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| copy number variation analysis: Cytogenomics Thomas Liehr, 2021-05-25 Cytogenomics demonstrates that chromosomes are crucial in understanding the human genome and that new high-throughput approaches are central to advancing cytogenetics in the 21st century. After an introduction to (molecular) cytogenetics, being the basic of all cytogenomic research, this book highlights the strengths and newfound advantages of cytogenomic research methods and technologies, enabling researchers to jump-start their own projects and more effectively gather and interpret chromosomal data. Methods discussed include banding and molecular cytogenetics, molecular combing, molecular karyotyping, next-generation sequencing, epigenetic study approaches, optical mapping/karyomapping, and CRISPR-cas9 applications for cytogenomics. The book's second half demonstrates recent applications of cytogenomic techniques, such as characterizing 3D chromosome structure across different tissue types and insights into multilayer organization of chromosomes, role of repetitive elements and noncoding RNAs in human genome, studies in topologically associated domains, interchromosomal interactions, and chromoanagenesis. This book is an important reference source for researchers, students, basic and translational scientists, and clinicians in the areas of human genetics, genomics, reproductive medicine, gynecology, obstetrics, internal medicine, oncology, bioinformatics, medical genetics, and prenatal testing, as well as genetic counselors, clinical laboratory geneticists, bioethicists, and fertility specialists. - Offers applied approaches empowering a new generation of cytogenomic research using a balanced combination of classical and advanced technologies - Provides a framework for interpreting chromosome structure and how this affects the functioning of the genome in health and disease - Features chapter contributions from international leaders in the field |
| copy number variation analysis: Single-cell Sequencing and Methylation Buwei Yu, Jiaqiang Zhang, Yiming Zeng, Li Li, Xiangdong Wang, 2020-10-14 With the rapid development of biotechnologies, single-cell sequencing has become an important tool for understanding the molecular mechanisms of diseases, defining cellular heterogeneities and characteristics, and identifying intercellular communications and single-cell-based biomarkers. Providing a clear overview of the clinical applications, the book presents state-of-the-art information on immune cell function, cancer progression, infection, and inflammation gained from single-cell DNA or RNA sequencing. Furthermore, it explores the role of target gene methylation in the pathogenesis of diseases, with a focus on respiratory cancer, infection and chronic diseases. As such it is a valuable resource for clinical researchers and physicians, allowing them to refresh their knowledge and improve early diagnosis and therapy for patients. |
| copy number variation analysis: Pharmacoepigenetics Ramón Cacabelos, 2019-06-04 Pharmacoepigenetics provides a comprehensive volume on the role of epigenetics and epigenomics in drug discovery and development, providing a detailed, but accessible, view of the field, from basic principles, to applications in disease therapeutics. Leading international researchers from across academia, clinical settings and the pharmaceutical industry discuss the influence of epigenetics and epigenomics in human pathology, epigenetic biomarkers for disease prediction, diagnosis, and treatment, current epigenetic drugs, and the application of epigenetic procedures in drug development. Throughout the book, chapter authors offer a balanced and objective discussion of the future of pharmacoepigenetics and its crucial contribution to the growth of precision and personalized medicine. - Fully examines the influence of epigenetics and epigenomics in human pathology, epigenetic biomarkers for disease prediction, diagnosis, treatment, current epigenetic drugs and the application of epigenetic procedures in drug development - Features chapter contributions from leading international researchers in academia, clinical settings and the pharmaceutical industry - Instructs researchers, students and clinicians on how to better interpret and employ pharmacoepigenetics in drug development, efficiency and safety - Provides a balanced and objective discussion of the future of pharmacoepigenetics and its crucial role in precision medicine |
| copy number variation analysis: Genotyping Stefan J. White, Stuart Cantsilieris, 2016-11-08 This volume explores a broad range of different genotyping techniques. Genotyping: Methods and Protocols consists of chapters that cover numerous topics such as: an overview of multiplexed microsatellite analysis; High Resolution Melt analysis and TaqMan-based assays; in situ analysis of variants in single RNA molecules; the MassARRAY system and Molecular Inversion Probes; Pulsed Field Gel Electrophoresis, Paralogue Ratio Test, and Multiplex Ligation-Dependent Probe Amplification; long-range PCR combined with PacBio sequencing; Targeted Locus Amplification; Multilocus Sequence Typing and rapid SNP detection with pyrosequencing; and genotyping-by-sequencing for plant analysis. Finally, the volume concludes with a summary of pertinent points to describe genetic variation. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Thorough and practical, Genotyping: Methods and Protocols is a valuable resource for anyone interested in learning more about the diverse field of genotyping. |
