Skip to main content
SpringerLink
Log in
Book cover

Copy Number Variants

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Derek M. Bickhart

    1. Research Microbiologist/Bioinformatician, USDA ARS DFRC, Madison, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • 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: Methods in Molecular Biology (MIMB, volume 1833)

This is a preview of subscription content, log in via an institution to check access.

Access this book

Log in via an institution
eBook USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

Table of contents (17 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Identification of Copy Number Variants from SNP Arrays Using PennCNV

    • Li Fang, Kai Wang
    Pages 1-28

  3. Using SAAS-CNV to Detect and Characterize Somatic Copy Number Alterations in Cancer Genomes from Next Generation Sequencing and SNP Array Data

    • Zhongyang Zhang, Ke Hao
    Pages 29-47

  4. Statistical Detection of Genome Differences Based on CNV Segments

    • Yang Zhou, Derek M. Bickhart, George E. Liu
    Pages 49-59

  5. Whole-Genome Shotgun Sequence CNV Detection Using Read Depth

    • Fatma Kahveci, Can Alkan
    Pages 61-72

  6. Read Depth Analysis to Identify CNV in Bacteria Using CNOGpro

    • Ola Brynildsrud
    Pages 73-81

  7. Using HaMMLET for Bayesian Segmentation of WGS Read-Depth Data

    • John Wiedenhoeft, Alexander Schliep
    Pages 83-93

  8. Split-Read Indel and Structural Variant Calling Using PINDEL

    • Kai Ye, Li Guo, Xiaofei Yang, Eric-Wubbo Lamijer, Keiran Raine, Zemin Ning
    Pages 95-105

  9. Detecting Small Inversions Using SRinversion

    • Ruoyan Chen, Yu Lung Lau, Wanling Yang
    Pages 107-114

  10. Detection of CNVs in NGS Data Using VS-CNV

    • Nathan Fortier, Gabe Rudy, Andreas Scherer
    Pages 115-127

  11. Structural Variant Breakpoint Detection with novoBreak

    • Zechen Chong, Ken Chen
    Pages 129-141

  12. Use of RAPTR-SV to Identify SVs from Read Pairing and Split Read Signatures

    • Derek M. Bickhart
    Pages 143-153

  13. Versatile Identification of Copy Number Variants with Canvas

    • Sergii Ivakhno, Eric Roller
    Pages 155-168

  14. A Randomized Iterative Approach for SV Discovery with SVelter

    • Xuefang Zhao
    Pages 169-177

  15. Analysis of Population-Genetic Properties of Copy Number Variations

    • Lingyang Xu, Liu Yang, Derek M. Bickhart, JunYa Li, George E. Liu
    Pages 179-186

  16. Validation of Genomic Structural Variants Through Long Sequencing Technologies

    • Xuefang Zhao
    Pages 187-192

  17. Structural Variation Detection and Analysis Using Bionano Optical Mapping

    • Saki Chan, Ernest Lam, Michael Saghbini, Sven Bocklandt, Alex Hastie, Han Cao et al.
    Pages 193-203

  18. Correction to: Analysis of Population-Genetic Properties of Copy Number Variations

    • Lingyang Xu, Liu Yang, Derek M. Bickhart, JunYa Li, George E. Liu
    Pages E1-E1

  19. Back Matter

    Pages 205-206
    Download chapter PDF
Back to top

Keywords

About this book

This volume offers detailed step-by-step instructions to allow beginners and experts alike to run appropriate copy number variants (CNV) detection software on a dataset of choice and discern between false positive noise and true positive CNV signals. Chapters guide readers through single nucleotide polymorphism (SNP) chips, optical mapping assembly techniques, and current open-source programs specializing in CNV detection.  Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Copy Number Variants: Methods and Protocols aims to provide guidance to Bioinformaticians and Molecular Biologists who are interested in identifying copy number variants (CNV) with a wide variety of experimental media

Editors and Affiliations

  • Research Microbiologist/Bioinformatician, USDA ARS DFRC, Madison, USA

    Derek M. Bickhart

Bibliographic Information

  • Book Title: Copy Number Variants

  • Book Subtitle: Methods and Protocols

  • Editors: Derek M. Bickhart

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-8666-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2018

  • Hardcover ISBN: 978-1-4939-8665-1Published: 24 July 2018

  • Softcover ISBN: 978-1-4939-9359-8Published: 10 December 2019

  • eBook ISBN: 978-1-4939-8666-8Published: 23 July 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 206

  • Number of Illustrations: 11 b/w illustrations, 25 illustrations in colour

  • Topics: Bioinformatics

Publish with us

Policies and ethics

Back to top

Search

Navigation