Jan 22, 2015

Alternative splicing QTLs in European and African populations using Altrans, a novel method for splice junction quantification

BioRxiv : the Preprint Server for Biology
Halit Ongen, Emmanouil T Dermitzakis

Abstract

With the advent of RNA-sequencing technology we now have the power to detect different types of alternative splicing and how DNA variation affects splicing. However, given the short read lengths used in most population based RNA-sequencing experiments, quantifying transcripts accurately remains a challenge. Here we present a novel method, Altrans, for discovery of alternative splicing quantitative trait loci (asQTLs). To assess the performance of Altrans we compared it to Cufflinks, a well-established transcript quantification method. Simulations show that in the presence of transcripts absent from the annotation, Altrans performs better in quantifications than Cufflinks. We have applied Altrans and Cufflinks to the Geuvadis dataset, which comprises samples from European and African populations, and discovered (FDR = 1%) 1806 and 243 asQTLs with Altrans, and 1596 and 288 asQTLs with Cufflinks for Europeans and Africans, respectively. Although Cufflinks results replicated better across the two populations, this likely due to the increased sensitivity of Altrans in detecting harder to detect associations. We show that, by discovering a set of asQTLs in a smaller subset of European samples and replicating these in the remaining la...Continue Reading

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Mentioned in this Paper

Quantitative Trait Loci
Genome
Sequence Determinations, RNA
Virus Replication
Evaluation
Sequencing
Nuclear mRNA Cis Splicing, via Spliceosome
RNA Splicing
Simulation
Black African

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