| copy number variation analysis: Long-Range Control of Gene Expression Veronica van Heyningen, Robert E Hill, 2011-09-02 Long-Range Control of Gene Expression covers the current progress in understanding the mechanisms for genomic control of gene expression, which has grown considerably in the last few years as insight into genome organization and chromatin regulation has advanced. Discusses the evolution of cis-regulatory sequences in drosophila Includes information on genomic imprinting and imprinting defects in humans Includes a chapter on epigenetic gene regulation in cancer |
| copy number variation analysis: Genomic Disorders James R. Lupski, Pawel T. Stankiewicz, 2007-11-10 A grand summary and synthesis of the tremendous amount of data now available in the post genomic era on the structural features, architecture, and evolution of the human genome. The authors demonstrate how such architectural features may be important to both evolution and to explaining the susceptibility to those DNA rearrangements associated with disease. Technologies to assay for such structural variation of the human genome and to model genomic disorders in mice are also presented. Two appendices detail the genomic disorders, providing genomic features at the locus undergoing rearrangement, their clinical features, and frequency of detection. |
| copy number variation analysis: Applied Multivariate Data Analysis Brian Everitt, 1991 |
| copy number variation analysis: Human Genome Structure, Function and Clinical Considerations Luciana Amaral Haddad, 2021-06-07 This book provides a detailed evidence-based overview of the latest developments in how the structure of the human genome is relevant to the health professional. It features comprehensive reviews of genome science including human chromosomal and mitochondrial DNA structure, protein-coding and noncoding genes, and the diverse classes of repeat elements of the human genome. These concepts are then built upon to provide context as to how they functionally relate to differences in phenotypic traits that can be observed in human populations. Guidance is also provided on how this information can be applied by the medical practitioner in day-to-day clinical practice. Human Genome Structure, Function and Clinical Considerations collates the latest developments in genome science and current methods for genome analysis that are relevant for the clinician, researcher and scientist who utilises precision medicine techniques and is an essential resource for any such practitioner. |
| copy number variation analysis: Computational Exome and Genome Analysis Peter N. Robinson, Rosario Michael Piro, Marten Jager, 2017-09-13 Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline. |
| copy number variation analysis: Cell-free DNA as Diagnostic Markers Valentina Casadio, Samanta Salvi, 2019-02-04 This book describes the most important techniques used for studying cfDNA in the different samples; serum, plasma, urine. Chapters detail methods on liquid biopsy for cancer disease, methods in cancer, epigenetic modifications, fetal and pediatric diseases, physical activity, and urinary cell free DNA. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Cell-Free DNA as Diagnostic Markers: Methods and Protocols aims to ensure successful results in the further study of this vital field. |
| copy number variation analysis: Gene-Environment Interactions in Psychiatry Bart Ellenbroek, Ji Un Youn, 2016-07-26 Gene-Environment Interactions in Psychiatry: Nature, Nurture, Neuroscience begins with the basic aspects of gene–environment studies, such as basic genetics, principles of animals modeling, and the basic processes of how environmental factors affect brain and behavior, with part two describing the most important psychiatric disorders in detail. Each chapter has a similar structure that includes a general description of the disorder that is followed by an analysis of the role of genes and how they are affected by environmental factors. Each chapter ends with a description of the most relevant animal models, again focusing on gene–environment interactions. The book concludes with a critical evaluation of the current research and an outlook for the (possible) future, offering a vignette into the fascinating world of nature, nurture, and neuroscience. - Written to provide in-depth basic knowledge on gene–environment interactions for graduate students, postgraduate students, clinicians, and scientists - Includes descriptions of the major psychiatric disorders - Provides detailed descriptions of animal models and basic genetic information - Presents well-illustrated color figures to explain complex features in a simple manner |
| copy number variation analysis: Visualizing the Semantic Web Vladimir Geroimenko, 2003 Dealing with visualization of the second-generation Web, this text presentsresearch on topics such as: visualization of semantic information and metadata;querying XML documents; topic map visualization; visual modelling of XML/RDFontologies; e-commerce and Web search applications; and more. |
