Detection of Epistatic Effects in Genetic Data PDF Download
Are you looking for read ebook online? Search for your book and save it on your Kindle device, PC, phones or tablets. Download Detection of Epistatic Effects in Genetic Data PDF full book. Access full book title Detection of Epistatic Effects in Genetic Data by Erik Michael Ferragut. Download full books in PDF and EPUB format.
Author: Erik Michael Ferragut
Publisher:
ISBN:
Category :
Languages : en
Pages : 400
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Book Description
Author: Erik Michael Ferragut
Publisher:
ISBN:
Category :
Languages : en
Pages : 400
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Book Description
Author: William Bateson
Publisher:
ISBN:
Category : Electronic books
Languages : en
Pages : 238
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Book Description
Bateson named the science "genetics" in 1905-1906. This is the first textbook in English on the subject of genetics.
Author: Ka-Chun Wong
Publisher:
ISBN: 9781071609477
Category : Electronic books
Languages : en
Pages : 402
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Book Description
Author: Jingky Pamesa Lozano
Publisher: Cuvillier Verlag
ISBN: 373693582X
Category : Mathematics
Languages : en
Pages : 210
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Book Description
Genetic studies have utilized the Transmission Disequilibrium Test (TDT) to investigate the effect of genes and their interactions (epistasis) on complex diseases such as diabetes mellitus, Alzheimer’s disease, ischaemic heart disease and cancer. The TDT has been frequently used as a statistical method to analyze genetic effects in family studies due to its robustness to population stratification. The original TDT method by Spielman et al. (Am J Hum Genet, 1993) was designed for qualitative traits (e.g. disease classification: affected / unaffected) but variations have been developed for its application in quantitative traits (QTs) such as blood sugar level, radiation sensitivity and measures of coronary artery calcification. However, the occurrence of nonnormally distributed quantitative traits in candidate gene analysis poses difficulties for statistical methods that are sensitive to distributional assumptions. This study introduces the Generalized Quantitative Transmission Disequilibrium Test (GQTDT) - a statistical method for quantitative traits based on generalized additive models incorporating parental mating type (parental genotype combination) indicator and different parameters of the distribution of the QT response variable in the statistical model. It aims to determine genetic effects (i.e. main effects and epistasis) affecting QTs in family-based studies. The method is based on the Generalized Additive Model for Location, Scale and Shape (GAMLSS, Rigby and Stasinopoulus, Appl Stat, 2005) which allows not only the mean but also other parameters of the conditional distribution of the quantitative trait to be included in the model. The power and type I error of the GQTDT to detect genetic main effects and epistasis were investigated in simulation studies. It has also been applied to real data to determine its applicability in different settings and compare its findings with existing biological data. Genotype data from family trios (parents and one offspring) as well as phenotype data of the offspring were used in the analysis. In the simulation studies, two unlinked biallelic loci and QTs influenced by one or two loci and epistasis were created. The QTs were simulated either as normally distributed or skewed to the right which are commonly encountered in genetic data. Different scenarios such as presence of population stratification and other covariates were also simulated in the data to determine its possible effects in the GQTDT analysis of genetic main effects and epistasis. The performance of the GQTDT in determining genetic main effects is satisfactory both in the normally distributed and skewed quantitative traits. When a fitted distribution is specified in the analysis, higher power can be achieved. In terms of detecting epistasis, good power is noted when the distribution of the quantitative trait is normal. When detecting epistasis in skewed traits, the power is not as high as the power in the normally distributed traits but higher compared to the benchmark method, the Quantitative Transmission Disequilibrium Test with parental mating type indicator (QTDTM; Gauderman, Genet Epi, 2003). The power of the GQTDT is also higher with higher minor allele frequencies, correctly assumed analysis genetic model, larger “true” effect size and bigger sample size. Slightly elevated type I error may be observed in analyzing skewed quantitative traits but like other TDT-like tests, the GQTDT is also robust to the effects of population stratification which causes spurious association. Its application to real data detected genetic main effects and epistasis with known biological evidence.
