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

Author

Listed:
  • Nava Ehsan

    (The Scripps Research Institute)

  • Bence M. Kotis

    (The Scripps Research Institute)

  • Stephane E. Castel

    (Columbia University
    New York Genome Center)

  • Eric J. Song

    (The Scripps Research Institute)

  • Nicholas Mancuso

    (University of Southern)

  • Pejman Mohammadi

    (The Scripps Research Institute
    Center for Immunity and Immunotherapies, Seattle Children’s Research Institute
    University of Washington School of Medicine
    University of Washington)

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 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.

Suggested Citation

  • Nava Ehsan & Bence M. Kotis & Stephane E. Castel & Eric J. Song & Nicholas Mancuso & Pejman Mohammadi, 2024. "Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-44710-8
    DOI: 10.1038/s41467-024-44710-8
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