PT  - JOURNAL ARTICLE
AU  - Nava Ehsan
AU  - Bence M. Kotis
AU  - Stephane E. Castel
AU  - Eric J. Song
AU  - Nicholas Mancuso
AU  - Pejman Mohammadi
TI  - Haplotype-aware modeling of <em>cis</em>-regulatory effects highlights the gaps remaining in eQTL data
AID  - 10.1101/2022.01.28.478116
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.01.28.478116
4099  - http://biorxiv.org/content/early/2022/01/28/2022.01.28.478116.short
4100  - http://biorxiv.org/content/early/2022/01/28/2022.01.28.478116.full
AB  - 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 accurate quantification of the cis-regulatory effects in genes with multiple conditionally independent eQTLs. Applying aFC-n to 458,465 eQTLs in the Genotype-Tissue Expression (GTEx) project data, we demonstrate significant improvement in accuracy over the current tools for estimating the eQTL effect size and predicting genetically regulated gene expression. We characterize some of the empirical properties of the eQTL data and use this framework to assess the current state of eQTL data in terms of characterizing cis-regulatory landscape in individual genomes. Notably, we show that 77.4% of the genes with an allelic imbalance in a sample show 0.5 log2 fold or more of residual imbalance after accounting for the eQTL data underlining the remaining gap in characterizing regulatory landscape in individual genomes. We further contrast this gap across tissue types, and ancestry backgrounds to identify its correlates and guide future studies.Competing Interest StatementStephane E. Castel is a co-founder, Chief Technology Officer, and stock owner at Variant Bio.