| copy number variation analysis: Proceedings of the International Conference on Advanced Intelligent Systems and Informatics 2018 Aboul Ella Hassanien, Mohamed F. Tolba, Khaled Shaalan, Ahmad Taher Azar, 2018-08-28 This book presents the proceedings of the 4th International Conference on Advanced Intelligent Systems and Informatics 2018 (AISI2018), which took place in Cairo, Egypt from September 1 to 3, 2018. This international and interdisciplinary conference, which highlighted essential research and developments in the field of informatics and intelligent systems, was organized by the Scientific Research Group in Egypt (SRGE). The book is divided into several main sections: Intelligent Systems; Robot Modeling and Control Systems; Intelligent Robotics Systems; Machine Learning Methodology and Applications; Sentiment Analysis and Arabic Text Mining; Swarm Optimizations and Applications; Deep Learning and Cloud Computing; Information Security, Hiding, and Biometric Recognition; and Data Mining, Visualization and E-learning. |
| copy number variation analysis: Parametric Statistical Change Point Analysis Jie Chen, A.K. Gupta, 2013-11-11 Recently there has been a keen interest in the statistical analysis of change point detec tion and estimation. Mainly, it is because change point problems can be encountered in many disciplines such as economics, finance, medicine, psychology, geology, litera ture, etc. , and even in our daily lives. From the statistical point of view, a change point is a place or time point such that the observations follow one distribution up to that point and follow another distribution after that point. Multiple change points problem can also be defined similarly. So the change point(s) problem is two fold: one is to de cide if there is any change (often viewed as a hypothesis testing problem), another is to locate the change point when there is a change present (often viewed as an estimation problem). The earliest change point study can be traced back to the 1950s. During the fol lowing period of some forty years, numerous articles have been published in various journals and proceedings. Many of them cover the topic of single change point in the means of a sequence of independently normally distributed random variables. Another popularly covered topic is a change point in regression models such as linear regres sion and autoregression. The methods used are mainly likelihood ratio, nonparametric, and Bayesian. Few authors also considered the change point problem in other model settings such as the gamma and exponential. |
| copy number variation analysis: Mitosis and Meiosis Part A , 2018-05-24 Mitosis and Meiosis, Part A, Volume 144, a new volume in the Methods in Cell Biology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Unique to this updated volume are chapters on Analyzing the Spindle Assembly Checkpoint in human cell culture, an Analysis of CIN, a Functional analysis of the tubulin code in mitosis, Employing CRISPR/Cas9 genome engineering to dissect the molecular requirements for mitosis, Applying the auxin-inducible degradation (AID) system for rapid protein depletion in mammalian cells, Small Molecule Tools in Mitosis Research, Optogenetic control of mitosis with photocaged chemical, and more. - Contains contributions from experts in the field from across the world - Covers a wide array of topics on both mitosis and meiosis - Includes relevant, analysis based topics |
| copy number variation analysis: Gene Quantification Francois Ferre, 2012-12-06 Geneticists and molecular biologists have been interested in quantifying genes and their products for many years and for various reasons (Bishop, 1974). Early molecular methods were based on molecular hybridization, and were devised shortly after Marmur and Doty (1961) first showed that denaturation of the double helix could be reversed - that the process of molecular reassociation was exquisitely sequence dependent. Gillespie and Spiegelman (1965) developed a way of using the method to titrate the number of copies of a probe within a target sequence in which the target sequence was fixed to a membrane support prior to hybridization with the probe - typically a RNA. Thus, this was a precursor to many of the methods still in use, and indeed under development, today. Early examples of the application of these methods included the measurement of the copy numbers in gene families such as the ribosomal genes and the immunoglo bulin family. Amplification of genes in tumors and in response to drug treatment was discovered by this method. In the same period, methods were invented for estimating gene num bers based on the kinetics of the reassociation process - the so-called Cot analysis. This method, which exploits the dependence of the rate of reassociation on the concentration of the two strands, revealed the presence of repeated sequences in the DNA of higher eukaryotes (Britten and Kohne, 1968). An adaptation to RNA, Rot analysis (Melli and Bishop, 1969), was used to measure the abundance of RNAs in a mixed population. |
| copy number variation analysis: Cell Biology by the Numbers Ron Milo, Rob Phillips, 2015-12-07 A Top 25 CHOICE 2016 Title, and recipient of the CHOICE Outstanding Academic Title (OAT) Award. How much energy is released in ATP hydrolysis? How many mRNAs are in a cell? How genetically similar are two random people? What is faster, transcription or translation?Cell Biology by the Numbers explores these questions and dozens of others provid |
