Epidemiology written by Robert C. Elston and published by John Wiley & Sons. This book was released on 2002-04-22 with total page 860 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Human Genetics and Genetic Epidemiology" ist der 3. Band aus der sehr erfolgreichen Reihe 'Wiley Biostatistics Reference Series', die auf Artikeln der "Encyclopedia of Biostatistics" basiert. Dieser Band gibt einen topaktuellen und umfassenden Überblick über ein Forschungsgebiet, das insbesondere im Zuge des Human-Genomprojekts eine regelrechte Explosion an Forschungsaktivitäten erlebt hat. Enthalten sind komplett aktualisierte Artikel aus der "Encyclopedia of Biostatistics" sowie über 25% neue Artikel. Mit einem komplexen System an Querverweisen, die das Auffinden der gewünschten Information erheblich erleichtern. Eine interessante Lektüre für Genetiker, Epidemiologen, Biostatistiker und Forscher in diesen Bereichen.

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 Novel Approaches to the Analysis of Family Data in Genetic Epidemiology written by Xiangqing Sun and published by Frontiers Media SA. This book was released on 2016-08-17 with total page 86 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome-wide association studies (GWAS) for complex disorders with large case-control populations have been performed on hundreds of traits in more than 1200 published studies (http://www.genome.gov/gwastudies/) but the variants detected by GWAS account for little of the heritability of these traits, leading to an increasing interest in using family based designs. While GWAS studies are designed to find common variants with low to moderate attributable risks, family based studies are expected to find rare variants with high attributable risk. Because family-based designs can better control both genetic and environmental background, this study design is robust to heterogeneity and population stratification. Moreover, in family-based analysis, the background genetic variation can be modeled to control the residual variance which could increase the power to identify disease associated rare variants. Analysis of families can also help us gain knowledge about disease transmission and inheritance patterns. Although a family-based design has the advantage of being robust to false positives, novel and powerful methods to analyze families in genetic epidemiology continue to be needed, especially for the interaction between genetic and environmental factors associated with disease. Moreover, with the rapid development of sequencing technology, advances in approaches to the design and analysis of sequencing data in families are also greatly needed. The 11 articles in this book all introduce new methodology and, using family data, substantial new findings are presented in the areas of infectious diseases, diabetes, eye traits, autism spectrum disorder and prostate cancer.

Download or read book Phenotypes and Genotypes written by Florian Frommlet and published by Springer. This book was released on 2016-02-12 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Genetics of Bone Biology and Skeletal Disease written by Rajesh V. Thakker and published by Academic Press. This book was released on 2017-10-31 with total page 878 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetics of Bone Biology and Skeletal Disease, Second Edition, is aimed at students of bone biology and genetics and includes general introductory chapters on bone biology and genetics. More specific disease orientated chapters comprehensively summarize the clinical, genetic, molecular, animal model, molecular pathology, diagnostic, counseling, and treatment aspects of each disorder. The book is organized into five sections that each emphasize a particular theme, general background to bone biology, general background to genetics and epigenetics, disorders of bone and joint, parathyroid and related disorders, and vitamin D and renal disorders. The first section is specifically devoted to providing an overview of bone biology and structure, joint and cartilage biology, principles of endocrine regulation of bone, and the role of neuronal regulation and energy homeostasis. The second section reviews the principles and progress of medical genetics and epigenetics related to bone disease, including genome-wide association studies (GWAS), genomic profiling, copy number variation, prospects of gene therapy, pharmacogenomics, genetic testing and counseling, as well as the generation and utilizing of mouse models. The third section details advances in the genetics and molecular biology of bone and joint diseases, both monogenic and polygenic, as well as skeletal dysplasias, and rarer bone disorders. The fourth section highlights the central role of the parathyroids in calcium and skeletal homeostasis by reviewing the molecular genetics of: hyperparathyroidism, hypoparathyrodism, endocrine neoplasias, and disorders of the PTH and calcium-sensing receptors. The fifth section details molecular and cellular advances across associated renal disorders such as vitamin D and rickets. Identifies and analyzes the genetic basis of bone disorders in humans and demonstrates the utility of mouse models in furthering the knowledge of mechanisms and evaluation of treatments Demonstrates how the interactions between bone and joint biology, physiology, and genetics have greatly enhanced the understanding of normal bone function as well as the molecular pathogenesis of metabolic bone disorders Summarizes the clinical, genetic, molecular, animal model, molecular pathology, diagnostic, counseling, and treatment aspects of each disorder

Download or read book Genetic Association Studies written by Mehmet Tevfik Dorak and published by Garland Science. This book was released on 2016-09-26 with total page 331 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic Association Studies is designed for students of public health, epidemiology, and the health sciecnes, covering the main principles of molecular genetics, population genetics, medical genetics, epidemiology and statistics. It presents a balanced view of genetic associations with coverage of candidate gene studies as well as genome-wide association studies. All aspects of a genetic association study are included, from the lab to analysis and interpretation of results, but also bioinformatics approaches to causality assessment. The role of the environment in genetic disease is also highlighted. Genetic Association Studies will enable readers to understand and critique genetic association studies and set them on the way to designing, executing, analyzing, interpreting, and reporting their own.

Download or read book Statistical Issues in Genome wide Association Studies written by David William Fardo and published by . This book was released on 2008 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first replicable finding from a genome-wide association study was published in 2005 (Klein et al., 2005). Since then, genome-wide association has been responsible for the discovery of nearly 100 novel genetic loci conferring risk for 40 common diseases (Pearson and Manolio, 2008). Many similar studies have been conducted with varying degrees of success, and statistical advancements continue to enhance the ability of these studies to succeed. This dissertation presents original contributions to benefit the design and analysis of genome-wide association studies. Disease traits measured on a continuous scale generally provide greater study power than binary traits. However, these measurements can be difficult and costly to obtain and may need to be adjusted in the analysis by many other confounding factors which must also be collected. Chapter 1 details rules to analyze a dichotomized version of a quantitative trait in a family-based genome-wide association study while maintaining power levels comparable to that of analyzing the original trait. These rules are illustrated by an application to an asthma study.