Copy number variants : methods and protocols
著者
書誌事項
Copy number variants : methods and protocols
（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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