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Allele-Specific Expression Analysis in Cancer Using Next-Generation Sequencing Data

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1878)

Abstract

Allele-specific expression arises when transcriptional activity at the different alleles of a gene differs considerably. Although extensive research has been carried out to detect and characterize this phenomenon, the landscape of allele-specific expression in cancer is still poorly understood. In this chapter, we describe a fast and reliable analysis pipeline to study allele-specific expression in cancer using next-generation sequencing data. The pipeline provides a gene-level analysis approach that exploits paired germline DNA and tumor RNA sequencing data and benefits from parallel computation resources when available.

Key words

Allele-specific features Genome analysis Parallel computation Transcriptome analysis Next-generation sequencing SNPs 
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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Centre for Integrative Biology (CIBIO)University of TrentoTrentoItaly

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