Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
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T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies. Further, we characterize highly coordinated genetic effects on gene expression, methylation, and histone variation through quantitative trait locus (QTL) mapping and allele-specific (AS) analyses. Finally, we demonstrate colocalization of molecular trait QTLs at 345 unique immune disease loci. This expansive, high-resolution atlas of multi-omics changes yields insights into cell-type-specific correlation between diverse genomic inputs, more generalizable correlations between these inputs, and defines molecular events that may underpin complex disease risk.
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eQTL effect and sample sizes were used from the Blueprint study on bulk RNA-seq of FACS sorted Monocytes and T cells57.
“We used eQTL effect and sample sizes from the Blueprint study on bulk RNA-seq of FACS sorted Monocytes and T cells57.”
From scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies (2021) · cites this paper as [57]
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References 73 · Cited by 679
Research works printed but not linked: 1
- Carrillo de Santa Pau E. Juan D. Pancaldi V. Were F. Martin-Subero I. Rico D. Valencia A. Searching for the chromatin determinants of human hematopoiesis bioRxiv 2016
- Authors
- Chen, L., Ge, B., Casale, F. P., Vasquez, L., Kwan, T., Garrido-Martín, D., Watt, S., Yan, Y., Kundu, K., Ecker, S., Datta, A., Richardson, D., Burden, F., Mead, D., Mann, A. L., Fernandez, J. M., Rowlston, S., Wilder, S. P., Farrow, S., Shao, X., Lambourne, J. J., Redensek, A., Albers, C. A., Amstislavskiy, V., Ashford, S., Berentsen, K., Bomba, L., Bourque, G., Bujold, D., Busche, S., Caron, M., Chen, S.-H., Cheung, W., Delaneau, O., Dermitzakis, E. T., Elding, H., Colgiu, I., Bagger, F. O., Flicek, P., Habibi, E., Iotchkova, V., Janssen-Megens, E., Kim, B., Lehrach, H., Lowy, E., Mandoli, A., Matarese, F., Maurano, M. T., Morris, J. A., Pancaldi, V., Pourfarzad, F., Rehnstrom, K., Rendon, A., Risch, T., Sharifi, N., Simon, M.-M., Sultan, M., Valencia, A., Walter, K., Wang, S.-Y., Frontini, M., Antonarakis, S. E., Clarke, L., Yaspo, M.-L., Beck, S., Guigo, R., Rico, D., Martens, J. H. A., Ouwehand, W. H., Kuijpers, T. W., Paul, D. S., Stunnenberg, H. G., Stegle, O., Downes, K., Pastinen, T., & Soranzo, N.
- Affiliations
- University of Cambridge (GB)
- McGill University (CA)
- European Bioinformatics Institute (GB)
- Wellcome Sanger Institute (GB)
- Universitat Pompeu Fabra (ES)
- Spanish National Cancer Research Centre (ES)
- National Health Service (GB)
- Radboud University Nijmegen (NL)
- Max Planck Institute for Molecular Genetics (DE)
- University of Geneva (CH)
- NYU Langone Health (US)
- Sanquin (NL)
- University College London (GB)
- McGill University and Génome Québec Innovation Centre (CA)
- Corresponding author
- Pastinen, Tomi
- Soranzo, Nicole
- ORCID
- Chen, Lu
- Ge, Bing
- Casale, Francesco Paolo
- Vasquez, Louella
- Kwan, Tony
- Garrido-Martín, Diego
- Watt, Stephen
- Kundu, Kousik
- Ecker, Simone
- Datta, Avik
- Richardson, David
- Burden, Frances
- Mead, Daniel
- Mann, Alice L.
- Wilder, Steven P.
- Shao, Xiaojian
- Lambourne, John J.
- Amstislavskiy, Vyacheslav
- Ashford, Sofie
- Berentsen, Kim
- Bomba, Lorenzo
- Bourque, Guillaume
- Bujold, David
- Busche, Stephan
- Caron, Maxime
- Chen, Shu-Huang
- Cheung, Warren
- Dermitzakis, Emmanouil T.
- Bagger, Frederik O.
- Flicek, Paul
- Habibi, Ehsan
- Iotchkova, Valentina
- Kim, Bowon
- Lowy, Ernesto
- Maurano, Matthew T.
- Morris, John A.
- Rendon, Augusto
- Sultan, Marc
- Valencia, Alfonso
- Walter, Klaudia
- Wang, Shuang-Yin
- Frontini, Mattia
- Antonarakis, Stylianos E.
- Clarke, Laura
- Yaspo, Marie-Laure
- Beck, Stephan
- Rico, Daniel
- Martens, Joost H.A.
- Ouwehand, Willem H.
- Kuijpers, Taco W.
- Paul, Dirk S.
- Stunnenberg, Hendrik G.
- Stegle, Oliver
- Downes, Kate
- Pastinen, Tomi
- Soranzo, Nicole
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2016-11
- Volume
- 167
- Issue
- 5
- Pages
- 1398-1414.e24
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC5119954
- OpenAlex
- W2553059833
- Cited by
- 679
- References
- 73
- Citations by year
- 2026: 34 · 2025: 51 · 2024: 85 · 2023: 86 · 2022: 83 · 2021: 86 · 2020: 73 · 2019: 77 · 2018: 56 · 2017: 42 · 2016: 4
- FWCI
- 47.72
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Cell (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (publishedVersion, cc-by)
- SERVAL (Université de Lausanne) (publishedVersion, cc-by)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion, other-oa)
- Radboud Repository (Radboud University) (submittedVersion, other-oa)
- National University of Singapore (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Max Planck Digital Library (submittedVersion, other-oa)
- IRIS (submittedVersion, cc-by)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (submittedVersion, cc-by)
- Radboud Repository (Radboud University) (submittedVersion)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- McGill University
- Genome Canada
- NHS Blood and Transplant
- Wellcome Trust (WT 098051, 257082, WT091310)
- European Bioinformatics Institute
- European Molecular Biology Laboratory (SEV-2012–0208)
- National Institute for Health and Care Research (NF-SI-0512-10165, NF-SI-0510-10214, RP-PG-0310-1002, NF-SI-0513-10151)
- British Heart Foundation (G0800270, SP/09/002, RG/13/13/30194, RE/13/6/30180, RG/08/014/24067, RG/09/012/28096)
- University of Cambridge
- University of Oxford
- European Commission (282510, 257082)
- Ministerio de Economía y Competitividad (SEV‐2012‐0208, PT13/0001))
- Lundbeckfonden (R193-2015-1611, R182-2014-3881)
- Max-Planck-Gesellschaft
- Canadian Institutes of Health Research (120608_1)
- Medical Research Council (G0800270, EU FP7, MR/L003120/1)
- Instituto de Salud Carlos III (PT13/0001)
- NIHR Cambridge Biomedical Research Centre
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- epigenetic variation, transcriptional variation, immune cells, T cells, DNA methylation, gene expression, cis-regulatory effects, quantitative trait loci, allele-specific expression, colocalization, multi-omics integration
- MeSH terms
- Adult, Aged, Female, Hematopoietic Stem Cells, Humans, Immune System Diseases, Male, Middle Aged, Monocytes, Neutrophils, T-Lymphocytes, Transcription, Genetic, Alternative Splicing, Genetic Predisposition to Disease, Quantitative Trait Loci, Histone Code, Young Adult, Epigenomics
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