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Genomic Structural Variants in Nervous System Disorders

  • Book
  • © 2022

Overview

Editors:
  1. Christos Proukakis

    1. Queen Square Institute of Neurology, University College London, London, UK

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Neuromethods (NM, volume 182)

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Table of contents (14 protocols)

  1. Front Matter

    Pages i-xvi
    Download chapter PDF

  2. snakeSV: Flexible Framework for Large-Scale SV Discovery

    • Ricardo A. Vialle, Towfique Raj
    Pages 1-14

  3. Detecting Tandem Repeat Expansions Using Short-Read Sequencing for Clinical Use

    • Mark F. Bennett, Arianna Tucci, Melanie Bahlo
    Pages 15-42

  4. Transposable Element Structural Variants in Parkinson’s Disease: Focusing on Genotyping Alu Transposable Element Insertions with TypeTE

    • Kimberley Billingsley, Jainy Thomas, Clément Goubert
    Pages 43-62

  5. Analysis of the Retrotransposon SINE-VNTR-Alu (SVA) Polymorphisms in the Genetics and Pathophysiology of Complex Diseases

    • Sulev Kõks, Lewis M. Singleton, John P. Quinn, Vivien J. Bubb, Abigail L. Pfaff
    Pages 63-77

  6. Long-Read Sequencing and Analysis of Variable Number Tandem Repeats

    • Meredith M. Course, Kathryn Gudsnuk, Paul N. Valdmanis
    Pages 79-94

  7. Multiplex CRISPR/Cas9-Guided No-Amp Targeted Sequencing Panel for Spinocerebellar Ataxia Repeat Expansions

    • Yu-Chih Tsai, Faria Zafar, Zachary T. McEachin, Ian McLaughlin, Marka Van Blitterswijk, Janet Ziegle et al.
    Pages 95-120

  8. Detecting the NOTCH2NLC Repeat Expansion in Neuronal Intranuclear Inclusion Disease

    • Satomi Mitsuhashi, Atsushi Fujita, Naomichi Matsumoto
    Pages 121-138

  9. Analysis of the Hexanucleotide Repeat Domain in the TAF1 SVA Retrotransposon in X-Linked Dystonia-Parkinsonism

    • Charles Jourdan Reyes, Theresa Lüth, Joanne Trinh
    Pages 139-153

  10. Neurogenetic Variant Analysis by Optical Genome Mapping for Structural Variation Detection-Balanced Genomic Rearrangements, Copy Number Variants, and Repeat Expansions/Contractions

    • Hayk Barseghyan, Andy W. C. Pang, Yang Zhang, Nikhil S. Sahajpal, Yannick Delpu, Chi-Yu Jill Lai et al.
    Pages 155-172

  11. Copy Number Variation Analysis from SNP Genotyping Microarrays in Large Cohorts of Neurological Disorders

    • Eduardo Pérez-Palma, Lisa-Marie Niestroj, Miguel Inca-Martínez, Camilo Villaman, Elif Irem Sarihan, Dennis Lal et al.
    Pages 173-195

  12. Locus-Specific DNA Methylation Profiling of Human LINE-1 Retrotransposons

    • Francisco J. Sanchez-Luque, Marie-Jeanne H. C. Kempen, Geoffrey J. Faulkner
    Pages 197-227

  13. Combined Fluorescent In Situ Hybridization (FISH) and Immunofluorescence for the Targeted Detection of Somatic Copy Number Variants in Synucleinopathies

    • Monica Emili Garcia-Segura, Diego Perez-Rodriguez, Christos Proukakis
    Pages 229-243

  14. Visualization of Defined Gene Sequences in Single Nuclei by DNA In Situ Hybridization (DISH)

    • Chris Park, Gwendolyn E. Kaeser, Jerold Chun
    Pages 245-256

  15. Assessing Mitochondrial DNA Deletions and Copy-Number Changes in Microdissected Neurons

    • Christian Dölle, Gonzalo S. Nido, Irene Flønes, Charalampos Tzoulis
    Pages 257-270

  16. Back Matter

    Pages 271-272
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Keywords

About this book

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. 


Editors and Affiliations

  • Queen Square Institute of Neurology, University College London, London, UK

    Christos Proukakis

Bibliographic Information

  • Book Title: Genomic Structural Variants in Nervous System Disorders

  • Editors: Christos Proukakis

  • Series Title: Neuromethods

  • DOI: https://doi.org/10.1007/978-1-0716-2357-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-2356-5Published: 01 June 2022

  • Softcover ISBN: 978-1-0716-2359-6Published: 02 June 2023

  • eBook ISBN: 978-1-0716-2357-2Published: 31 May 2022

  • Series ISSN: 0893-2336

  • Series E-ISSN: 1940-6045

  • Edition Number: 1

  • Number of Pages: XVI, 272

  • Number of Illustrations: 23 b/w illustrations, 48 illustrations in colour

  • Topics: Neurosciences

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