Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
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.
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 Clément Goubert
4.Analysis of the Retrotransposon SINE-VNTR-Alu (SVA) Polymorphisms in the Genetics and Pathophysiology of Complex Diseases
Sulev Kõks, 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 Schüle
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 Lüth, 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 Pérez-Palma, Lisa-Marie Niestroj, Miguel Inca-Martínez, 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 Dölle, Gonzalo S. Nido, Irene Flønes, and Charalampos Tzoulis
Subject Index List...
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.
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.
snakeSV: Flexible Framework for Large-Scale SV Discovery.- Detecting Tandem Repeat Expansions using Short Read Sequencing for Clinical Use.- Transposable Element Structural Variants in Parkinson's Disease, Focusing on Genotyping Alu Transposable Element Insertions with TypeTE.- Analysis of the Retrotransposon SINE-VNTR-Alu (SVA) Polymorphisms in the Genetics and Pathophysiology of Complex Diseases.- Long-Read Sequencing and Analysis of Variable Number Tandem Repeats.- Multiplex CRISPR/Cas9-Guided No-Amp Targeted Sequencing Panel for Spinocerebellar Ataxia Repeat Expansions.- Detecting the NOTCH2NLC Repeat Expansion in Neuronal Intranuclear Inclusion Disease.- Analysis of the Hexanucleotide Repeat Domain in the TAF1 SVA Retrotransposon in X-Linked Dystonia-Parkinsonism.- Neurogenetic Variant Analysis by Optical Genome Mapping for Structural Variation Detection-Balanced Genomic Rearrangements, Copy Number Variants, and Repeat Expansions/Contractions.- Copy Number Variation Analysisfrom SNP Genotyping Microarrays in Large Cohorts of Neurological Disorders.- Locus-Specific DNA Methylation Profiling of Human LINE-1 Retrotransposons.- Combined Fluorescent In-Situ Hybridization (FISH) and Immunofluorescence for the Targeted Detection of Somatic Copy Number Variants in Synucleinopathies.- Visualization of Defined Gene Sequences in Single Cell Nuclei by DNA In Situ Hybridization (DISH).- Assessing Mitochondrial DNA Deletions and Copy Number Changes in Microdissected Neurons.
Inhaltsverzeichnis
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 Clément Goubert
4.Analysis of the Retrotransposon SINE-VNTR-Alu (SVA) Polymorphisms in the Genetics and Pathophysiology of Complex Diseases
Sulev Kõks, 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 Schüle
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 Lüth, 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 Pérez-Palma, Lisa-Marie Niestroj, Miguel Inca-Martínez, 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 Dölle, Gonzalo S. Nido, Irene Flønes, and Charalampos Tzoulis
Subject Index List...
Klappentext
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.
Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
