ScReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets.

ABSTRACT:

Background

Recently, pioneering expression quantitative trait loci (eQTL) studies on single cell RNA sequencing (scRNA-seq) data have revealed new and cell-specific regulatory single nucleotide variants (SNVs). Here, we present an alternative QTL-related approach applicable to transcribed SNV loci from scRNA-seq data: scReQTL. ScReQTL uses Variant Allele Fraction (VAF_RNA) at expressed biallelic loci, and corelates it to gene expression from the corresponding cell.

Results

Our approach employs the advantage that, when estimated from multiple cells, VAF_RNA can be used to assess effects of SNVs in a single sample or individual. In this setting scReQTL operates in the context of identical genotypes, where it is likely to capture RNA-mediated genetic interac

SUBMITTER: Liu H 

PROVIDER: S-EPMC7791999 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature