MBASED: Allele-specific Expression Detection in Cancer Tissues and Cell Lines

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2014 Oct 16

PMID 25315065

Citations 71

Authors

Oleg Mayba

Houston N Gilbert

Jinfeng Liu

Peter M Haverty

Suchit Jhunjhunwala

Zhaoshi Jiang

Colin Watanabe

Zemin Zhang

Affiliations

Soon will be listed here.

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.

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