Copy Number Variants: Methods and Protocols

ISBN-13: 9781493993598 / Angielski / Miękka / 2019 / 206 str.

Derek M. Bickhart

Spis treści

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

 

Blurb

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