Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood
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Abstract
Abstract Understanding the difference in genetic regulation of gene expression between brain and blood is important for discovering genes for brain-related traits and disorders. Here, we estimate the correlation of genetic effects at the top-associated cis -expression or -DNA methylation (DNAm) quantitative trait loci ( cis -eQTLs or cis -mQTLs) between brain and blood ( r b ). Using publicly available data, we find that genetic effects at the top cis -eQTLs or mQTLs are highly correlated between independent brain and blood samples ( $$\hat r_b = 0.70$$ r ^ b = 0.70 for cis -eQTLs and $$\hat r_ b = 0.78$$ r ^ b = 0.78 for cis -mQTLs). Using meta-analyzed brain cis -eQTL/mQTL data ( n = 526 to 1194), we identify 61 genes and 167 DNAm sites associated with four brain-related phenotypes, most of which are a subset of the discoveries (97 genes and 295 DNAm sites) using data from blood with larger sample sizes ( n = 1980 to 14,115). Our results demonstrate the gain of power in gene discovery for brain-related phenotypes using blood cis -eQTL/mQTL data with large sample sizes.
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Using LDSC on a meta-analysis of all 11 clinically-ascertained datasets, the liability-scale heritability of PD was estimated as 0.22 (95% CI 0.18-0.26).
“Using LDSC on a meta-analysis of all 11 clinically-ascertained datasets from our GWAS and estimated the liability-scale heritability of PD as 0.22 (95% CI 0.18 – 0.26), only slightly lower than a previous estimate derived using GCTA (0.27, 95% CI 0.17 – 0.38) (2,16,30).”
From Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies (2019) · cites this paper as [16]
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“Let d = b= − b> (5) The sampling variance of d can be written as V d = V b= + V b> − 2θ V b= V b> (6) where b= and b> are the estimated effect sizes of the top associated cis-eQTL for a gene in two tissues, V b= and V b> are the sampling variance for b= and b> , respectively, and θ is sampling correlation between b= a…”
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eQTLGen Consortium, Stahl, E. A., BIOS Consortium, the Bipolar Disorder Working Group of the Psychiatric Genomics Consortium, Breen, G., Forstner, A. J., McQuillin, A., Ripke, S., Trubetskoy, V., Mattheisen, M., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0397-8 · Cited by 1,519 · see citing works
Self-citationGenomic and phenotypic insights from an atlas of genetic effects on DNA methylation
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Self-citationPorcu, E., Rüeger, S., Lepik, K., eQTLGen Consortium, Agbessi, M., Ahsan, H., Alves, I., Andiappan, A., Arindrarto, W., Awadalla, P., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10936-0 · Cited by 322 · see citing works
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Wiklund, P., Karhunen, V., Richmond, R. C., Parmar, P., Rodriguez, A., De Silva, M., Wielscher, M., Rezwan, F. I., Richardson, T. G., Veijola, J., et al. (2019) · Clinical Epigenetics · doi:10.1186/s13148-019-0683-4 · Cited by 120 · see citing works
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The endocytic membrane trafficking pathway plays a major role in the risk of Parkinson's disease
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- Authors
- Qi, T., Wu, Y., Zeng, J., Zhang, F., Xue, A., Jiang, L., Zhu, Z., Kemper, K., Yengo, L., Zheng, Z., eQTLGen Consortium, Agbessi, M., Ahsan, H., Alves, I., Andiappan, A., Awadalla, P., Battle, A., Beutner, F., Jan Bonder, M., Boomsma, D., Christiansen, M., Claringbould, A., Deelen, P., Esko, T., Favé, M.-J., Franke, L., Frayling, T., Gharib, S., Gibson, G., Hemani, G., Jansen, R., Kähönen, M., Kalnapenkis, A., Kasela, S., Kettunen, J., Kim, Y., Kirsten, H., Kovacs, P., Krohn, K., Kronberg-Guzman, J., Kukushkina, V., Kutalik, Z., Lee, B., Lehtimäki, T., Loeffler, M., Marigorta, U. M., Metspalu, A., Milani, L., Müller-Nurasyid, M., Nauck, M., Nivard, M., Penninx, B., Perola, M., Pervjakova, N., Pierce, B., Powell, J., Prokisch, H., Psaty, B., Raitakari, O., Ring, S., Ripatti, S., Rotzschke, O., Ruëger, S., Saha, A., Scholz, M., Schramm, K., Seppälä, I., Stumvoll, M., Sullivan, P., Teumer, A., Thiery, J., Tong, L., Tönjes, A., van Dongen, J., van Meurs, J., Verlouw, J., Völker, U., Võsa, U., Yaghootkar, H., Zeng, B., Marioni, R. E., Montgomery, G. W., Deary, I. J., Wray, N. R., Visscher, P. M., McRae, A. F., & Yang, J.
