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Bioinformatics Tools For Detection And Clinical Interpretation Of Genomic Variations
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Book Synopsis Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations by : Ali Samadikuchaksaraei
Download or read book Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations written by Ali Samadikuchaksaraei and published by BoD – Books on Demand. This book was released on 2019-09-04 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic variations and phenotypic diversity are closely linked and form the underlying mechanism for development of many human diseases. This book addresses the methods of detection, analysis, and interpretation of genomic variations in clinically relevant scenarios. If your research or clinical practice involves handling of genomic sequencing data, this book is for you. Topics covered include: methods for identifying genetic diversity, the workflow for analyzing whole exome and whole genome sequencing data, local ancestry deconvolution models, the value of molecular patterns and pattern biomarkers in cancer diagnosis and prognosis, and genotyping and profiling resistance-associated variants of hepatitis C. If your research or clinical practice involves handling of genomic sequencing data, this book is for you.
Book Synopsis Bioinformatics Workflows for Genomic Variant Discovery, Interpretation and Prioritization by : Osman Ugur Sezerman
Download or read book Bioinformatics Workflows for Genomic Variant Discovery, Interpretation and Prioritization written by Osman Ugur Sezerman and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Next-generation sequencing (NGS) techniques allow high-throughput detection of a vast amount of variations in a cost-efficient manner. However, there still are inconsistencies and debates about how to process and analyse this ,Äòbig data,Äô. To accurately extract clinically relevant information from genomics data, choosing appropriate tools, knowing how to best utilize them and interpreting the results correctly is crucial. This chapter reviews state-of-the-art bioinformatics approaches in clinically relevant genomic variant detection. Best practices of reads-to-variant discovery workflows for germline and somatic short genomic variants are presented along with the most commonly utilized tools for each step. Additionally, methods for detecting structural variations are overviewed. Finally, approaches and current guidelines for clinical interpretation of genomic variants are discussed. As emphasized in this chapter, data processing and variant discovery steps are relatively well-understood. The differences in prioritization algorithms on the other hand can be perplexing, thus creating a bottleneck during interpretation. This review aims to shed light on the pros and cons of these differences to help experts give more informed decisions.
Book Synopsis Bioinformatics for Diagnosis, Prognosis and Treatment of Complex Diseases by : Bairong Shen
Download or read book Bioinformatics for Diagnosis, Prognosis and Treatment of Complex Diseases written by Bairong Shen and published by Springer Science & Business Media. This book was released on 2013-11-25 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book introduces the bioinformatics tools, databases and strategies for the translational research, focuses on the biomarker discovery based on integrative data analysis and systems biological network reconstruction. With the coming of personal genomics era, the biomedical data will be accumulated fast and then it will become reality for the personalized and accurate diagnosis, prognosis and treatment of complex diseases. The book covers both state of the art of bioinformatics methodologies and the examples for the identification of simple or network biomarkers. In addition, bioinformatics software tools and scripts are provided to the practical application in the study of complex diseases. The present state, the future challenges and perspectives were discussed. The book is written for biologists, biomedical informatics scientists and clinicians, etc. Dr. Bairong Shen is Professor and Director of Center for Systems Biology, Soochow University; he is also Director of Taicang Center for Translational Bioinformatics.
Book Synopsis Human Genome Informatics by : Christophe Lambert
Download or read book Human Genome Informatics written by Christophe Lambert and published by Academic Press. This book was released on 2018-08-02 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: Human Genome Informatics: Translating Genes into Health examines the most commonly used electronic tools for translating genomic information into clinically meaningful formats. By analyzing and comparing interpretation methods of whole genome data, the book discusses the possibilities of their application in genomic and translational medicine. Topics such as electronic decision-making tools, translation algorithms, interpretation and translation of whole genome data for rare diseases are thoroughly explored. In addition, discussions of current human genome databases and the possibilities of big data in genomic medicine are presented. With an updated approach on recent techniques and current human genomic databases, the book is a valuable source for students and researchers in genome and medical informatics. It is also ideal for workers in the bioinformatics industry who are interested in recent developments in the field. Provides an overview of the most commonly used electronic tools to translate genomic information Brings an update on the existing human genomic databases that directly impact genome interpretation Summarizes and comparatively analyzes interpretation methods of whole genome data and their application in genomic medicine
Book Synopsis Evolution of Translational Omics by : Institute of Medicine
Download or read book Evolution of Translational Omics written by Institute of Medicine and published by National Academies Press. This book was released on 2012-09-13 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Handbook of Statistical Genomics by : David J. Balding
Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1828 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.
Book Synopsis Biological Sequence Analysis by : Richard Durbin
Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.
Book Synopsis Genomic Applications in Pathology by : George Jabboure Netto
Download or read book Genomic Applications in Pathology written by George Jabboure Netto and published by Springer. This book was released on 2018-12-21 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The recent advances in genomics are continuing to reshape our approach to diagnostics, prognostics and therapeutics in oncologic and other disorders. A paradigm shift in pharmacogenomics and in the diagnosis of genetic inherited diseases and infectious diseases is unfolding as the result of implementation of next generation genomic technologies. With rapidly growing knowledge and applications driving this revolution, along with significant technologic and cost changes, genomic approaches are becoming the primary methods in many laboratories and for many diseases. As a result, a plethora of clinical genomic applications have been implemented in diagnostic pathology laboratories, and the applications and demands continue to evolve rapidly. This has created a tremendous need for a comprehensive resource on genomic applications in clinical and anatomic pathology. We believe that our current textbook provides such a resource to practicing molecular pathologists, hematopathologists and other subspecialized pathologists, general pathologists, pathology and other trainees, oncologists, geneticists and a growing spectrum of other clinicians. With periodic updates and a sufficiently rapid time from submission to publication, this textbook will be the resource of choice for many professionals and teaching programs. Its focus on genomics parallels the evolution of these technologies as primary methods in the clinical lab. The rapid evolution of genomics and its applications in medicine necessitates the (frequent) updating of this publication. This text will provide a state-of-the art review of the scientific principles underlying next generation genomic technologies and the required bioinformatics approaches to analyses of the daunting amount of data generated by current and emerging genomic technologies. Implementation roadmaps for various clinical assays such as single gene, gene panels, whole exome and whole genome assays will be discussed together with issues related to reporting and the pathologist’s role in interpretation and clinical integration of genomic tests results. Genomic applications for site-specific solid tumors and hematologic neoplasms will be detailed. Genomic applications in pharmacogenomics, inherited genetic diseases and infectious diseases will also be discussed. The latest iteration of practice recommendations or guidelines in genomic testing put forth by stakeholder professional organizations such as the College of American Pathology and the Association for Molecular Pathology, will be discussed as well as regulatory issues and laboratory accreditation related to genomic testing. All chapters will be written by experts in their fields and will include the most up to date scientific and clinical information.
Download or read book Genomic Medicine written by Laura J. Tafe and published by Springer Nature. This book was released on 2019-09-26 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of Molecular Diagnostics is rapidly evolving and molecular characterization of neoplasms is becoming an increasingly important part of the pathologic work up and diagnosis of many tumor types. This work provides a high-yield reference book that compiles critical information related to molecular biomarkers for various solid tumor and hematologic malignancy subtypes. It is succinct yet comprehensive enough to be suitable for fellows in training and medical professionals with an interest in molecular pathology and biomarkers. The book covers many aspects of molecular diagnostics, from techniques to applications and comprehensive summaries of the current molecular biomarkers of critical importance in solid and liquid tumors. Attention is also specifi cally devoted to bioinformatics and next generation sequencing, as well as pre-analytical issues that must be considered for accurate interpretation of molecular results in the context of overall patient care. This text focuses on clinical utility and validity and serves as an “owner’s manual” in Genomic Diagnostics for the practicing pathologist, pathology fellows and residents and other health care providers. Physicians will find this book invaluable as a quick reference for current molecular testing modalities and guidelines, tumor board preparation, deciding which test to order and interpreting genomic laboratory results. In addition, it is an accessible for trainees as a board review preparation reference.
Book Synopsis Detection of Clinically Relevant Copy-number Variants from Short-read Sequencing Data for Genomic Diagnostics by : Ramakrishnan Rajagopalan
Download or read book Detection of Clinically Relevant Copy-number Variants from Short-read Sequencing Data for Genomic Diagnostics written by Ramakrishnan Rajagopalan and published by . This book was released on 2021 with total page 150 pages. Available in PDF, EPUB and Kindle. Book excerpt: The overall goal of clinical genomic diagnostics is to identify pathogenic genetic variants that cause disease. Genetic variants can be classified into different subtypes based on the nature of the variant (sequence, copy-number, and structural variants), and current standard of care protocols require different diagnostic assays to detect these subtypes. Patients with suspected genetic disease often receive both chromosomal microarray array (CMA) testing for genome-wide copy number variant detection and exome sequencing for sequence variant detection to cover the spectrum of variant subtypes and sizes during their diagnostic odyssey. While short-read NGS testing, such as exome and genome, can detect both copy number and sequence variants, its implementation into the clinical lab has been hampered by both the lack of clinical standards and technical challenges concerning performance. Although not a currently offered clinical test, the identification of both copy number and sequencing variants from the same data would reduce the time to diagnosis, the costs involved, and significantly impact patient care. Using a cohort of 307 samples with clinical CMA and exome sequencing data, this thesis presents high quality, clinical-grade technical validation study and a new approach to tackling the major issue of false positives with current algorithms for CNV detection from exomes. A novel reproducibility framework was developed to assess the effect of control cohorts, and an R package for scalability in high-performance computing environments to analyze large exome sequencing cohorts. Application of the tools developed in this thesis to a cohort of 546 patients with rare pediatric disorders revealed eight novel diagnoses (1.5%) over their standard of care testing, and application to routine clinical epilepsy and hearing loss next-generation sequencing panels provided a minimum additional diagnostic yield of 2%. Over the next few years, genome sequencing is poised to become a first-tier diagnostic test, with the capability to detect all major classes of variation, including structural variants. Building on the exome work, I have developed a clinical-grade analytical workflow to integrate copy number and structural variants using 48 index samples with genome sequencing data and improved the false-positive rate. Application of this workflow to a cohort of 14 patients with clinically diagnosed Alagille Syndrome, but without a molecular diagnosis, revealed four novel diagnoses that were not detectable by the prior standard of care tests. These findings included a submicroscopic inversion in the gene JAG1 and a deletion in NOTCH2, the first-ever pathogenic copy number variant identified in this gene. Further, applying these methods to a cohort of 15 patients with nonsyndromic hearing loss revealed three novel diagnoses. The case series presented in this work argues the advantage of genome sequencing over the current standard of care tests for variants undetectable by their standard of care testing. Together, the frameworks presented in this thesis improved the current standard of care exome test and laid the groundwork for a future clinical test, genome sequencing. In addition, I demonstrated the clinical utility of the tools developed in this work showing how these approaches resulted in novel diagnoses and developed recommendations for broader application in clinical diagnostic settings. Keywords: copy-number variants, next-generation sequencing, Short-read sequencing, structural variation
Book Synopsis Bioinformatics for Beginners by : Supratim Choudhuri
Download or read book Bioinformatics for Beginners written by Supratim Choudhuri and published by Elsevier. This book was released on 2014-05-09 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools provides a coherent and friendly treatment of bioinformatics for any student or scientist within biology who has not routinely performed bioinformatic analysis. The book discusses the relevant principles needed to understand the theoretical underpinnings of bioinformatic analysis and demonstrates, with examples, targeted analysis using freely available web-based software and publicly available databases. Eschewing non-essential information, the work focuses on principles and hands-on analysis, also pointing to further study options. Avoids non-essential coverage, yet fully describes the field for beginners Explains the molecular basis of evolution to place bioinformatic analysis in biological context Provides useful links to the vast resource of publicly available bioinformatic databases and analysis tools Contains over 100 figures that aid in concept discovery and illustration
Book Synopsis Assessing Genomic Sequencing Information for Health Care Decision Making by : Institute of Medicine
Download or read book Assessing Genomic Sequencing Information for Health Care Decision Making written by Institute of Medicine and published by National Academies Press. This book was released on 2014-08-19 with total page 104 pages. Available in PDF, EPUB and Kindle. Book excerpt: Rapid advances in technology have lowered the cost of sequencing an individual's genome from the several billion dollars that it cost a decade ago to just a few thousand dollars today and have correspondingly greatly expanded the use of genomic information in medicine. Because of the lack of evidence available for assessing variants, evaluation bodies have made only a few recommendations for the use of genetic tests in health care. For example, organizations, such as the Evaluation of Genomic Applications in Practice and Prevention working group, have sought to set standards for the kinds of evaluations needed to make population-level health decisions. However, due to insufficient evidence, it has been challenging to recommend the use of a genetic test. An additional challenge to using large-scale sequencing in the clinic is that it may uncover "secondary," or "incidental," findings - genetic variants that have been associated with a disease but that are not necessarily related to the conditions that led to the decision to use genomic testing. Furthermore, as more genetic variants are associated with diseases, new information becomes available about genomic tests performed previously, which raises issues about how and whether to return this information to physicians and patients and also about who is responsible for the information. To help develop a better understanding of how genomic information is used for healthcare decision making, the Roundtable on Translating Genomic-Based Research for Health of the Institute of Medicine held a workshop in Washington,DC in February 2014. Stakeholders, including clinicians, researchers, patients, and government officials, discussed the issues related to the use of genomic information in medical practice. Assessing Genomic Sequencing Information for Health Care Decision Making is the summary of that workshop. This report compares and contrasts evidence evaluation processes for different clinical indications and discusses key challenges in the evidence evaluation process.
Download or read book Bioinformatics written by David Edwards and published by Springer. This book was released on 2014-10-07 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics is a relatively new field of research. It evolved from the requirement to process, characterize, and apply the information being produced by DNA sequencing technology. The production of DNA sequence data continues to grow exponentially. At the same time, improved bioinformatics such as faster DNA sequence search methods have been combined with increasingly powerful computer systems to process this information. Methods are being developed for the ever more detailed quantification of gene expression, providing an insight into the function of the newly discovered genes, while molecular genetic tools provide a link between these genes and heritable traits. Genetic tests are now available to determine the likelihood of suffering specific ailments and can predict how plant cultivars may respond to the environment. The steps in the translation of the genetic blueprint to the observed phenotype is being increasingly understood through proteome, metabolome and phenome analysis, all underpinned by advances in bioinformatics. Bioinformatics is becoming increasingly central to the study of biology, and a day at a computer can often save a year or more in the laboratory. The volume is intended for graduate-level biology students as well as researchers who wish to gain a better understanding of applied bioinformatics and who wish to use bioinformatics technologies to assist in their research. The volume would also be of value to bioinformatics developers, particularly those from a computing background, who would like to understand the application of computational tools for biological research. Each chapter would include a comprehensive introduction giving an overview of the fundamentals, aimed at introducing graduate students and researchers from diverse backgrounds to the field and bring them up-to-date on the current state of knowledge. To accommodate the broad range of topics in applied bioinformatics, chapters have been grouped into themes: gene and genome analysis, molecular genetic analysis, gene expression analysis, protein and proteome analysis, metabolome analysis, phenome data analysis, literature mining and bioinformatics tool development. Each chapter and theme provides an introduction to the biology behind the data describes the requirements for data processing and details some of the methods applied to the data to enhance biological understanding.
Book Synopsis Current Protocols in Bioinformatics by : Andreas D. Baxevanis
Download or read book Current Protocols in Bioinformatics written by Andreas D. Baxevanis and published by Current Protocols. This book was released on 2003 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current Protocols in Bioinformatics is the only publication that responds to the need for both a current and updateable source of bioinformatics methodology. This unique publication assures that you have access to a full range of bioinformatics protocols written by globally-recognized experts in the field, and that these proto-cols are updated and revised as new developments and innovations occur.
Book Synopsis Computational Exome and Genome Analysis by : Peter N. Robinson
Download or read book Computational Exome and Genome Analysis written by Peter N. Robinson and published by CRC Press. This book was released on 2017-09-13 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Molecular Genetic Pathology by : Liang Cheng
Download or read book Molecular Genetic Pathology written by Liang Cheng and published by Springer. This book was released on 2013-03-05 with total page 1136 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Genetic Pathology, Second Edition presents up-to-date material containing fundamental information relevant to the clinical practice of molecular genetic pathology. Fully updated in each area and expanded to include identification of new infectious agents (H1N1), new diagnostic biomarkers and biomarkers for targeted cancer therapy. This edition is also expanded to include the many new technologies that have become available in the past few years such as microarray (AmpliChip) and high throughput deep sequencing, which will certainly change the clinical practice of molecular genetic pathology. Part I examines the clinical aspects of molecular biology and technology, genomics. Poharmacogenomics and proteomics, while Part II covers the clinically relevant information of medical genetics, hematology, transfusion medicine, oncology, and forensic pathology. Supplemented with many useful figures and presented in a helpful bullet-point format, Molecular Genetic Pathology, Second Edition provides a unique reference for practicing pathologists, oncologists, internists, and medical genetisists. Furthermore, a book with concise overview of the field and highlights of clinical applications will certainly help those trainees, including pathology residents, genetics residents, molecular pathology fellows, internists, hematology/oncology fellows, and medical technologists in preparing for their board examination/certification.
Book Synopsis Precision Cancer Medicine by : Sameek Roychowdhury
Download or read book Precision Cancer Medicine written by Sameek Roychowdhury and published by Springer Nature. This book was released on 2020-01-02 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic sequencing technologies have augmented the classification of cancer beyond tissue of origin and towards a molecular taxonomy of cancer. This has created opportunities to guide treatment decisions for individual patients with cancer based on their cancer’s unique molecular characteristics, also known as precision cancer medicine. The purpose of this text will be to describe the contribution and need for multiple disciplines working together to deliver precision cancer medicine. This entails a multi-disciplinary approach across fields including molecular pathology, computational biology, clinical oncology, cancer biology, drug development, genetics, immunology, and bioethics. Thus, we have outlined a current text on each of these fields as they work together to overcome various challenges and create opportunities to deliver precision cancer medicine. As trainees and junior faculty enter their respective fields, this text will provide a framework for understanding the role and responsibility for each specialist to contribute to this team science approach.