| copy number variation analysis: Interactive Web-Based Data Visualization with R, plotly, and shiny Carson Sievert, 2020-01-30 The richly illustrated Interactive Web-Based Data Visualization with R, plotly, and shiny focuses on the process of programming interactive web graphics for multidimensional data analysis. It is written for the data analyst who wants to leverage the capabilities of interactive web graphics without having to learn web programming. Through many R code examples, you will learn how to tap the extensive functionality of these tools to enhance the presentation and exploration of data. By mastering these concepts and tools, you will impress your colleagues with your ability to quickly generate more informative, engaging, and reproducible interactive graphics using free and open source software that you can share over email, export to pdf, and more. Key Features: Convert static ggplot2 graphics to an interactive web-based form Link, animate, and arrange multiple plots in standalone HTML from R Embed, modify, and respond to plotly graphics in a shiny app Learn best practices for visualizing continuous, discrete, and multivariate data Learn numerous ways to visualize geo-spatial data This book makes heavy use of plotly for graphical rendering, but you will also learn about other R packages that support different phases of a data science workflow, such as tidyr, dplyr, and tidyverse. Along the way, you will gain insight into best practices for visualization of high-dimensional data, statistical graphics, and graphical perception. The printed book is complemented by an interactive website where readers can view movies demonstrating the examples and interact with graphics. |
| copy number variation analysis: 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) IEEE Staff, 2021-12-09 We solicit high quality original research papers (including significant work in progress) in any aspect of bioinformatics, genomics, and biomedicine New computational techniques and methods and their application in life science and medical domains are especially encouraged |
| copy number variation analysis: Mobile DNA: Finding Treasure in Junk Haig H. Kazazian, 2011 Annotation What we now know about mobile DNA--and the substantial roles it plays in humans, animals, and plants. & bull; & bull;Mobile DNA accounts for more than half of our genome: This book explains the important role it plays in shaping evolutionary change. & bull;A rich, thorough, and accessible introduction for all serious students, practitioners, and researchers in human and medical genetics, molecular biology, or evolutionary biology. & bull;By one of the field's leading researchers, Dr. Haig Kazazian. This book thoroughly reviews our current scientific understanding of the significant role that mobile genetic elements play in the evolution and function of genomes and organisms--from plants and animals to humans. Highly regarded geneticist Haig Kazazian offers an accessible intellectual history of the field's research strategies and concerns, explaining how advances opened up new questions, and how new tools and capabilities have encouraged progress in the field. Kazazian introduces the key strategies and approaches taken in leading laboratories (including his own) to gain greater insight into the large proportion of our genome that derives from mobile genetic elements, including viruses, plasmids, and transposons. He also presents intriguing insights into long-term research strategies that may lead to an even deeper understanding. |
| copy number variation analysis: The 48 Laws of Power Robert Greene, 2023-10-31 Amoral, cunning, ruthless, and instructive, this multi-million-copy New York Times bestseller is the definitive manual for anyone interested in gaining, observing, or defending against ultimate control – from the author of The Laws of Human Nature. In the book that People magazine proclaimed “beguiling” and “fascinating,” Robert Greene and Joost Elffers have distilled three thousand years of the history of power into 48 essential laws by drawing from the philosophies of Machiavelli, Sun Tzu, and Carl Von Clausewitz and also from the lives of figures ranging from Henry Kissinger to P.T. Barnum. Some laws teach the need for prudence (“Law 1: Never Outshine the Master”), others teach the value of confidence (“Law 28: Enter Action with Boldness”), and many recommend absolute self-preservation (“Law 15: Crush Your Enemy Totally”). Every law, though, has one thing in common: an interest in total domination. In a bold and arresting two-color package, The 48 Laws of Power is ideal whether your aim is conquest, self-defense, or simply to understand the rules of the game. |
| copy number variation analysis: ADHD Hojka Gregoric Kumperscak, 2021-11-24 Attention Deficit Hyperactivity Disorder (ADHD) is the most prevalent neurodevelopmental disorder. Previously, it was considered a disorder that affected children only. Recently, however, there is no doubt that ADHD can affect adults as well, but with different clinical presentation. Thus, it is critical to understand how the clinical picture of the disorder changes with development. Traditional ADHD diagnostic procedures are broadening and incorporating new entities like endophenotypes. Comorbidity is a rule, especially if ADHD is not recognized and treated early. New genetic studies bring deeper and more concise knowledge about the disorder’s etiology. This book addresses these aspects of ADHD to bring about more clarity and understanding of the disorder. |
