Cytogenomics

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

Cytogenetics is the study of chromosome morphology, structure, pathology, function, and behavior. The field has evolved to embrace molecular cytogenetic changes, now termed cytogenomics. Cytogeneticists utilize an assortment of procedures to investigate the full complement of chromosomes and/or a targeted region within a specific chromosome in metaphase or interphase. Tools include routine analysis of G-banded chromosomes, specialized stains that address specific chromosomal structures, and molecular probes, such as fluorescence in situ hybridization (FISH) and chromosome microarray analysis, which employ a variety of methods to highlight a region as small as a single, specific genetic sequence under investigation. The AGT Cytogenetics Laboratory Manual, Fourth Edition offers a comprehensive description of the diagnostic tests offered by the clinical laboratory and explains the science behind them. One of the most valuable assets is its rich compilation of laboratory-tested protocols currently being used in leading laboratories, along with practical advice for nearly every area of interest to cytogeneticists. In addition to covering essential topics that have been the backbone of cytogenetics for over 60 years, such as the basic components of a cell, use of a microscope, human tissue processing for cytogenetic analysis (prenatal, constitutional, and neoplastic), laboratory safety, and the mechanisms behind chromosome rearrangement and aneuploidy, this edition introduces new and expanded chapters by experts in the field. Some of these new topics include a unique collection of chromosome heteromorphisms; clinical examples of genomic imprinting; an example-driven overview of chromosomal microarray; mathematics specifically geared for the cytogeneticist; usage of ISCN’s cytogenetic language to describe chromosome changes; tips for laboratory management; examples of laboratory information systems; a collection of internet and library resources; and a special chapter on animal chromosomes for the research and zoo cytogeneticist. The range of topics is thus broad yet comprehensive, offering the student a resource that teaches the procedures performed in the cytogenetics laboratory environment, and the laboratory professional with a peer-reviewed reference that explores the basis of each of these procedures. This makes it a useful resource for researchers, clinicians, and lab professionals, as well as students in a university or medical school setting.

This second edition focuses on the study of human interphase chromosomes and its relation to health and disease. Orchestrated organization and behavior of the human genome in interphase nuclei at chromosomal level has been repeatedly shown to play a significant role in almost all basic biological processes involved in the processing and inheritance of genetic information within and between species. Accordingly, post-genomic bioscience appeals to basic and applied studies of interphase nuclei genetics and genomics with special attention to interphase chromosome behavior in health and disease. Additionally, elucidating the role of interphase chromosome behavior during development, chromosome/DNA replication, DNA reparation opens new horizons for basic and applied bioscience Studies of interphase nuclei have an appreciable impact on different areas of biomedical sciences such as cell biology, neurobiology, cancer research, developmental biology, epigenetics, cytogenetics, and medical genetics, as a whole. Moreover, development of innovative and emergent technologies to analyze interphase nuclei are closely associated with application of these techniques in diagnostic and research practices to solve reproductive problems (including infertility and spontaneous abortions), to investigate congenital malformations (including those produced by aneuploidy and other chromosome abnormalities); genetic diseases (including cardiac, immune, neurological and psychiatric diseases), and cancer. This second edition serves as a source of updated valuable information and promising ideas for a wide audience of professionals in biomedicine including researchers, scientists, and healthcare professionals in human genetics, cytogenetics, and developmental biology.

This book provides a detailed and up-to-dated information on the genomes belonging to three major life forms on Earth – archaea, prokaryotes and eukaryotes. Each section describes about the genome of a specific group of organisms, such as viruses, archaea, bacteria, eukaryotes and organellar genomes. Individual chapters provide details of their organization, structure, evolution, sequencing strategies and functions. Further, this book discusses the technologies that are applied for genome sequencing; assembly, annotation and gene prediction. Other topics include the genomes of important model organisms, mitochondria genome of Neanderthal fossil, etc. This book also examines the evolution of chloroplast and mitochondria genomes by comparing with bacteria, addresses the diseases that occur in humans due to the mutations in mitochondrial genome, gene therapy and engineering of chloroplast and mitochondrial genomes. Lastly, it features an overview of the role of proteomics, exposomics, connectomics, metabolomics, and microbiomics. This book is a fascinating read for students, lecturers and researchers in the field of genetics, genomics, microbiology and life sciences.

