Where Are the Disease-Associated eQTLs?
Open accessAbstract
Most disease-associated variants, although located in putatively regulatory regions, do not have detectable effects on gene expression. One explanation could be that we have not examined gene expression in the cell types or conditions that are most relevant for disease. Even large-scale efforts to study gene expression across tissues are limited to human samples obtained opportunistically or postmortem, mostly from adults. In this review we evaluate recent findings and suggest an alternative strategy, drawing on the dynamic and highly context-specific nature of gene regulation. We discuss new technologies that can extend the standard regulatory mapping framework to more diverse, disease-relevant cell types and states.
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Single-cell eQTL mapping identifies cell type–specific genetic control of autoimmune disease
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Systematic differences in discovery of genetic effects on gene expression and complex traits
Mostafavi, H., Spence, J. P., Naqvi, S., & Pritchard, J. K. (2023) · Nature Genetics · doi:10.1038/s41588-023-01529-1 · Cited by 336 · see citing works
Graph representation learning in biomedicine and healthcare
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“By re-imagining genome-wide-association studies and expression-quantitative-trait-loci studies 203 as networks, biologically meaningful modules can be discovered that highlight key genes involved in the underlying mechanisms of a disease 204 .”
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Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity
Gazal, S., Weissbrod, O., Hormozdiari, F., Dey, K. K., Nasser, J., Jagadeesh, K. A., Weiner, D. J., Shi, H., Fulco, C. P., O’Connor, L. J., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01087-y · Cited by 181 · see citing works
Human immune diversity: from evolution to modernity
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Single-cell genomics meets human genetics
Cuomo, A. S. E., Nathan, A., Raychaudhuri, S., MacArthur, D. G., & Powell, J. E. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00599-5 · Cited by 124 · see citing works
Scalable genetic screening for regulatory circuits using compressed Perturb-seq
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Hold out the genome: a roadmap to solving the cis-regulatory code
de Boer, C. G., & Taipale, J. (2024) · Nature · doi:10.1038/s41586-023-06661-w · Cited by 107 · see citing works
Expression quantitative trait locus studies in the era of single-cell omics
Luo, J., Wu, X., Cheng, Y., Chen, G., Wang, J., & Song, X. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1182579 · Cited by 11 · see citing works
- Authors
- Umans, B. D., Battle, A., & Gilad, Y.
- Affiliations
- University of Chicago (US)
- Johns Hopkins University (US)
- Corresponding author
- Umans, Benjamin D.
- Battle, Alexis
- Gilad, Yoav
- Venue
- Trends in Genetics
- Publisher
- Elsevier BV
- Published
- 2021-02
- Volume
- 37
- Issue
- 2
- Pages
- 109-124
- ISSN
- 0168-9525 (ISSN-L)
- PMC
- PMC8162831
- OpenAlex
- W3083216853
- Cited by
- 296
- References
- 132
- Citations by year
- 2026: 41 · 2025: 65 · 2024: 66 · 2023: 57 · 2022: 41 · 2021: 25 · 2020: 1
- FWCI
- 4.42
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Trends in Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (R35GM131726, R01GM120167)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- disease-associated variants, expression quantitative trait loci, gene expression regulation, regulatory mapping, cell type-specific gene expression, tissue-specific gene expression, cell states, regulatory variants
- MeSH terms
- Animals, Gene Expression Regulation, Humans, Regulatory Sequences, Nucleic Acid, Gene Expression, Genetic Predisposition to Disease, Quantitative Trait Loci
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