Genome wide discovery of genetic variants affecting alternative splicing patterns in human using bioinformatics method

Abstract

The alternative splicing pattern of transcription units can be influenced by the genotype of a neighboring locus, which is termed splicing quantitative trait locus (sQTL). Here we report a comprehensive catalog of sQTLs discovered from the public RNA-seq and matched genotype datasets of three European ancestries. Each pair of RNA-seq and genotype dataset was analyzed with IVAS, a locally developed R/Bioconductor package for sQTL discovery. A meta-analysis was applied to the three result sets to reach a consensus of 2525 sQTLs (FDR < 0.05). Among them, nine independent sQTLs overlapped the known signals in the catalog of genome-wide association studies. Interestingly, six of these sQTLs are associated with the alternative exons, whose absence would hamper the protein function by omitting a critical/conserved domain. Altogether, we report the list of candidate sQTLs, and it might be useful for the explanations of trait-associated polymorphisms.

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