Systematic identification of trans eQTLs as putative drivers of known disease associations
Open accessAbstract
Lude Franke and colleagues report the results of a large expression QTL study performed on peripheral blood samples from 5,311 individuals. They identify trans-eQTL effects for 103 independent loci that were previously associated with complex traits at genome-wide significance, suggesting that this approach can provide insights into the downstream effects of many trait-associated variants. Identifying the downstream effects of disease-associated SNPs is challenging. To help overcome this problem, we performed expression quantitative trait locus (eQTL) meta-analysis in non-transformed peripheral blood samples from 5,311 individuals with replication in 2,775 individuals. We identified and replicated trans eQTLs for 233 SNPs (reflecting 103 independent loci) that were previously associated with complex traits at genome-wide significance. Some of these SNPs affect multiple genes in trans that are known to be altered in individuals with disease: rs4917014, previously associated with systemic lupus erythematosus (SLE)1, altered gene expression of C1QB and five type I interferon response genes, both hallmarks of SLE2,3,4. DeepSAGE RNA sequencing showed that rs4917014 strongly alters the 3′ UTR levels of IKZF1 in cis, and chromatin immunoprecipitation and sequencing analysis of the trans-regulated genes implicated IKZF1 as the causal gene. Variants associated with cholesterol metabolism and type 1 diabetes showed similar phenomena, indicating that large-scale eQTL mapping provides insight into the downstream effects of many trait-associated variants.
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rs2011946 is associated with CXCR4 expression in whole blood (p-value = 1.82 × 10−6).
“We also found that rs2011946 is associated with CXCR4 expression in whole blood (p-value = 1.82 × 10−6) [33].”
From Shared genetic risk between corticobasal degeneration, progressive supranuclear palsy, and frontotemporal dementia (2017) · cites this paper as [33]
The paper discusses blood eQTL associations generally (main text, page unavailable), but the passages in our copy do not report an association between rs2011946 and CXCR4 expression. Searches for rs2011946, CXCR4, and the stated p-value found no matching result, so the specific claim cannot be verified from our copy. (LLM, conf=0.72)
Experimental — accuracy not yet measuredSMR analysis identified two potential causal genes, CDC42 (rs2268177; PSMR=1.07 × 10−12) and VEZT (rs14121; PSMR=3.41 × 10−6), underlying endometriosis loci at 1p36.12 and 12q22, respectively.
“The SMR analysis identified two potential causal genes, CDC42 (rs2268177; PSMR=1.07 × 10−12) and VEZT (rs14121; PSMR=3.41 × 10−6), underlying endometriosis loci at 1p36.12 and 12q22, respectively (Supplementary Data 14).”
From Meta-analysis identifies five novel loci associated with endometriosis highlighting key genes involved in hormone metabolism (2017) · cites this paper as [31]
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Self-citationWang, T., Peng, Q., Liu, B., Liu, Y., & Wang, Y. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.00418 · Cited by 27 · see citing works
- Authors
- Westra, H.-J., Peters, M. J., Esko, T., Yaghootkar, H., Schurmann, C., Kettunen, J., Christiansen, M. W., Fairfax, B. P., Schramm, K., Powell, J. E., Zhernakova, A., Zhernakova, D. V., Veldink, J. H., Van den Berg, L. H., Karjalainen, J., Withoff, S., Uitterlinden, A. G., Hofman, A., Rivadeneira, F., 't Hoen, P. A. C., Reinmaa, E., Fischer, K., Nelis, M., Milani, L., Melzer, D., Ferrucci, L., Singleton, A. B., Hernandez, D. G., Nalls, M. A., Homuth, G., Nauck, M., Radke, D., Völker, U., Perola, M., Salomaa, V., Brody, J., Suchy-Dicey, A., Gharib, S. A., Enquobahrie, D. A., Lumley, T., Montgomery, G. W., Makino, S., Prokisch, H., Herder, C., Roden, M., Grallert, H., Meitinger, T., Strauch, K., Li, Y., Jansen, R. C., Visscher, P. M., Knight, J. C., Psaty, B. M., Ripatti, S., Teumer, A., Frayling, T. M., Metspalu, A., van Meurs, J. B. J., & Franke, L.