| copy number variation analysis: Statistical Analysis of Next Generation Sequencing Data Somnath Datta, Dan Nettleton, 2016-09-17 Next Generation Sequencing (NGS) is the latest high throughput technology to revolutionize genomic research. NGS generates massive genomic datasets that play a key role in the big data phenomenon that surrounds us today. To extract signals from high-dimensional NGS data and make valid statistical inferences and predictions, novel data analytic and statistical techniques are needed. This book contains 20 chapters written by prominent statisticians working with NGS data. The topics range from basic preprocessing and analysis with NGS data to more complex genomic applications such as copy number variation and isoform expression detection. Research statisticians who want to learn about this growing and exciting area will find this book useful. In addition, many chapters from this book could be included in graduate-level classes in statistical bioinformatics for training future biostatisticians who will be expected to deal with genomic data in basic biomedical research, genomic clinical trials and personalized medicine. About the editors: Somnath Datta is Professor and Vice Chair of Bioinformatics and Biostatistics at the University of Louisville. He is Fellow of the American Statistical Association, Fellow of the Institute of Mathematical Statistics and Elected Member of the International Statistical Institute. He has contributed to numerous research areas in Statistics, Biostatistics and Bioinformatics. Dan Nettleton is Professor and Laurence H. Baker Endowed Chair of Biological Statistics in the Department of Statistics at Iowa State University. He is Fellow of the American Statistical Association and has published research on a variety of topics in statistics, biology and bioinformatics. |
| copy number variation analysis: Neuronal and Synaptic Dysfunction in Autism Spectrum Disorder and Intellectual Disability Carlo Sala, Chiara Verpelli, 2016-04-30 Neuronal and Synaptic Dysfunction in Autism Spectrum Disorder and Intellectual Disability provides the latest information on Autism spectrum disorders (ASDs), the lifelong neurodevelopmental disorders that present in early childhood and affect how individuals communicate and relate to others and their surroundings. In addition, three quarters of ASD patients also manifest severe intellectual disability. Though certain genes have been implicated, ASDs remain largely a mystery, and research looking into causes and cellular deficits are crucial for better understanding of neurodevelopmental disorders. Despite the prevalence and insidious nature of this disorder, this book remains to be an extensive resource of information and background on the state of current research in the field. The book serves as a reference for this purpose, and discusses the crucial role synaptic activity plays in proper brain function. In addition, the volume discusses the neurodevelopmental synaptopathies and serves as a resource for scientists and clinicians in all biomedical science specialties. This research has been crucial for recent studies that have provided a rationale for the development of pharmacological agents able to counteract functional synaptic anomalies and potentially ameliorate some ASD symptoms. - Introduces the genetic and non-genetic causes of autism and associated intellectual disabilities - Describes the genes implicated in autistic spectrum disorders and their function - Considers major individual genetic causes of autism, Rett syndrome, Fragile X syndrome, and other autism spectrum disorders, as well as their classification as synaptopathies - Presents a thorough discussion of the clinical aspects of multiple neurodevelopmental disorders and the experimental models that exist to study their pathophysiology in vitro and in vivo, including animal models and patient-derived stem cell culture |
| copy number variation analysis: Applications of RNA-Seq and Omics Strategies Fabio Marchi, Priscila Cirillo, Elvis Cueva Mateo, 2017-09-13 The large potential of RNA sequencing and other omics techniques has contributed to the production of a huge amount of data pursuing to answer many different questions that surround the science's great unknowns. This book presents an overview about powerful and cost-efficient methods for a comprehensive analysis of RNA-Seq data, introducing and revising advanced concepts in data analysis using the most current algorithms. A holistic view about the entire context where transcriptome is inserted is also discussed here encompassing biological areas with remarkable technological advances in the study of systems biology, from microorganisms to precision medicine. |
| copy number variation analysis: Molecular Biology of the Cell , 2002 |
| copy number variation analysis: Copy Number Variation and Disease Hildegard Kehrer-Sawatzki, Dr. David N. Cooper, 2009 For evolutionary biologists as well as for human and cancer geneticist Copy number variants (CNVs) are an important source of human genomic diversity. They impact upon a diverse array of specialist fields such as evolutionary biology, predisposition to inherited disease (monogenic and complex), cancer genetics, inter-individual variation in diverse human populations, and somatic mosaicism. The important advances in CNV research that have been made over the last few years have greatly increased the awareness of the extent to which CNVs contribute to the diversity of human phenotypes, including `single gene defects' and genomic disorders. Indeed, CNVs are now being widely investigated in genome-wide association studies to determine their influence on human disease susceptibility. This special issue comprises a unique collection of review and original articles, which together reflect the current knowledge of CNVs while posing key questions about the structure, function and evolution of this key type of polymorphic variation in the human genome. Thus it is an invaluable source of information for evolutionary biologists as well as for human and cancer geneticists. |
