Genome-wide association studies and genomic prediction / edited by Cedric Gondro, Julius van der Werf, Ben Hayes.

Contributor(s): Gondro, Cedric [editor.] | Werf, Julius van der [editor.] | Hayes, Ben (Ben J.) [editor.]
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 1019.Publisher: New York : Humana Press, [2013]Copyright date: ©2013Description: 1 online resource (xi, 566 pages)Content type: text Media type: computer Carrier type: online resourceISBN: 9781627034470; 1627034471Subject(s): Molecular genetics | Variation (Biology) | Molecular Epidemiology | Genetic Services | Epidemiologic Research Design | Genetic Techniques | Computational Biology | Diagnostic Techniques and Procedures | Genetic Association Studies | Genetics | Diagnostic Services | Oligonucleotide Array Sequence Analysis | Epidemiologic Methods | Biology | Health Services | Investigative Techniques | Sequence Analysis | Preventive Health Services | Diagnosis | Health Care Facilities, Manpower, and Services | Biological Science Disciplines | Analytical, Diagnostic and Therapeutic Techniques and Equipment | Public Health | Community Health Services | Delivery of Health Care | Environment and Public Health | Natural Science Disciplines | Disciplines and Occupations | Genomics | Genome-Wide Association Study | Genetic Testing | Molecular genetics | Variation (Biology) | Biology | Health & Biological Sciences | Genetics | Biophysics | genomica | genomics | bioinformatics | humane genetica | human genetics | Genome informatics | GenoominformaticaGenre/Form: Electronic books. Additional physical formats: Print version:: Genome-wide Association Studies and Genomic Prediction.DDC classification: 572.8 LOC classification: QH440.5Online resources: Click here to access online
Contents:
R for genome-wide association studies / Cedric Gondro, Laercio R. Porto-Neto, Seung Hwan Lee -- Descriptive statistics of data : understanding the data set and phenotypes of interest / Sonja Dominik -- Designing a GWAS : power, sample size, and data structure / Roderick D. Ball -- Managing large SNP datasets with SNPpy / Faheem Mitha -- Quality control for genome-wide association studies / Cedric Gondro, Seung Hwan Lee, Hak Kyo Lee, Laercio R. Porto-Neto -- Overview of statistical methods for genome-wide association studies (GWAS) / Ben Hayes -- Statistical analysis of genomic data / Roderick D. Ball -- Using PLINK for genome-wide association studies (GWAS) and data analysis / Miguel E. Rentería, Adrian Cortes, Sarah E. Medland -- Genome-wide complex trait analysis (GCTA) : Methods, data analyses, and interpretations / Jian Yang, Sang Hong Lee, Michael E. Goddard, Peter M. Visscher -- Bayesian methods applied to GWAS / Rohan L. Fernando, Dorian Garrick -- Implementing a QTL detection study (GWAS) using genomic prediction methodology / Dorian J. Garrick, Rohan L. Fernando -- Genome-enabled prediction using the BLR (Bayesian Linear Regression) R-package / Gustavo de los Campos, Paulino Pérez, Ana I. Vazquez, José Crossa -- Genomic best linear unbiased prediction (gBLUP) for the estimation of genomic breeding values / Samuel A. Clark, Julius van der Werf -- Detecting regions of homozygosity to map the cause of recessively inherited disease / James W. Kijas -- Use of ancestral haplotypes in genome-wide association studies / Tom Druet, Frédéric Farnir -- Genotype phasing in populations of closely related individuals / John M. Hickey -- Genotype imputation to increase sample size in pedigreed populations / John M. Hickey, Matthew A. Cleveland, Christian Maltecca, Gregor Gorjanc, Birgit Gredler, Andreas Kranis -- Validation of genome-wide association studies (GWAS) results / John M. Henshall -- Detection of signatures of selection using FST / Laercio R. Porto-Neto, Seung Hwan Lee, Hak Kyo Lee, Cedric Gondro -- Association weight matrix : a network-based approach towards functional genome-wide association studies / Antonio Reverter, Marina R.S. Fortes -- Mixed effects structural equation models and phenotypic causal networks / Bruno Dourado Valente, Guilherme Jordão Magalhães Rosa -- Epistasis, complexity, and multifactor dimensionality reduction / Qinxin Pan, Ting Hu, Jason H. Moore -- Applications of multifactor dimensionality reduction to genome-wide data using the R package 'MDR' / Stacey Winham -- Higher order interactions : detection of epistasis using machine learning and evolutionary computation / Ronald M. Nelson, Marcin Kierczak, Örjan Carlborg -- Incorporating prior knowledge to increase the power of genome-wide association studies / Ashley Petersen, Justin Spratt, Nathan L. Tintle -- Genomic selection in animal breeding programs / Julius van der Werf.
Summary: "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."-- Back cover.
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Includes bibliographical references and index.

