Mapping the Genetic Architecture of Gene Regulation in Whole Blood
Open accessAbstract
BACKGROUND: We aimed to assess whether whole blood expression quantitative trait loci (eQTLs) with effects in cis and trans are robust and can be used to identify regulatory pathways affecting disease susceptibility. MATERIALS AND METHODS: We performed whole-genome eQTL analyses in 890 participants of the KORA F4 study and in two independent replication samples (SHIP-TREND, N = 976 and EGCUT, N = 842) using linear regression models and Bonferroni correction. RESULTS: In the KORA F4 study, 4,116 cis-eQTLs (defined as SNP-probe pairs where the SNP is located within a 500 kb window around the transcription unit) and 94 trans-eQTLs reached genome-wide significance and overall 91% (92% of cis-, 84% of trans-eQTLs) were confirmed in at least one of the two replication studies. Different study designs including distinct laboratory reagents (PAXgene™ vs. Tempus™ tubes) did not affect reproducibility (separate overall replication overlap: 78% and 82%). Immune response pathways were enriched in cis- and trans-eQTLs and significant cis-eQTLs were partly coexistent in other tissues (cross-tissue similarity 40-70%). Furthermore, four chromosomal regions displayed simultaneous impact on multiple gene expression levels in trans, and 746 eQTL-SNPs have been previously reported to have clinical relevance. We demonstrated cross-associations between eQTL-SNPs, gene expression levels in trans, and clinical phenotypes as well as a link between eQTLs and human metabolic traits via modification of gene regulation in cis. CONCLUSIONS: Our data suggest that whole blood is a robust tissue for eQTL analysis and may be used both for biomarker studies and to enhance our understanding of molecular mechanisms underlying gene-disease associations.
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Whole blood cell studies were included in the Alzheimer's disease-relevant tissue class due to their high correlation of eQTLs with Alzheimer's disease-relevant tissues (70% with brain; 51-70% for monocytes and lymphoblastoid cell lines) and their large sample sizes.
“While their specificity may be lower for identifying Alzheimer’s disease risk eQTLs, we included whole blood cell studies in our Alzheimer’s disease–relevant tissue class due to their high correlation of eQTLs with Alzheimer’s disease–relevant tissues (70% with brain164; 51–70% for monocytes and lymphoblastoid cell lines165) and their large sample sizes that allow for increased discovery power.”
From Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing (2019) · cites this paper as [165]
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“B 2708 subjects Biostatistics Gene expression data [125]”
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Self-citationAssociation between DNA Methylation in Whole Blood and Measures of Glucose Metabolism: KORA F4 Study
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“In addition, statistical arguments strongly support the inference that in many cases there may be multiple independently acting SNPs responsible for the eQTL effect at each locus [32–34].”
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Self-citationIdentification of blood eQTLs in older adults
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Self-citationTomofuji, Y., Mu, Z., Mire, H. M., Zhao, Y., Liu, C.-J., Jayanthi, V., Sugiarto, N. W., Accelerating Medicines Partnership: RA/SLE Network, Sparks, J. A., & Raychaudhuri, S. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.29.741564
- Authors
- Schramm, K., Marzi, C., Schurmann, C., Carstensen, M., Reinmaa, E., Biffar, R., Eckstein, G., Gieger, C., Grabe, H.-J., Homuth, G., Kastenmüller, G., Mägi, R., Metspalu, A., Mihailov, E., Peters, A., Petersmann, A., Roden, M., Strauch, K., Suhre, K., Teumer, A., Völker, U., Völzke, H., Wang-Sattler, R., Waldenberger, M., Meitinger, T., Illig, T., Herder, C., Grallert, H., & Prokisch, H.
- Affiliations
- Helmholtz Munich (DE)
- Universitätsmedizin Greifswald (DE)
- Deutsches Diabetes-Zentrum e.V. (DE)
- University of Tartu (EE)
- Estonian Biocentre (EE)
- Institut für Humangenetik (DE)
- Düsseldorf University Hospital (DE)
- Medizinische Hochschule Hannover (DE)
- Corresponding author
- Prokisch, Holger
- ORCID
- Schramm, Katharina
- Schurmann, Claudia
- Biffar, Reiner
- Eckstein, Gertrud
- Gieger, Christian
- Grabe, Hans-Jörgen
- Homuth, Georg
- Mägi, Reedik
- Metspalu, Andres
- Peters, Annette
- Petersmann, Astrid
- Roden, Michael
- Strauch, Konstantin
- Suhre, Karsten
- Teumer, Alexander
- Völker, Uwe
- Völzke, Henry
- Meitinger, Thomas
- Herder, Christian
- Grallert, Harald
- Prokisch, Holger
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-04-16
- Volume
- 9
- Issue
- 4
- Pages
- e93844
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3989189
- OpenAlex
- W2052628795
- Cited by
- 33
- References
- 37
- Citations by year
- 2026: 1 · 2025: 1 · 2022: 3 · 2021: 3 · 2020: 2 · 2019: 5 · 2018: 3 · 2017: 5 · 2016: 4 · 2015: 5 · 2014: 1
- FWCI
- 3.28
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Open access LMU (Ludwid Maxmilian's Universitat Munchen) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion)
- mediaTUM (Technical University of Munich) (submittedVersion, other-oa)
- Site cant be reached (submittedVersion, cc-by)
- Funders
- Qatar Foundation
- European Commission (313010, 2007–2013, SF0180142s08, FP7 2007-2013, 277984, FP7/2007, 03ZIK012)
- Bundesministerium für Bildung und Forschung (03IS2061A, 03ZIK012, 01GS0834, 0315494A)
- Bundesministerium für Gesundheit
- Siemens
- Tartu Ülikool
- Universität Greifswald
- Ministry of Cultural Affairs
- Weill Cornell Medical College
- Weill Cornell Medicine - Qatar
- European Regional Development Fund (FP7/2007‐2013, 2007 – 2013)
- Münchner Zentrum für Gesundheitswissenschaften
- 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, whole blood gene expression, cis-eQTL, trans-eQTL, immune pathways, metabolic phenotypes, disease susceptibility, biomarkers
- MeSH terms
- Blood, Chromosome Mapping, Gene Expression Regulation, Genetic Markers, Humans, Linear Models, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Gene Regulatory Networks, Genetic Association Studies
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