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van der Wijst MGP, de Vries DH, Groot HE, Trynka G, Hon CC, Bonder MJ, Stegle O, Nawijn MC, Idaghdour Y, van der Harst P, Ye CJ, Powell J, Theis FJ, Mahfouz A, Heinig M, Franke L. The single-cell eQTLGen consortium. eLife 2020; 9:e52155. [PMID: 32149610 PMCID: PMC7077978 DOI: 10.7554/elife.52155] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/03/2020] [Indexed: 12/17/2022] Open
Abstract
In recent years, functional genomics approaches combining genetic information with bulk RNA-sequencing data have identified the downstream expression effects of disease-associated genetic risk factors through so-called expression quantitative trait locus (eQTL) analysis. Single-cell RNA-sequencing creates enormous opportunities for mapping eQTLs across different cell types and in dynamic processes, many of which are obscured when using bulk methods. Rapid increase in throughput and reduction in cost per cell now allow this technology to be applied to large-scale population genetics studies. To fully leverage these emerging data resources, we have founded the single-cell eQTLGen consortium (sc-eQTLGen), aimed at pinpointing the cellular contexts in which disease-causing genetic variants affect gene expression. Here, we outline the goals, approach and potential utility of the sc-eQTLGen consortium. We also provide a set of study design considerations for future single-cell eQTL studies.
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Affiliation(s)
- MGP van der Wijst
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - DH de Vries
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - HE Groot
- Department of Cardiology, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - G Trynka
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Open TargetsHinxtonUnited Kingdom
| | - CC Hon
- RIKEN Center for Integrative Medical SciencesYokahamaJapan
| | - MJ Bonder
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ)HeidelbergGermany
- Genome Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - O Stegle
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ)HeidelbergGermany
- Genome Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - MC Nawijn
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - Y Idaghdour
- Program in Biology, Public Health Research Center, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - P van der Harst
- Department of Cardiology, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - CJ Ye
- Institute for Human Genetics, Bakar Computational Health Sciences Institute, Bakar ImmunoX Initiative, Department of Medicine, Department of Bioengineering and Therapeutic Sciences, Department of Epidemiology and Biostatistics, Chan Zuckerberg Biohub, University of California San FranciscoSan FranciscoUnited States
| | - J Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute, UNSW Cellular Genomics Futures Institute, University of New South WalesSydneyAustralia
| | - FJ Theis
- Institute of Computational Biology, Helmholtz Zentrum MünchenNeuherbergGermany
- Department of Mathematics, Technical University of MunichGarching bei MünchenGermany
| | - A Mahfouz
- Leiden Computational Biology Center, Leiden University Medical CenterLeidenNetherlands
- Delft Bioinformatics Lab, Delft University of TechnologyDelftNetherlands
| | - M Heinig
- Institute of Computational Biology, Helmholtz Zentrum MünchenNeuherbergGermany
- Department of Informatics, Technical University of MunichGarching bei MünchenGermany
| | - L Franke
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center GroningenGroningenNetherlands
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