| copy number variation analysis: The Transforming Principle Maclyn McCarty, 1986 Forty years ago, three medical researchers--Oswald Avery, Colin MacLeod, and Maclyn McCarty--made the discovery that DNA is the genetic material. With this finding was born the modern era of molecular biology and genetics. |
| copy number variation analysis: Copy Number Variants Derek M. Bickhart, 2018-07-24 This volume offers detailed step-by-step instructions to allow beginners and experts alike to run appropriate copy number variants (CNV) detection software on a dataset of choice and discern between false positive noise and true positive CNV signals. Chapters guide readers through single nucleotide polymorphism (SNP) chips, optical mapping assembly techniques, and current open-source programs specializing in CNV detection. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Copy Number Variants: Methods and Protocols aims to provide guidance to Bioinformaticians and Molecular Biologists who are interested in identifying copy number variants (CNV) with a wide variety of experimental media |
| copy number variation analysis: Population Neuroscience Tomas Paus, 2013-03-23 Is Newton’s brain different from Rembrandt’s? Does a mother’s diet during pregnancy impact brain growth? Do adolescent peers leave a signature in the social brain? Does the way we live in our middle years affect how our brains age? To answer these and many other questions, we can now turn to population neuroscience. Population neuroscience endeavors to identify environmental and genetic factors that shape the function and structure of the human brain; it uses the tools and knowledge of genetics (and the “omics” sciences), epidemiology and neuroscience. This text attempts to provide a bridge spanning these three disciplines so that their practitioners can communicate easily with each other when working together on large-scale imaging studies of the developing, mature and aging brain. By understanding the processes driving variations in brain function and structure across individuals, we will also be able to predict an individual’s risk of (or resilience against) developing a brain disorder. In the long term, the hope is that population neuroscience will lay the foundation for personalized preventive medicine and, in turn, reduce the burden associated with complex, chronic disorders of brain and body. |
| copy number variation analysis: The Nonhuman Primate in Nonclinical Drug Development and Safety Assessment Joerg Bluemel, Sven Korte, Emanuel Schenck, Gerhard Weinbauer, 2015-03-13 The Nonhuman Primate in Drug Development and Safety Assessment is a valuable reference dedicated to compiling the latest research on nonhuman primate models in nonclinical safety assessment, regulatory toxicity testing and translational science. By covering important topics such as study planning and conduct, inter-species genetic drift, pathophysiology, animal welfare legislation, safety assessment of biologics and small molecules, immunotoxicology and much more, this book provides scientific and technical insights to help you safely and successfully use nonhuman primates in pharmaceutical toxicity testing. A comprehensive yet practical guide, this book is intended for new researchers or practicing toxicologists, toxicologic pathologists and pharmaceutical scientists working with nonhuman primates, as well as graduate students preparing for careers in this area. - Covers important topics such as species selection, study design, experimental methodologies, animal welfare and the 3Rs (Replace, Refine and Reduce), social housing, regulatory guidelines, comparative physiology, reproductive biology, genetic polymorphisms and more - Includes practical examples on techniques and methods to guide your daily practice - Offers a companion website with high-quality color illustrations, reference values for safety assessment and additional practical information such as study design considerations, techniques and procedures and dosing and sampling volumes |
| copy number variation analysis: Computational Genomics with R Altuna Akalin, 2020-12-16 Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015. |
| copy number variation analysis: Evolution of Translational Omics Institute of Medicine, Board on Health Sciences Policy, Board on Health Care Services, Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials, 2012-09-13 Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials. |
| copy number variation analysis: ISCN 2013 International Standing Committee on Human Cytogenetic Nomenclature, 2013 This publication extends the now classic system of human cytogenetic nomenclature prepared by an expert committee and published in collaboration with Cytogenetic and Genome Research' since 1963. Revised and finalized by the ISCN Committee and its advisors at a meeting in Seattle, Wash., in April 2012, the ISCN 2013 updates, revises and incorporates all previous human cytogenetic nomenclature recommendations into one systematically organized publication that supersedes all previous ISCN recommendations. There are several new features in ISCN 2013: an update of the microarray nomenclature, many more illustrative examples of uses of nomenclature in all sections some definitions including chromothripsis and duplication a new chapter for nomenclature that can be used for any region-specific assay. The ISCN 2013 is an indispensable reference volume for human cytogeneticists, technicians and students for the interpretation and communication of human cytogenetic nomenclature. |
