ReQTL: identifying correlations between expressed SNVs and gene expression using RNA-sequencing data

摘要

Motivation: By testing for associations between DNA genotypes and gene expression levels, expression quantitative trait locus (eQTL) analyses have been instrumental in understanding how thousands of single nucleotide variants (SNVs) may affect gene expression. As compared to DNA genotypes, RNA genetic variation represents a phenotypic trait that reflects the actual allele content of the studied system. RNA genetic variation at expressed SNV loci can be estimated using the proportion of alleles bearing the variant nucleotide (variant allele fraction, VAF(RNA)). VAF(RNA) is a continuous measure which allows for precise allele quantitation in loci where the RNA alleles do not scale with the genotype count. We describe a method to correlate VAF(RNA) with gene expression and assess its ability to identify genetically regulated expression solely from RNA-sequencing (RNA-seq) datasets.