Hierarchical Analysis of RNA-Seq Reads Improves the Accuracy of Allele-specific Expression.

Narayanan Raghupathy, The Jackson Laboratory
Kwangbom Choi, The Jackson Laboratory
Matthew J Vincent, The Jackson Laboratory
Glen L Beane, The Jackson Laboratory
Keith Sheppard, The Jackson Laboratory
Steven C. Munger, The Jackson Laboratory
Ron Korstanje, The Jackson Laboratory
Fernando Pardo-Manual de Villena
Gary Churchill, The Jackson Laboratory


Motivation: Allele-specific expression (ASE) refers to the differential abundance of the allelic copies of a transcript. RNA sequencing (RNA-Seq) can provide quantitative estimates of ASE for genes with transcribed polymorphisms. When short-read sequences are aligned to a diploid transcriptome, readmapping ambiguities confound our ability to directly count reads. Multi-mapping reads aligning equally well to multiple genomic locations, isoforms, or alleles can comprise the majority (>85%) of reads. Discarding them can result in biases and substantial loss of information. Methods have been developed that use weighted allocation of read counts but these methods treat the different types of multi-reads equivalently. We propose a hierarchical approach to allocation of read counts that first resolves ambiguities among genes, then among isoforms, and lastly between alleles. We have implemented our model in EMASE software (Expectation-Maximization for Allele Specific Expression) to estimate total gene expression, isoform usage, and ASE based on this hierarchical allocation.

Results: Methods that align RNA-Seq reads to a diploid transcriptome incorporating known genetic variants improve estimates of ASE and total gene expression compared to methods that use reference genome alignments. Weighted allocation methods outperform methods that discard multi-reads. Hierarchical allocation of reads improves estimation of ASE even when data are simulated from a nonhierarchical model. Analysis of RNA-Seq data from F1 hybrid mice using EMASE reveals widespread ASE associated with cis-acting polymorphisms and a small number of parent-of-origin effects.

Availability: EMASE software is available at https://github.com/churchill-lab/emase.

Contact: Gary.Churchill@jax.org.

Supplementary information: Supplementary data are available at Bioinformatics online.

Bioinformatics 2018 Feb 12 [Epub ahead of print]