Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data.

ABSTRACT: Expression Quantitative Trait Loci (eQTLs) are critical to understanding the mechanisms underlying disease-associated genomic loci. Nearly all protein-coding genes in the human genome have been associated with one or more eQTLs. Here we introduce a multi-variant generalization of allelic Fold Change (aFC), aFC-n, to enable quantification of the cis-regulatory effects in multi-eQTL genes under the assumption that all eQTLs are known and conditionally independent. Applying aFC-n to 458,465 eQTLs in the Genotype-Tissue Expression (GTEx) project data, we demonstrate significant improvements in accuracy over the original model in estimating the eQTL effect sizes and in predicting genetically regulated gene expression over the current tools. We characterize some of the empirical properties of th

SUBMITTER: Ehsan N 

PROVIDER: S-EPMC10789818 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature