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This volume covers the detection of structural variants (SVs), which require different strategies than the ones used for single nucleotide variants (SNVs). This book aims to provide readers with a combination of the latest “wet lab” methods and computational pipelines that target all SV classes. The chapters in this book cover topics such as detection of transposable elements (TEs) from short read data; long read sequencing used for multiple variable number tandem repeat analysis; genomic mosaicism in the nervous system; and optical genome mapping. In the Neuromethods series style, chapters include the kind of detail and key advice from the specialists needed to get successful results in your laboratory. Cutting-edge and comprehensive, Genomic Structural Variants in Nervous System Disorders is a valuable resource for scientists and researchers interested in learning more about this important field.
The past few years have witnessed extraordinary advances in molecular genetic techniques and the accumulation of structural genomics information and resources in both human and model organisms. With the development of new technologies and the availability of resources like the sequence of eukaryotic genomes, problems of a previously unthinkable sco
Neurodegenerative diseases represent a large group of neurological disorders with heterogeneous clinical and pathological presentations--often affecting a specific subset of cells in particular anatomical regions. These complex and often overlapping features presents a challenge in identifying the cause behind the vulnerability of these cell populations and anatomical area. However, with recent advancements in omics technology, the complexity of the mammalian brain is being rapidly teased out. Two of these technologies offer a unique perspective and deeper resolution to study the heterogeneity in the brain: long-read sequencing and single-cell microfluidics. In this dissertation, I demonstrate the use of one or both technologies to further characterize the heterogeneity in human brain and its relationship to various neurodegenerative diseases. My initial work identifies a novel genomic structural variant in the gene SNCA, a causal gene in Parkinson's disease (PD) and other synucleinopathies. These intron-less sequences are known as gencDNAs (genomic cDNA) and are found in human cortical neurons of both PD and age-matched controls in a mosaic manner. Furthermore, it is unveiled that a small subset of copies contains point mutations in loci reported to cause monogenic PD, if mutated in its native counterpart, when using long-read amplicon sequencing. Though much is unknown about of SNCA gencDNAs, it is hypothesized to be created due to a reverse transcription event and re-inserted back into the genome. My subsequent work combines both single-cell RNA sequencing and long-read sequencing to examine and compare the transcriptome of various neurodegenerative diseases in the frontal cortex at a single cell resolution. Despite being a synucleinopathy, dementia with Lewy bodies (DLB) has more transcriptomic similarities to Alzheimer's disease (AD) than with PD. While profiling the isoforms of selected genes within these diseases, a vast number of novel isoforms are also identified, with some specific to a particular cell type, such as NRGN. Finally, some major isoform switching is observed in at a cell type resolution, even in genes that were not differentially expressed in our short-read RNA-seq data, such as BIN1 in DLB oligodendrocyte and CLU in AD and DLB excitatory neurons. This dissertation further illuminates the heterogeneity in the human brain at a genomic and transcriptomic layer in the context of various neurodegeneration using long-read sequencing and single cell microfluidics.
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.
At last, here is a baseline book for anyone who is confused by cryptic computer programs, algorithms and formulae, but wants to learn about applied bioinformatics. Now, anyone who can operate a PC, standard software and the internet can also learn to understand the biological basis of bioinformatics, of the existence as well as the source and availability of bioinformatics software, and how to apply these tools and interpret results with confidence. This process is aided by chapters that introduce important aspects of bioinformatics, detailed bioinformatics exercises (including solutions), and to cap it all, a glossary of definitions and terminology relating to bioinformatics.
Completely updated for its Fourth Edition, this book is the most comprehensive, current review of the molecular and genetic basis of neurologic and psychiatric diseases. More than 120 leading experts provide a fresh, new assessment of recent molecular, genetic, and genomic advances, offer new insights into disease pathogenesis, describe the newest available therapies, and explore promising areas of therapeutic development. This edition features an updated section on psychiatric disease and expanded, updated chapters on human genomics, gene therapy, and ethical issues. Six new chapters cover congenital myasthenic syndromes, hereditary spastic paraplegia, ion channel disorders, the phakomatoses, beta-galactosidase deficiency, and prion diseases. A Neurologic Gene Map describes the chromosome locus of all the genetic diseases and their gene product where known. The fully searchable online text will be available on a companion Website. (www.rosenbergneuroandpsychdisease.com)
This newest volume of Advances in Neurobiology discusses the utilization of genomic and proteomic technologies, to address facets of neurobiology including development and epigenetic regulation, functions in learning and memory, and changes associated with neurological and psychiatric disorders.
Rosenberg’s Molecular and Genetic Basis of Neurologic and Psychiatric Disease, Sixth Edition: Volume One, provides a comprehensive introduction and reference to the foundations and key practical aspects relevant to neurologic and psychiatric disease. A favorite of over three generations of students, clinicians and scholars, this new edition retains and expands the informative, concise and critical tone of the first edition. This is an essential reference for general medical practitioners, neurologists, psychiatrists, geneticists, and related professionals, and for the neuroscience and neurology research community. The content covers all aspects essential to the practice of neurogenetics to inform clinical diagnosis, treatment and genetic counseling. Every chapter has been thoroughly revised or newly commissioned to reflect the latest scientific and medical advances by an international team of leading scientists and clinicians. The contents have been expanded to include disorders for which a genetic basis has been recently identified, together with abundant original illustrations that convey and clarify the key points of the text in an attractive, didactic format. Comprehensive coverage of the neurogenetic foundation of neurological and psychiatric disease Provides a detailed introduction on both the clinical and basic research implications of molecular and genetics surrounding the brain Includes new chapters on molecular genomics, CRISPR and the most recent updates in molecular genetics
Preceded by Genomics and clinical medicine / edited by Dhavendra Kumar. [First edition]. 2008.