Main description:

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.

Contents:

Acknowledgement...

Series Preface...

Preface...

Table of Contents...

Contributing Authors...

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

Ricardo A. Vialle, and Towfique Raj

2. Detecting Tandem Repeat Expansions using Short Read Sequencing for Clinical Use

Mark F. Bennett, Arianna Tucci, and Melanie Bahlo

3. Transposable Element Structural Variants in Parkinson's Disease, Focusing on Genotyping Alu Transposable Element Insertions with TypeTE

Kimberley Billingsley, Jainy Thomas, and Clement Goubert

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

Sulev Koks, Lewis Singleton, John P. Quinn, Vivien J. Bubb, and Abigail L. Pfaff

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

Meredith M. Course, Kathryn Gudsnuk, and Paul N. Valdmanis

6. 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, and Birgitt Schule

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

Satomi Mitsuhashi, Atsushi Fujita, and Naomichi Matsumoto

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

Charles Jourdan Reyes, Theresa Luth, and Joanne Trinh

9. 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, Joyce Lee, Chloe Tessereau, Mark Oldakowski, Ravindra B. Kolhe, Henry Houlden, Peter L. Nagy, Aaron D. Bossler, Alka Chaubey, and Alex R. Hastie

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

Eduardo Perez-Palma, Lisa-Marie Niestroj, Miguel Inca-Martinez, Camilo Villaman, Elif Irem Sarihan, Dennis Lal, and Ignacio Mata

11. Locus-Specific DNA Methylation Profiling of Human LINE-1 Retrotransposons Francisco J. Sanchez-Luque, Marie-Jeanne H.C. Kempen, and Geoffrey J. Faulkner

12. 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, and Christos Proukakis

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

Chris Park, Gwendolyn E. Kaeser, and Jerold Chun

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

Christian Doelle, Gonzalo S. Nido, Irene Flones, and Charalampos Tzoulis

Subject Index List...