Phenotype-Specific Enrichment of Mendelian Disorder Genes near GWAS Regions across 62 Complex Traits
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Abstract
Although recent studies provide evidence for a common genetic basis between complex traits and Mendelian disorders, a thorough quantification of their overlap in a phenotype-specific manner remains elusive. Here, we have quantified the overlap of genes identified through large-scale genome-wide association studies (GWASs) for 62 complex traits and diseases with genes containing mutations known to cause 20 broad categories of Mendelian disorders. We identified a significant enrichment of genes linked to phenotypically matched Mendelian disorders in GWAS gene sets; of the total 1,240 comparisons, a higher proportion of phenotypically matched or related pairs (n = 50 of 92 [54%]) than phenotypically unmatched pairs (n = 27 of 1,148 [2%]) demonstrated significant overlap, confirming a phenotype-specific enrichment pattern. Further, we observed elevated GWAS effect sizes near genes linked to phenotypically matched Mendelian disorders. Finally, we report examples of GWAS variants localized at the transcription start site or physically interacting with the promoters of genes linked to phenotypically matched Mendelian disorders. Our results are consistent with the hypothesis that genes that are disrupted in Mendelian disorders are dysregulated by non-coding variants in complex traits and demonstrate how leveraging findings from related Mendelian disorders and functional genomic datasets can prioritize genes that are putatively dysregulated by local and distal non-coding GWAS variants.
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For many traits, there is clear convergence between common-variant association signals and genes implicated in monogenic forms of the same disease, as well as enrichment of GWAS signals in regulatory elements active in cell types consistent with known disease biology.
“For many traits, there is clear convergence between common-variant association signals and genes implicated in monogenic forms of the same disease, as well as enrichment of GWAS signals in regulatory elements specifically active in cell types consistent with known disease biology60,61.”
From A brief history of human disease genetics (2020) · cites this paper as [61]
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- Authors
- Freund, M. K., Burch, K. S., Shi, H., Mancuso, N., Kichaev, G., Garske, K. M., Pan, D. Z., Miao, Z., Mohlke, K. L., Laakso, M., Pajukanta, P., Pasaniuc, B., & Arboleda, V. A.
- Affiliations
- University of California, Los Angeles (US)
- University of North Carolina at Chapel Hill (US)
- University of Eastern Finland (FI)
- Corresponding author
- Freund, Malika Kumar
- Arboleda, Valerie A.
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2018-10
- Volume
- 103
- Issue
- 4
- Pages
- 535-552
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC6174356
- OpenAlex
- W2804434811
- Cited by
- 102
- References
- 105
- Citations by year
- 2026: 9 · 2025: 14 · 2024: 10 · 2023: 10 · 2022: 19 · 2021: 17 · 2020: 15 · 2019: 6 · 2018: 1
- FWCI
- 5.97
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- UNC Libraries
- Funders
- National Institutes of Health (T32HG002536)
- NIH (DP5OD024579, R01HG009120, R01MH115676, R01HG006399, U01CA194393, F31HL142180, HL-095056, HL-28481)
- National Institute of Mental Health (T32MH073526)
- National Cancer Institute (T32LM012424)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- monogenic disorders, complex traits, overlapping genes, non-coding variants, transcription start sites, promoter interactions, gene expression dysregulation, disease gene prioritization, genetic overlap
- MeSH terms
- Female, Humans, Male, Phenotype, Promoter Regions, Genetic, Genetic Predisposition to Disease, Multifactorial Inheritance, Polymorphism, Single Nucleotide, Transcription Initiation Site, Quantitative Trait Loci, Genome-Wide Association Study
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