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MBASED: allele-specific expression detection in cancer tissues and cell lines

Oleg Mayba1*, Houston N Gilbert2, Jinfeng Liu1, Peter M Haverty1, Suchit Jhunjhunwala1, Zhaoshi Jiang1, Colin Watanabe1 and Zemin Zhang1*

Author Affiliations

1 Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco 94080, CA, USA

2 Department of Biostatistics, Genentech Inc, South San Francisco 94080, CA, USA

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Genome Biology 2014, 15:405  doi:10.1186/s13059-014-0405-3

Published: 7 August 2014

Abstract

Allele-specific gene expression, ASE, is an important aspect of gene regulation. We developed a novel method MBASED, meta-analysis based allele-specific expression detection for ASE detection using RNA-seq data that aggregates information across multiple single nucleotide variation loci to obtain a gene-level measure of ASE, even when prior phasing information is unavailable. MBASED is capable of one-sample and two-sample analyses and performs well in simulations. We applied MBASED to a panel of cancer cell lines and paired tumor-normal tissue samples, and observed extensive ASE in cancer, but not normal, samples, mainly driven by genomic copy number alterations.