PlantOmics: The Omics of Plant Science provides a comprehensive account of the latest trends and developments of omics technologies or approaches and their applications in plant science. Thirty chapters written by 90 experts from 15 countries are included in this state-of-the-art book. Each chapter describes one topic/omics such as: omics in model plants, spectroscopy for plants, next generation sequencing, functional genomics, cyto-metagenomics, epigenomics, miRNAomics, proteomics, metabolomics, glycomics, lipidomics, secretomics, phenomics, cytomics, physiomics, signalomics, thiolomics, organelle omics, micro morphomics, microbiomics, cryobionomics, nanotechnology, pharmacogenomics, and computational systems biology for plants. It provides up to date information, technologies, and their applications that can be adopted and applied easily for deeper understanding plant biology and therefore will be helpful in developing the strategy for generating cost-effective superior plants for various purposes. In the last chapter, the editors have proposed several new areas in plant omics that may be explored in order to develop an integrated meta-omics strategy to ensure the world and earth’s health and related issues. This book will be a valuable resource to students and researchers in the field of cutting-edge plant omics.

Cytogenetics - Past, Present, and Further Perspectives discusses events that influenced the development of cytogenetics as a specialty within biology, with special attention paid to methodological achievements developed worldwide that have driven the field forward. Improvements to the resolution of chromosome analysis followed closely the introduction of innovative analytical technologies. In that sense, this book reviews and provides a brief account of the structure of chromosomes and stresses the high structural conservation in different species with an emphasis on aspects that require further research. However, it should be kept in mind that the future of cytogenetics will likely depend on improved knowledge of chromosome structure and function.

The experimental data that have been generated using new molecular techniques associated with the completion of genome projects have changed our perception of the structural features, functional implications and evolutionary dynamics of repetitive DNA sequences. This volume of Genome Dynamics provides a valuable update on recent developments in research into multigene families, centromeres, telomeres, microsatellite DNA, satellite DNA, and transposable elements. Each chapter presents a review by distinguished experts and analyzes repetitive DNA diversity and abundance, as well as the impact on genome structure, function and evolution. This publication is targeted at scientists and scholars at every level, from students to faculty members, and, indeed, anyone involved or interested in genetics, molecular evolution, molecular biology as well as genomics will find it a valuable source of up-to-date information.

In this thoroughly revised and expanded third edition of the highly praised classic, The Principles of Clinical Cytogenetics, a panel of hands-on experts update their descriptions of the basic concepts and interpretations involved in chromosome analysis to include the many advances that have occurred in the field. Among the highlights are a full chapter devoted to advances in chromosome microarray, soon to become a standard of care in this field, as well as an update on chromosome nomenclature as reflected in ISCN 2009. Other features include an update on automation to reflect the current state of the art, an update on hematopoietic neoplasms to reflect the new WHO guidelines, and updates on all regulatory changes that have been implemented. Cutting edge and readily accessible, The Principles of Clinical Cytogenetics, Third Edition offers physicians who depend on the cytogenetics laboratory for the diagnosis of their patients, students in cytogenetics programs, graduate and medical students studying for board examinations, cytogenetics technologists, and cytogeneticists a clear understanding of what happens in the cytogenetics laboratory to facilitate accurate and timely diagnoses.

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.

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.