| copy number variation analysis: Iscn 2020 Jean McGowan-Jordan, Ros J. Hastings, Sarah Moore, 2020-12-31 This reprint of 'Cytogenetic and Genome Research' contains contributions discussing the subject in-depth. 'Cytogenetic and Genome Research' is a well-respected, international peer-reviewed journal in genetics. |
| copy number variation analysis: Deep Sequencing Data Analysis Noam Shomron, 2013-07-20 The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) apparatuses which, in essence, read billions of nucleotides per reaction. Effectively, when carefully planned, any experimental question which can be translated into reading nucleic acids can be applied.In Deep Sequencing Data Analysis, expert researchers in the field detail methods which are now commonly used to study the multi-facet deep sequencing data field. These included techniques for compressing of data generated, Chromatin Immunoprecipitation (ChIP-seq), and various approaches for the identification of sequence variants. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of necessary materials and reagents, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data analysis procedures for deep sequencing data interpretation. |
| copy number variation analysis: Large-scale Simultaneous Hypothesis Testing Bradley Efron, 2003 |
| copy number variation analysis: Digital PCR George Karlin-Neumann, Francisco Bizouarn, 2018-05-01 This volume explores and explains how digital PCRs (dPCRs) help in the study of numerous topics, such as infectious diseases, evolution of cancer and treatment responses, somatic mosaicism, genome editing and cell therapy, and food testing for GMOs and pathogens. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and thorough, Digital PCR: Methods and Protocols is a valuable resource for specialists in various fields, including geneticists, neurologists, immunologists, oncologists, and researchers who are interested in environmental sciences.” |
| copy number variation analysis: Clinical Bioinformatics Ronald Trent, 2016-08-23 In Clinical Bioinformatics, Second Edition, leading experts in the field provide a series of articles focusing on software applications used to translate information into outcomes of clinical relevance. Recent developments in omics, such as increasingly sophisticated analytic platforms allowing changes in diagnostic strategies from the traditional focus on single or small number of analytes to what might be possible when large numbers or all analytes are measured, are now impacting patient care. Covering such topics as gene discovery, gene function (microarrays), DNA sequencing, online approaches and resources, and informatics in clinical practice, this volume concisely yet thoroughly explores this cutting-edge subject. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Clinical Bioinformatics, Second Edition serves as an ideal guide for scientists and health professionals working in genetics and genomics. |
| copy number variation analysis: The Ubiquitin System Milton J. Schlesinger, Avram Hershko, 1988 |
Copy number variation analysis using Axiom arrays
The analysis software offers two CNV analysis methods: (1) fixed-region analysis when breakpoints of CNV regions of interest are known a priori and there is little breakpoint …
doi: 10.1007/978-1-4939-7778-9 9 - McCarroll Lab
Here, we share a detailed protocol for analyzing copy number variation with ddPCR including (1) designing successful assays targeting genomic segments of interest, (2) using those assays in …
Introduction to Copy Number Analysis - Bionano Genomics
Bionano provides two type of Copy Number (CN) pipelines, a fractional CN pipeline and an integer CN pipeline. Released as part of Bionano Solve v3.4, the fractional CN pipeline is …
Copy Number Variations (CNVs) - The University of Alabama …
Copy number variations (CNVs) • Stretches of genomic DNA present in more than or less than two copies that can range in size from kilobases (kb) to megabases (Mb) • Cannot be …
Droplet Digital PCR: High-Resolution Copy Number Variation …
Copy number variation (CNV), including genomic deletions or duplications, is a prominent source of interindividual variability, and copy number variation of specific loci has been associated …
An approach for determination of copy number variation …
The ability to determine Copy Number Variation (CNV) from short-read Next Generation Sequencing (NGS) data would enable laboratories to determine both CNV and Single …
DNA Copy Number and Loss of Heterozygosity Analysis …
Detection of copy-number variants and chromosomal aberrations in GenomeStudio® software. Illumina has developed several algorithms for detecting copy number variants (CNVs) and …
Performing CNV Analysis in GenomeStudio using cnvPartition 1
cnvPartition is a plug-in software program provided by Illumina that works from within the GenomeStudio Genotyping module to identify regions of copy number variation in a …
Axiom Copy Number Data Analysis - assets.thermofisher.com
This Guide provides information and instructions for performing copy number variation (CNV) data analysis on Applied Biosystems Axiom arrays.
