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.
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Notes
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Only dbSNP 144 common SNPs represented in the 1000 Genome Project genotype data and with global MAF greater or equal to 1% were considered.
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Romanel, A. (2019). Allele-Specific Expression Analysis in Cancer Using Next-Generation Sequencing Data. In: Krasnitz, A. (eds) Cancer Bioinformatics. Methods in Molecular Biology, vol 1878. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8868-6_7
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DOI: https://doi.org/10.1007/978-1-4939-8868-6_7
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