Online resource; title from PDF title page (Springer, viewed Jun. 12, 2013).

R for genome-wide association studies / Cedric Gondro, Laercio R. Porto-Neto, Seung Hwan Lee -- Descriptive statistics of data : understanding the data set and phenotypes of interest / Sonja Dominik -- Designing a GWAS : power, sample size, and data structure / Roderick D. Ball -- Managing large SNP datasets with SNPpy / Faheem Mitha -- Quality control for genome-wide association studies / Cedric Gondro, Seung Hwan Lee, Hak Kyo Lee, Laercio R. Porto-Neto -- Overview of statistical methods for genome-wide association studies (GWAS) / Ben Hayes -- Statistical analysis of genomic data / Roderick D. Ball -- Using PLINK for genome-wide association studies (GWAS) and data analysis / Miguel E. Rentería, Adrian Cortes, Sarah E. Medland -- Genome-wide complex trait analysis (GCTA) : Methods, data analyses, and interpretations / Jian Yang, Sang Hong Lee, Michael E. Goddard, Peter M. Visscher -- Bayesian methods applied to GWAS / Rohan L. Fernando, Dorian Garrick -- Implementing a QTL detection study (GWAS) using genomic prediction methodology / Dorian J. Garrick, Rohan L. Fernando -- Genome-enabled prediction using the BLR (Bayesian Linear Regression) R-package / Gustavo de los Campos, Paulino Pérez, Ana I. Vazquez, José Crossa -- Genomic best linear unbiased prediction (gBLUP) for the estimation of genomic breeding values / Samuel A. Clark, Julius van der Werf -- Detecting regions of homozygosity to map the cause of recessively inherited disease / James W. Kijas -- Use of ancestral haplotypes in genome-wide association studies / Tom Druet, Frédéric Farnir -- Genotype phasing in populations of closely related individuals / John M. Hickey -- Genotype imputation to increase sample size in pedigreed populations / John M. Hickey, Matthew A. Cleveland, Christian Maltecca, Gregor Gorjanc, Birgit Gredler, Andreas Kranis -- Validation of genome-wide association studies (GWAS) results / John M. Henshall -- Detection of signatures of selection using FST / Laercio R. Porto-Neto, Seung Hwan Lee, Hak Kyo Lee, Cedric Gondro -- Association weight matrix : a network-based approach towards functional genome-wide association studies / Antonio Reverter, Marina R.S. Fortes -- Mixed effects structural equation models and phenotypic causal networks / Bruno Dourado Valente, Guilherme Jordão Magalhães Rosa -- Epistasis, complexity, and multifactor dimensionality reduction / Qinxin Pan, Ting Hu, Jason H. Moore -- Applications of multifactor dimensionality reduction to genome-wide data using the R package 'MDR' / Stacey Winham -- Higher order interactions : detection of epistasis using machine learning and evolutionary computation / Ronald M. Nelson, Marcin Kierczak, Örjan Carlborg -- Incorporating prior knowledge to increase the power of genome-wide association studies / Ashley Petersen, Justin Spratt, Nathan L. Tintle -- Genomic selection in animal breeding programs / Julius van der Werf.

"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."-- Back cover.

English.

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