NanoString®: Product Manual | nCounter® Data Analysis …
The nCounter® Custom Copy Number Variation (CNV) Assay utilizes NanoString’s unique direct and multiplexed detection of nucleic acids in solution to generate estimates of copy number …
Copy number variation analysis using the QuantStudio 3D …
Copy number variation (CNV) is an imbalance in the genome that increases or decreases the wild type copy number of a locus in comparison to a reference genome.
conumee: Enhanced copy-number variation analysis using …
for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays. Imports methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges,
Influences of rare copy-number variation on human complex …
The human genome contains hundreds of thousands of regions harboring copy-number variants (CNV). However, the phenotypic effects of most such polymorphisms are unknown because …
Analysis of copy number variation: design pipeline and …
Recent studies using microarray-based technologies have revealed the true extent and importance of structural variation within the genome. This variation, known as copy number …
Validation of copy number variation analysis for next ... - Nature
The identification of large structural variants and copy number variants (CNVs) encapsulating the regions targeted by WES and custom gene panel assays have proved challenging in a clinical...
Genomic Variation Analysis: Copy Number Variation - Bio-Rad
Our primary application for the QX100TM Droplet DigitalTM PCR system is to determine copy number variation (CNV) within a particular highly duplicated region of the genome. One of our …
Optimal Sparse Segment Identification With Application in …
simulations and analysis of a real dataset on identification of copy number variants based on high-density SNP data. The results show that the LRS procedure can yield greater gain in …
Copy Number Variation Analysis Module
The Copy Number Variation Analysis Module for DiomniTM Design and Analysis (RUO) Software 3 is used to perform relative quantitation analysis of genomic DNA targets using the real-time …
Detection of genome-wide copy number variation using the …
The Axiom platform enables copy number analysis with two methods: the Fixed Region method for known small regions; and the Discovery de novo method enables detection of events for …
Performing CNV Analysis in GenomeStudio using cnvPartition 1
identify regions of copy number variation in a genotyping project’s sample, based on the intensity and allele frequency data contained in the project. It also works with GenomeStudio’s …
DNA Copy Number and Loss of Heterozygosity Analysis …
provides stronger resolution for detecting true copy number changes. Copy Number Estimation cnvPartition models LRRs and BAFs for each of 14 different copy number scenarios as simple …
Copy Number Variation (CNV) Analysis with BeadStudio
CNV Analysis is fully supported with BeadStudio software in combination with all Illumina Infinium® DNA Analysis BeadChips. Table 1: CNV Analysis Options Plug-in Function …
Copy Number Variation (CNV) Analysis with BeadStudio
CNV Analysis is fully supported with BeadStudio software in combination with all Illumina Infinium DNA Analysis BeadChips. Plug-ins include cnvPartition, QuantiSNP, dChip, Homozygosity …
Interpreting Infinium Assay Data for Whole-Genome …
Structural variation in the genome consists of several classes of variants. Illumina BeadChips based on the Infinium Assay can detect both copy number-variation (e.g., amplifications, …
Sample Types for Illumina Genotyping Assays
Numerous sample types have been shown to yield high-quality data for genotyping and copy number variation analysis with Illumina Assays. Both the Infinium HD and GoldenGate assays …
Expanding CNV Detection into the unSNPable Genome
CNV identification and analysis, Illumina has worked closely with deCODE Genetics to develop specific content for several new DNA Analysis BeadChips. This content was designed to target …
Copy Number Variations - Illumina
- Copy number polymorphism (relatively common CNV, with a fixed starting/ending position) - Copy number difference (between-species copy number differences, e.g chimpanzees and …
Genome-Wide Mapping of Copy Number Variations and …
(SNPs), copy number variations (CNVs), and copy-neutral loss of heterozygosity (LOH). SNPs involve the change in a single nucleotide, while CNVs and LOH encompass larger segments …
SNP Genotyping and Copy Number Analysis - Illumina
tent such as regions that show copy number varia-tion (CNV) and non-synonymous SNPs. Combining the Infinium Assay with BeadChips allows large-scale interrogation of variations in …
