Tools & best practices for the high-throughput production of allelic expression data from RNA-sequencing data

Allelic expression analysis has become important for integrating genome and transcriptome data to characterize various biological phenomena such as cis-regulatory variation and nonsense-mediated decay. Researchers at the New York Genome Center analyzed the properties of allelic expression read count data and technical sources of error, such as low-quality or double-counted RNA-seq reads, genotyping errors, allelic mapping bias, and technical covariates due to sample preparation and sequencing, and variation in total read depth. Here they provide guidelines for correcting such errors, show that our quality control measures improve the detection of relevant allelic expression, and introduce tools for the high-throughput production of allelic expression data from RNA-sequencing data.

Addtionally, the researchers describe a new tool in the Genome Analyzer Toolkit (GATK) software package for efficient retrieval of raw allelic count data from RNA-seq data, and analyze the properties of AE data and the sources of errors and technical variation, with suggested guidelines for accounting for them. While most types of errors may be rare, they are easily enriched among sites with allelic imbalance, and can sometimes mimic the biological signal of interest, thus warranting careful analysis. The focus here is on methods for obtaining accurate data of AE rather than building a graphical user interface (GUI) pipeline or downstream statistical analysis of its biological sources.


Allelic expression and its sources. a Schematic illustration of AE. b Biological sources of AE, with the x-axis denoting the approximate sharing of AE across tissues of an individual, and the y-axis having the estimated sharing of AE signal in one tissue across different individuals SNP single-nucleotide polymorphism

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Castel SE, Levy-Moonshine A, Mohammadi P, Banks E, Lappalainen T. (2015) Tools and best practices for data processing in allelic expression analysis. Genome Biol 16(1):195. [article]

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