Molecular Diagnostics, Third Edition, focuses on the technologies and applications that professionals need to work in, develop, and manage a clinical diagnostic laboratory. Each chapter contains an expert introduction to each subject that is next to technical details and many applications for molecular genetic testing that can be found in comprehensive reference lists at the end of each chapter. Contents are divided into three parts, technologies, application of those technologies, and related issues. The first part is dedicated to the battery of the most widely used molecular pathology techniques. New chapters have been added, including the various new technologies involved in next-generation sequencing (mutation detection, gene expression, etc.), mass spectrometry, and protein-specific methodologies. All revised chapters have been completely updated, to include not only technology innovations, but also novel diagnostic applications. As with previous editions, each of the chapters in this section includes a brief description of the technique followed by examples from the area of expertise from the selected contributor. The second part of the book attempts to integrate previously analyzed technologies into the different aspects of molecular diagnostics, such as identification of genetically modified organisms, stem cells, pharmacogenomics, modern forensic science, molecular microbiology, and genetic diagnosis. Part three focuses on various everyday issues in a diagnostic laboratory, from genetic counseling and related ethical and psychological issues, to safety and quality management. Presents a comprehensive account of all new technologies and applications used in clinical diagnostic laboratories Explores a wide range of molecular-based tests that are available to assess DNA variation and changes in gene expression Offers clear translational presentations by the top molecular pathologists, clinical chemists, and molecular geneticists in the field

Cytogenetic Laboratory Management: Chromosomal, FISH and Microarray-Based Best Practices and Procedures is a practical guide that describes how to develop and implement best practice processes and procedures in the genetic laboratory setting. The text first describes good laboratory practices, including quality management, design control of tests and FDA guidelines for laboratory developed tests, and pre-clinical validation study designs. The second focus of the book describes best practices for staffing and training, including cost of testing, staffing requirements, process improvement using Six Sigma techniques, training and competency guidelines and complete training programs for cytogenetic and molecular genetic technologists. The third part of the text provides step-wise standard operating procedures for chromosomal, FISH and microarray-based tests, including pre-analytic, analytic and post-analytic steps in testing, and divided into categories by specimen type, and test-type. All three sections of the book include example worksheets, procedures, and other illustrative examples that can be downloaded from the Wiley website to be used directly without having to develop prototypes in your laboratory. Providing both a wealth of information on laboratory management and molecular and cytogenetic testing, Cytogenetic Laboratory Management will be an essential tool for laboratorians world-wide in the field of laboratory testing and genetics testing in particular. This book gives the essentials of: Developing and implementing good quality management programs in laboratories Understanding design control of tests and pre-clinical validations studies and reports FDA guidelines for laboratory developed tests Use of reagents, instruments and equipment Cost of testing assessment and process improvement using Six Sigma methodology Staffing training and competency objectives Complete training programs for molecular and cytogenetic technologists Standard operating procedures for all components of chromosomal analysis, FISH and microarray testing of different specimen types This volume is a companion to Cytogenetic Abnormalities: Chromosomal, FISH and Microarray-Based Clinical Reporting. The combined volumes give an expansive approach to performing, reporting and interpreting cytogenetic laboratory testing and the necessary management practices, staff and testing requirements.

The first three editions of this acclaimed book presented a much-needed conceptual synthesis of this rapidly moving field. Now, Cancer Cytogenetics, Fourth Edition, offers a comprehensive, expanded, and up-to-date review of recent dramatic advances in this area, incorporating a vast amount of new data from the latest basic and clinical investigations. New contributors reflecting broader international authorship and even greater expertise Greater emphasis throughout on the clinical importance and application of information about cytogenetic and molecular aberrations Includes a complete coverage of chromosome aberrations in cancer based on an assessment of the 60,000 neoplasms cytogenetically investigated to date Now produced in full color for enhanced clarity Covers how molecular genetic data (PCR-based and sequencing information) are collated with the cytogenetic data where pertinent Discusses how molecular cytogenetic data (based on studies using FISH, CGH, SNP, etc) are fused with karyotyping data to enable an as comprehensive understanding of cancer cytogenetics as is currently possible

