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Methods Mol Biol. 2019;1878:125-137. doi: 10.1007/978-1-4939-8868-6_7.

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

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Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy.


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.


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

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