A meta-analysis of gene expression quantitative trait loci in brain
Open accessAbstract
Current catalogs of brain expression quantitative trait loci (eQTL) are incomplete and the findings do not replicate well across studies. All existing cortical eQTL studies are small and emphasize the need for a meta-analysis. We performed a meta-analysis of 424 brain samples across five studies to identify regulatory variants influencing gene expression in human cortex. We identified 3584 genes in autosomes and chromosome X with false discovery rate q<0.05 whose expression was significantly associated with DNA sequence variation. Consistent with previous eQTL studies, local regulatory variants tended to occur symmetrically around transcription start sites and the effect was more evident in studies with large sample sizes. In contrast to random SNPs, we observed that significant eQTLs were more likely to be near 5'-untranslated regions and intersect with regulatory features. Permutation-based enrichment analysis revealed that SNPs associated with schizophrenia and bipolar disorder were enriched among brain eQTLs. Genes with significant eQTL evidence were also strongly associated with diseases from OMIM (Online Mendelian Inheritance in Man) and the NHGRI (National Human Genome Research Institute) genome-wide association study catalog. Surprisingly, we found that a large proportion (28%) of ~1000 autosomal genes encoding proteins needed for mitochondrial structure or function were eQTLs (enrichment P-value=1.3 × 10(-9)), suggesting a potential role for common genetic variation influencing the robustness of energy supply in brain and a possible role in the etiology of some psychiatric disorders. These systematically generated eQTL information should be a valuable resource in determining the functional mechanisms of brain gene expression and the underlying biology of associations with psychiatric disorders.
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Quality control and analysis for all data types conformed to those developed in the authors' prior publications.
“Quality control and analysis for all data types conformed to those developed in our prior publications19.”
From Gene expression elucidates functional impact of polygenic risk for schizophrenia (2016) · cites this paper as [19]
Replication was lower for a meta-analysis of mixed brain regions (π1 = 0.62) and for blood eQTLs (π1 = 0.54).
“Replication was somewhat lower for a recent meta-analysis that included a mix of several distinct brain regions19 (π1 = 0.62), and for eQTLs detected in blood (π1 = 0.54)20.”
From Gene expression elucidates functional impact of polygenic risk for schizophrenia (2016) · cites this paper as [19]
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Natural selection and language genes in humans
DeSalle, R., Lepski, G. A., Arévalo, A. L., Bobo, D., LaVergne, N., Miyagawa, S., & Tattersall, I. (2026) · Scientific Reports · doi:10.1038/s41598-026-39032-2
- Authors
- Kim, Y., Xia, K., Tao, R., Giusti-Rodriguez, P., Vladimirov, V, van den Oord, E., & Sullivan, P. F.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- Johns Hopkins University (US)
- Corresponding author
- Kim, Y
- Venue
- Translational Psychiatry
- Published
- 2014-10-07
- Volume
- 4
- Issue
- 10
- Pages
- e459-e459
- ISSN
- 2158-3188 (ISSN-L)
- PMC
- PMC4350525
- OpenAlex
- W2055742054
- Cited by
- 73
- References
- 103
- Citations by year
- 2026: 1 · 2025: 3 · 2024: 3 · 2023: 4 · 2022: 3 · 2021: 3 · 2020: 10 · 2019: 8 · 2018: 12 · 2017: 10 · 2016: 11 · 2015: 5
- FWCI
- 1.15
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Translational Psychiatry (publishedVersion, cc-by-nc-sa)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-sa)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Funders
- Stanley Medical Research Institute
- National Institutes of Health
- National Institute of Mental Health (R01MH097283)
- 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
- expression quantitative trait loci, brain gene expression, human cortex, regulatory variants, single nucleotide polymorphisms, 5' untranslated region, schizophrenia, bipolar disorder, mitochondrial genes, brain energy metabolism, mental illness
- MeSH terms
- Bipolar Disorder, Brain, Humans, Schizophrenia, Gene Expression, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome-Wide Association Study
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