The 2016 edition of the International System for Human Cytogenomic Nomenclature (ISCN 2016) offers standard nomenclature that is used to describe any genomic rearrangement identified by techniques ranging from karyotyping to FISH, microarray, various region specific assays, and DNA sequencing. Suggestions from the international cytogenetics community have been reviewed by the Standing Committee, an international group of experts, nominated by their peers. This updated edition offers: * many new examples, particularly for microarray and region specific assays * trackable changes in the main text compared to the previous edition for easier identification * a nomenclature standard to facilitate the description of chromosome rearrangements characterized by DNA sequencing developed through collaboration between the Human Genome Variation Society (HGVS) and ISCN to accommodate the increased use of sequencing technologies in the characterization of chromosomal abnormalities The ISCN 2016 is an indispensable reference volume for human cytogeneticists, molecular geneticists, technicians, and students for the interpretation and communication of human cytogenetic and molecular cytogenomic nomenclature. After a long collaboration with Cytogenetic and Genome Research, ISCN is now again a part of this leading journal on chromosome and genome research, combining the day-to-day business with the latest findings.

Clinical Genomics provides an overview of the various next-generation sequencing (NGS) technologies that are currently used in clinical diagnostic laboratories. It presents key bioinformatic challenges and the solutions that must be addressed by clinical genomicists and genomic pathologists, such as specific pipelines for identification of the full range of variants that are clinically important. This book is also focused on the challenges of diagnostic interpretation of NGS results in a clinical setting. Its final sections are devoted to the emerging regulatory issues that will govern clinical use of NGS, and reimbursement paradigms that will affect the way in which laboratory professionals get paid for the testing. Simplifies complexities of NGS technologies for rapid education of clinical genomicists and genomic pathologists towards genomic medicine paradigm Tried and tested practice-based analysis for precision diagnosis and treatment plans Specific pipelines and meta-analysis for full range of clinically important variants

The role of molecular genetics in the treatment of malignancy continues to grow at an astonishing rate. Today’s subspecialized multidisciplinary approach to oncology has incorporated advances in targeted molecular therapy, prognosis, risk assessment, and prevention—all based at least in part on molecular diagnostics and imaging. Inside this cutting-edge resource, readers will explore broad, comprehensive perspectives on the current trends in molecular diagnosis of cancer and personalized cancer medicine. Authoritative discussions share insights from noted experts in cancer research, clinical trials, molecular diagnostics, personalized therapy, bioinformatics, and federal regulations. From the basic mechanisms of carcinogenesis to the most advanced molecular screening, staging, and treatment technologies, readers will discover clear and straightforward discussions directly relevant to patient diagnosis and care.

Personalized medicine, which simply means selection of treatment best suited for an individual, involves integration and translation of several new technologies in clinical care of patients. The scope is much broader than indicated by the term genomic medicine because many non-genomic factors are taken into consideration in developing personalized medicine. Basic technologies for personalized medicine, of which molecular diagnostics has the biggest share, are mentioned briefly and appropriate references are given for further information. Commercial aspects are discussed briefly in a chapter and detailed analysis of markets and companies involved in personalized medicine is presented in a special report on this topic. There is increasing interest in personalized medicine. Considerable advances have taken place in molecular biology and biotechnology to make personalized medicine a viable option, but some misconceptions still exist, both in the academic and commercial sectors. There is lack of a suitable source of information that provides both the fundamentals as well as applications of personalized medicine. As the latest version of the first monograph on personalized medicine published in 1998, this volume, Textbook of Personalized Medicine, summarizes the author’s efforts during the past decade, as well as reviews selected studies done during this period in a readable format for the physicians and scientists. It is hoped that physicians, pharmacists, scientists and interested lay readers with basic scientific knowledge will find this book useful.

This second edition volume expands on the first edition with more detailed methodologies on prenatal testing and diagnosis, and also covers next-generation sequencing techniques. The chapters in this book are divided into three sections: preimplantation genetic testing, traditional prenatal testing, and non-invasive prenatal testing. This book covers topics such as molecular testing for preimplantation genetic diagnosis of single gene disorders; DNA extraction from various types of prenatal specimens; prenatal diagnosis of cystic fibrosis and Tay-Sachs disease; chromosomal SNP microarrays; and isolation of cell-free DNA from maternal plasma. 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. Practical and thorough, Prenatal Diagnosis, Second Edition is a valuable resource for any researcher interested in reproducing these techniques in their clinical laboratories.