Author: Ronny C. Woodruff
Publisher: Springer Science & Business Media
ISBN: 9401152101
Category : Science
Languages : en
Pages : 561
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Book Description
Although debated since the time of Darwin, the evolutionary role of mutation is still controversial. In over 40 chapters from leading authorities in mutation and evolutionary biology, this book takes a new look at both the theoretical and experimental measurement and significance of new mutation. Deleterious, nearly neutral, beneficial, and polygenic mutations are considered in their effects on fitness, life history traits, and the composition of the gene pool. Mutation is a phenomenon that draws attention from many different disciplines. Thus, the extensive reviews of the literature will be valuable both to established researchers and to those just beginning to study this field. Through up-to-date reviews, the authors provide an insightful overview of each topic and then share their newest ideas and explore controversial aspects of mutation and the evolutionary process. From topics like gonadal mosaicism and mutation clusters to adaptive mutagenesis, mutation in cell organelles, and the level and distribution of DNA molecular changes, the foundation is set for continuing the debate about the role of mutation, fitness, and adaptability. It is a debate that will have profound consequences for our understanding of evolution.
Author: Ka-Chun Wong
Publisher: Humana
ISBN: 9781071609491
Category : Medical
Languages : en
Pages : 402
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Book Description
This volume explores methods and protocols for detecting epistasis from genetic data. Chapters provide methods and protocols demonstrating approaches to identify epistasis, genetic epistasis testing, genome-wide epistatic SNP networks, epistasis detection through machine learning, and complex interaction analysis using trigenic synthetic genetic array (τ-SGA). Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Epistasis: Methods and Protocols aims to ensure successful results in the further study of this vital field. "Simulating Evolution in Asexual Populations with Epistasis” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Author: José M Álvarez-Castro
Publisher: Frontiers Media SA
ISBN: 2889194442
Category : Ecology
Languages : en
Pages : 100
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Book Description
Ronald Fisher needed to develop elaborate models of genetic effects in order to set the foundations of Quantitative Genetics in his 1918 paper “The correlation between relatives on the supposition of Mendelian inheritance”. Since then, many significant implementations have been made to model genetic effects. However, at the verge of one century after Fisher’s kick-off, models of genetic effects keep on being discussed and implemented. Indeed, the relatively recent advent of QTL analyses challenged the state of the art of this field by providing researchers the opportunity to obtain and analyze estimates of genetic effects from real data. In this context, the development of this field was not exempt of some polemics, like the debate about the convenience of the functional and the statistical epistasis approaches. This research topic is meant to provide recent developments in models and estimation of genetic effects and to enrich the discussion about how and why models of genetic effects must be further developed and applied. The articles in this Research Topic shall thus extend, refine and/or provide a refresh look at Fisher’s original models of genetic effects and their application to genetic effects estimation and to improve our understanding of evolutionary processes and breeding programs.
Author: Jason B. Wolf
Publisher: Oxford University Press, USA
ISBN: 9780195128062
Category : Science
Languages : en
Pages : 348
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Book Description
Over the last two decades, research into epistasis has seen explosive growth and has moved the focus of research in evolutionary genetics from a traditional additive approach. We now know the effects of genes are rarely independent, and to reach a fuller understanding of the process of evolution we need to look at gene interactions as well as gene-environment interactions. This book is an overview of non-additive evolutionary genetics, integrating all work to date on all levels of evolutionary investigation of the importance of epistasis in the evolutionary process in general. It includes a historical perspective on this emerging field, in-depth discussion of terminology, discussions of the effects of epistasis at several different levels of biological organization and combinations of theoretical and experimental approaches to analysis.
Author: Carleigh Woodward
Publisher:
ISBN:
Category :
Languages : en
Pages : 166
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Book Description
Converging empirical evidence portrays epistasis (i.e., gene-gene interaction) as a ubiquitous property of genetic architectures and protagonist in complex trait variability. While researchers employ sophisticated technologies to detect epistasis, the scarcity of robust instances of detection in human populations is striking. To evaluate the empirical issues pertaining to epistatic detection, we analytically characterize the statistical detection problem and elucidate two candidate explanations. The first examines whether population-level manifestations of epistasis arising in nature are small; consequently, for sample-sizes employed in research, the power delivered by detectors may be disadvantageously small. The second considers whether gene-environmental association generates bias in estimates of genotypic values diminishing the power of detection. By simulation study, we adjudicate the merits of both explanations and the power to detect epistasis under four digenic architectures. In agreement with both explanations, our findings implicate small epistatic effect-sizes and gene-environmental association as mechanisms that obscure the detection of epistasis.
Author: Bruce Walsh
Publisher: Oxford University Press
ISBN: 0192566644
Category : Science
Languages : en
Pages : 1504
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Book Description
Quantitative traits-be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene-usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences.