- Affiliations
- The University of Queensland (AU)
- Ontario Institute for Cancer Research (CA)
- University of Chicago (US)
- Agency for Science, Technology and Research (SG)
- Johns Hopkins University (US)
- Leipzig Heart Institute (DE)
- Vrije Universiteit Amsterdam (NL)
- University of Washington (US)
- University Medical Center Groningen (NL)
- University of Tartu (EE)
- University of Exeter (GB)
- Georgia Institute of Technology (US)
- University of Bristol (GB)
- Tampere University (FI)
- University of Helsinki (FI)
- Leipzig University (DE)
- IFB Adiposity Diseases (DE)
- Universitätsmedizin Greifswald (DE)
- Helmholtz Munich (DE)
- University of Turku (FI)
- Karolinska Institutet (SE)
- Erasmus MC (NL)
- University of Edinburgh (GB)
- Corresponding author
- Yang, Jian
- ORCID
- Qi, Ting
- Wu, Yang
- Zeng, Jian
- Zhang, Futao
- Xue, Angli
- Jiang, Longda
- Zhu, Zhihong
- Kemper, Kathryn
- Zheng, Zhili
- Agbessi, Mawussé
- Ahsan, Habibul
- Alves, Isabel
- Andiappan, Anand
- Awadalla, Philip
- Battle, Alexis
- Boomsma, Dorret
- Claringbould, Annique
- Deelen, Patrick
- Esko, Tõnu
- Favé, Marie-Julie
- Franke, Lude
- Frayling, Timothy
- Gharib, Sina
- Hemani, Gibran
- Jansen, Rick
- Kähönen, Mika
- Kalnapenkis, Anette
- Kasela, Silva
- Kettunen, Johannes
- Kirsten, Holger
- Kovacs, Peter
- Krohn, Knut
- Kukushkina, Viktorija
- Lee, Bernett
- Lehtimäki, Terho
- Loeffler, Markus
- Marigorta, Urko M.
- Metspalu, Andres
- Milani, Lili
- Nauck, Matthias
- Nivard, Michel
- Penninx, Brenda
- Perola, Markus
- Pierce, Brandon
- Powell, Joseph
- Prokisch, Holger
- Psaty, Bruce
- Raitakari, Olli
- Ring, Susan
- Ripatti, Samuli
- Saha, Ashis
- Scholz, Markus
- Schramm, Katharina
- Seppälä, Ilkka
- Sullivan, Patrick
- Teumer, Alexander
- Thiery, Joachim
- Tönjes, Anke
- Verlouw, Joost
- Völker, Uwe
- Võsa, Urmo
- Yaghootkar, Hanieh
- Marioni, Riccardo E.
- Montgomery, Grant W.
- Deary, Ian J.
- Wray, Naomi R.
- Visscher, Peter M.
- McRae, Allan F.
- Yang, Jian
- Venue
- Nature Communications
- Published
- 2018-06-11
- Volume
- 9
- Issue
- 1
- Pages
- 2282-2282
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC5995828
- OpenAlex
- W2789305195
- Cited by
- 427
- References
- 71
- Citations by year
- 2026: 47 · 2025: 62 · 2024: 62 · 2023: 55 · 2022: 48 · 2021: 59 · 2020: 39 · 2019: 45 · 2018: 10
- FWCI
- 23.23
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion, cc-by)
- Amsterdam UMC (VU Amsterdam) - Institutional Repository (publishedVersion, other-oa)
- Explore Bristol Research (publishedVersion, cc-by)
- VU Research Portal (publishedVersion, other-oa)
- Tampere University Institutional Repository (Tampere University) (publishedVersion, cc-by)
- EUR Research Repository (Erasmus University Rotterdam) (acceptedVersion, public-domain)
- UTUPub (University of Turku) (submittedVersion, public-domain)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion, other-oa)
- RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Figshare (submittedVersion)
- Työväentutkimus Vuosikirja (submittedVersion)
- Site cant be reached (submittedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion)
- Bristol Research (University of Bristol) (submittedVersion, cc-by)
- Spiral (Imperial College London) (submittedVersion, cc-by)
- Tampere University Institutional Repository (Tampere University) (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- Wellcome Trust (208806/Z/17/Z)
- National Institutes of Health (GM 099568, AG042568)
- Medical Research Council (MR/K026992/1, MR/M013111/1, 1107258, 1113400, 1078037, 1078901)
- Australian Research Council (DP160103860, DP160101343, DP160102400, 1113400, DP160101056)
- National Health and Medical Research Council (1083656, 1113400, 1078901, 1107258, 1078037)
- National Institute on Aging (R01AG042568)
- National Institute of General Medical Sciences (P01GM099568, R01GM075091)
- 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 › Epigenetics and DNA Methylation
- Keywords
- cis-eQTL, DNA methylation, gene expression regulation, brain phenotypes
- MeSH terms
- Brain, DNA, Enhancer Elements, Genetic, Gene Expression Regulation, Genetic Markers, Humans, Phenotype, Promoter Regions, Genetic, Tissue Distribution, DNA Methylation, Quantitative Trait Loci, Genome-Wide Association Study, Transcriptome
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