Genetic variability in the regulation of gene expression in ten regions of the human brain
Open accessAbstract
Germ-line genetic control of gene expression occurs via expression quantitative trait loci (eQTLs). We present a large, exon-specific eQTL data set covering ten human brain regions. We found that cis-eQTL signals (within 1 Mb of their target gene) were numerous, and many acted heterogeneously among regions and exons. Co-regulation analysis of shared eQTL signals produced well-defined modules of region-specific co-regulated genes, in contrast to standard coexpression analysis of the same samples. We report cis-eQTL signals for 23.1% of catalogued genome-wide association study hits for adult-onset neurological disorders. The data set is publicly available via public data repositories and via http://www.braineac.org/. Our study increases our understanding of the regulation of gene expression in the human brain and will be of value to others pursuing functional follow-up of disease-associated variants.
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Genetic variants at the HLA-DQB1 locus discovered in the recent AD genetic meta-analysis included eQTLs for TNXB/TNXA in brain tissues.
“genetic variants at the HLA-DQB1 locus discovered in the recent AD genetic meta-analysis [84] included eQTLs for TNXB/TNXA in brain tissues [84, 85].”
From Sex-specific DNA methylation differences in Alzheimer’s disease pathology (2021) · cites this paper as [85]
The Results section, “Using cis-eQTL signals to interpret GWAS hits” (page not available), reports brain eQTLs for other disease-associated variants, including an Alzheimer’s disease variant regulating CR1. Searches for HLA-DQB1, TNXB, TNXA, and their combination found no passage linking the claimed locus to TNXB/TNXA expression in brain tissue. (LLM, conf=0.74)
Experimental — accuracy not yet measuredCommonMind Consortium eQTLs replicate most eQTLs found in other independent samples, with π1 values of 0.98 for GTEx v6, 0.75 for Harvard Brain Bank, 0.70 for BrainCloud, 0.79 for NIH, 0.93 for UKBEC, and 0.77 for HBCC.
“GTEx v6 is the largest public dataset of eQTLs from DLPFC tissue (n = 92) assayed by RNA-seq; its replication in CMC is π1 = 0.98.”
From Gene expression elucidates functional impact of polygenic risk for schizophrenia (2016) · cites this paper as [18]
The module memberships were confirmed in the BRAINEAC data for non-Alzheimer's disease control human brains.
“We confirmed these module memberships in the BRAINEAC data for non-Alzheimer’s disease control human brains generated in our own lab (Ramasamy et al., 2014).”
From Genetic variability in response to amyloid beta deposition influences Alzheimer’s disease risk (2019) · cites this paper as Ramasamy et al., 2014
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- Authors
- UK Brain Expression Consortium, Ramasamy, A., North American Brain Expression Consortium, Trabzuni, D., Guelfi, S., Varghese, V., Smith, C., Walker, R., De, T., Coin, L., de Silva, R., Cookson, M. R., Singleton, A. B., Hardy, J., Ryten, M., & Weale, M. E.
- Affiliations
- Guy's Hospital (GB)
- King Faisal Specialist Hospital & Research Centre (SA)
- UCL Queen Square Institute of Neurology (GB)
- University of Edinburgh (GB)
- Imperial College London (GB)
- The University of Queensland (AU)
- National Institutes of Health (US)
- Corresponding author
- Ryten, Mina
- Weale, Michael E
- ORCID
- Venue
- Nature Neuroscience
- Published
- 2014-08-31
- Volume
- 17
- Issue
- 10
- Pages
- 1418-1428
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- PMC
- PMC4208299
- OpenAlex
- W2094379190
- Cited by
- 644
- References
- 63
- Citations by year
- 2026: 14 · 2025: 29 · 2024: 32 · 2023: 33 · 2022: 45 · 2021: 72 · 2020: 77 · 2019: 72 · 2018: 82 · 2017: 72 · 2016: 67 · 2015: 45 · 2014: 2
- FWCI
- 40.72
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Neuroscience (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Funders
- Wellcome Trust (089698)
- Brain Research UK (UCC14182)
- National Institute for Health and Care Research (ACF-2007-18-011)
- Parkinson's UK (K-1212, G-0907)
- National Institutes of Health
- Medical Research Council (MR/K01417X/1, MC_G1000735, MR/L016400/1)
- National Institute on Aging (Z01AG000947, P30-AG-19610, K01AG000947, P30AG019610)
- National Institute of Neurological Disorders and Stroke (U24NS072026)
- 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, gene expression regulation, human brain regions, cis-eQTL, co-regulation, neurological disorders, mental illness, disease-associated variants
- MeSH terms
- Adolescent, Adult, Aged, Aged, 80 and over, Brain, Female, Gene Expression Regulation, Humans, Male, Middle Aged, Nervous System Diseases, Genetic Predisposition to Disease, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Gene Expression Profiling, Quantitative Trait Loci, Young Adult, Genetic Association Studies
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