Cancer Genomics and Proteomics pp 219-227

Part of the Methods in Molecular Biology book series (MIMB, volume 1176)

Computational Analysis in Cancer Exome Sequencing

Protocol

Abstract

Exome sequencing in cancer is a powerful tool for identifying mutational events across the coding region of human genes. Here, we describe computational methods that use exome sequencing reads from cancer samples to identify somatic single nucleotide variants (SNVs), copy number alterations, and short insertions and deletions (InDels). We further describe analytical methods to generate lists of driver genes with more mutational events than expected by chance.

Key words

Cancer Single nucleotide variant Copy number variation Exome sequencing Gene burden InDels 

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Department of PathologyYale University School of MedicineNew HavenUSA
  2. 2.W.M. Keck Foundation Biotechnology Resource Laboratory, Department of Molecular Biophysics and BiochemistryYale University School of MedicineNew HavenUSA

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