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Systematic differences in discovery of genetic effects on gene expression and complex traits

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Mostafavi, Hakhamanesh, Spence, Jeffrey P., Naqvi, Sahin, Pritchard, Jonathan K.·2023·Nature Genetics

DOI 10.1038/s41588-023-01529-1PMC PMC12270542

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Abstract

Most signals in genome-wide association studies (GWAS) of complex traits implicate noncoding genetic variants with putative gene regulatory effects. However, currently identified regulatory variants, notably expression quantitative trait loci (eQTLs), explain only a small fraction of GWAS signals. Here, we show that GWAS and cis-eQTL hits are systematically different: eQTLs cluster strongly near transcription start sites, whereas GWAS hits do not. Genes near GWAS hits are enriched in key functional annotations, are under strong selective constraint and have complex regulatory landscapes across different tissue/cell types, whereas genes near eQTLs are depleted of most functional annotations, show relaxed constraint, and have simpler regulatory landscapes. We describe a model to understand these observations, including how natural selection on complex traits hinders discovery of functionally relevant eQTLs. Our results imply that GWAS and eQTL studies are systematically biased toward different types of variant, and support the use of complementary functional approaches alongside the next generation of eQTL studies.

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Authors: Mostafavi, H., Spence, J. P., Naqvi, S., & Pritchard, J. K.
Affiliations: Stanford University (US)
Corresponding author: Mostafavi, Hakhamanesh
Pritchard, Jonathan K.
ORCID: Mostafavi, Hakhamanesh
Spence, Jeffrey P.
Naqvi, Sahin
Pritchard, Jonathan K.
Venue: Nature Genetics
Publisher: Springer Science and Business Media LLC
Published: 2023-10-19
Volume: 55
Issue: 11
Pages: 1866-1875
ISSN: 1061-4036 (ISSN-L)
1546-1718
DOI: 10.1038/s41588-023-01529-1
PMC: PMC12270542
OpenAlex: W4387782515
Cited by: 336
References: 80
Citations by year: 2026: 109 · 2025: 128 · 2024: 90 · 2023: 8
FWCI: 55.62
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Nature Genetics (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (R01HG008140, R01HG011432, U01HG012069)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Keywords: expression quantitative trait loci, cis-eQTL, complex traits, non-coding variants, transcription start sites, natural selection, selective constraint, regulatory landscape, tissue-specific gene expression
MeSH terms: Gene Expression Regulation, Gene Expression, Multifactorial Inheritance, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome-Wide Association Study

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Systematic differences in discovery of genetic effects on gene expression and complex traits

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