Copy Number Variants Methods and Protocols [Hardcover]

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.

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