- Affiliations
- University Medical Center Groningen (NL)
- Erasmus MC (NL)
- University of Tartu (EE)
- University of Exeter (GB)
- Universitätsmedizin Greifswald (DE)
- University of Helsinki (FI)
- University of Washington (US)
- Centre for Human Genetics (GB)
- Helmholtz Munich (DE)
- The University of Queensland (AU)
- University Medical Center Utrecht (NL)
- National Institute on Aging (US)
- National Institutes of Health (US)
- Finnish Institute for Health and Welfare (FI)
- University of Auckland (NZ)
- QIMR Berghofer Medical Research Institute (AU)
- Deutsches Diabetes-Zentrum e.V. (DE)
- Düsseldorf University Hospital (DE)
- University of Groningen (NL)
- Group Health Cooperative (US)
- Corresponding author
- Westra, Harm-Jan
- Franke, Lude
- ORCID
- Westra, Harm-Jan
- Peters, Marjolein J
- Esko, Tõnu
- Yaghootkar, Hanieh
- Schurmann, Claudia
- Kettunen, Johannes
- Fairfax, Benjamin P
- Schramm, Katharina
- Powell, Joseph E
- Zhernakova, Alexandra
- Zhernakova, Daria V
- Veldink, Jan H
- Karjalainen, Juha
- Withoff, Sebo
- Uitterlinden, André G
- Rivadeneira, Fernando
- Fischer, Krista
- Nelis, Mari
- Milani, Lili
- Melzer, David
- Ferrucci, Luigi
- Singleton, Andrew B
- Hernandez, Dena G
- Homuth, Georg
- Nauck, Matthias
- Radke, Dörte
- Völker, Uwe
- Perola, Markus
- Salomaa, Veikko
- Brody, Jennifer
- Gharib, Sina A
- Enquobahrie, Daniel A
- Montgomery, Grant W
- Makino, Seiko
- Prokisch, Holger
- Herder, Christian
- Roden, Michael
- Grallert, Harald
- Meitinger, Thomas
- Strauch, Konstantin
- Li, Yang
- Visscher, Peter M
- Knight, Julian C
- Psaty, Bruce M
- Ripatti, Samuli
- Teumer, Alexander
- Frayling, Timothy M
- Metspalu, Andres
- Franke, Lude
- Venue
- Nature Genetics
- Published
- 2013-09-08
- Volume
- 45
- Issue
- 10
- Pages
- 1238-1243
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC3991562
- OpenAlex
- W2135199713
- Cited by
- 1,658
- References
- 61
- Citations by year
- 2026: 37 · 2025: 65 · 2024: 65 · 2023: 76 · 2022: 95 · 2021: 141 · 2020: 178 · 2019: 173 · 2018: 179 · 2017: 208 · 2016: 189 · 2015: 147 · 2014: 94 · 2013: 7
- FWCI
- 95.69
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- public-domain
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion, public-domain)
- PubMed (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- Figshare (submittedVersion)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion)
- STM:n Hallinnonalan avoin julkaisuarkisto (Julkari) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- Funders
- Wellcome Trust (075491/Z/04/Z, 088891, 083270/Z/07/Z, 074318/Z/04/Z, 090532)
- National Institute for Health and Care Research (ACF-2008-13-017, CL-2012-13-004)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (918.66.620, 911-03-012, 916·10·135, 175.010.200)
- National Institutes of Health (Z99 AG999999)
- National Heart, Lung, and Blood Institute (R01HL073410, R01HL085251)
- 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 › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- trans-eQTL, expression quantitative trait loci, peripheral blood gene expression, systemic lupus erythematosus, C1QB, IKZF1, 3' UTR regulation, causal gene identification, cholesterol metabolism, type 1 diabetes, complex traits
- MeSH terms
- Diabetes Mellitus, Type 1, Humans, Lupus Erythematosus, Systemic, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Quantitative Trait Loci
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