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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 HaoEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1833)

Abstract

Somatic copy number alterations (SCNAs) are profound in cancer genomes at different stages: oncogenesis, progression, and metastasis. Accurate detection and characterization of SCNA landscape at genome-wide scale are of great importance. Next-generation sequencing and SNP array are current technology of choice for SCNA analysis. They are able to quantify SCNA with high resolution and meanwhile raise great challenges in data analysis. To this end, we have developed an R package saasCNV for SCNA analysis using (1) whole-genome sequencing (WGS), (2) whole-exome sequencing (WES) or (3) whole-genome SNP array data. In this chapter, we provide the features of the package and step-by-step instructions in detail.

Key words

Copy number variation Somatic copy number alteration SAAS-CNV Next-generation sequencing Whole-genome sequencing Whole-exome sequencing SNP array Segmentation Cancer genome 

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkUSA

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