Copy number variants : methods and protocols

著者

    • Bickhart, Derek M.

書誌事項

Copy number variants : methods and protocols

edited by Derek M. Bickhart

（Methods in molecular biology / John M. Walker, series editor, 1833）（Springer protocols）

Humana Press, 2018

  • : [hardback]

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注記

"Corrected publication 2018"--T.p. verso

Includes bibliographical references and index

内容説明・目次

内容説明

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

目次

1. Identification of Copy Number Variants from SNP Arrays using PennCNV Li Fang and Kai Wang 2. Using SAAS-CNV to Detect and Characterize Somatic Copy Number Alterations in Cancer Genomes from Next Generation Sequencing and SNP Array Data Zhongyang Zhang and Ke Hao 3. Statistical Detection of Genome Differences Based on CNV Segments Yang Zhou, Derek M. Bickhart, and George E. Liu 4. Whole Genome Shotgun Sequence CNV Detection using Read Depth Fatma Kahveci and Can Alkan 5. Read Depth Analysis to Identify CNV in Bacteria using CNOGpro Ola Brynildsrud 6. Using HaMMLET for Bayesian Segmentation of WGS read-depth Data John Wiedenhoeft and Alexander Schliep 7. Split-Read InDel and Structural Variant Calling Using PINDEL Kai Ye, Li Guo, Xiaofei Yang, Eric-Wubbo Lamijer, Keiran Raine, and Zemin Ning 8. Detecting Small Inversions using SRinversion Ruoyan Chen, Yu Lung Lau, and Wanling Yang 9. Detection of CNVs in NGS data using VS-CNV Nathan Fortier, Gabe Rudy, and Andreas Scherer 10. Structural Variant Breakpoint Detection with novoBreak Zechen Chong and Ken Chen 11. Use of RAPTR-SV to Identify SVs from Read Pairing and Split Read Signatures Derek M. Bickhart 12. Versatile Identification of Copy Number Variants with Canvas Sergii Ivakhno and Eric Roller 13. Markov Chain Monte Carlo SV Calling with SVelter Xuefang Zhao 14. Analysis of Population-genetic Properties of Copy Number Variations Lingyang Xu, Yang Liu, Derek M. Bickhart, JunYa Li, and George E. Liu 15. Validation of Genomic Structural Variants through Long Sequencing Technologies Xuefang Zhao 16. Structural Variation Detection and Analysis using Bionano Optical Mapping Saki Chan, Ernest Lam, Michael Saghbini, Sven Bocklandt, Alex Hastie, Han Cao, Erik Holmlin, and Mark Borodkin

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