Genetic determinants of blood gene expression and splicing and their contribution to molecular phenotypes and health outcomes

The biological mechanisms through which most non-protein-coding genetic variants affect disease risk are unknown. To investigate the gene-regulatory cascades that ensue from these variants, we mapped blood gene expression and splicing quantitative trait loci (QTLs) through bulk RNA-sequencing in 4,732 participants, and integrated these data with protein, metabolite and lipid QTLs in the same individuals. We identified cis-QTLs for the expression of 17,233 genes and 29,514 splicing events (in 6,853 genes). Using colocalization analysis, we identified 3,430 proteomic and metabolomic traits with a shared association signal with either gene expression or splicing. We quantified the relative contribution of the genetic effects at loci with shared etiology through statistical mediation, observing 222 molecular phenotypes significantly mediated by gene expression or splicing. We uncovered gene-regulatory mechanisms at GWAS disease loci with therapeutic implications, such as WARS1 in hypertension, IL7R in dermatitis and IFNAR2 in COVID-19. Our study provides an open-access and interactive resource of the shared genetic etiology across transcriptional phenotypes, molecular traits and health outcomes in humans (https://IntervalRNA.org.uk). ### Competing Interest Statement A.T. is supported by the Wellcome Trust (PhD studentship 222548/Z/21/Z). E.P. was funded by the EU/EFPIA Innovative Medicines Initiative Joint Undertaking BigData@Heart grant 116074 and is funded by the NIHR BTRU in Donor Health and Behaviour (NIHR203337) [*]. M.A.Q. is on the KOL panel for New England Biolabs. S.C.R was funded by a BHF Programme Grant (RG/18/13/33946) and the NIHR Cambridge BRC (BRC-1215-20014; NIHR203312). B.B.S. and H.R. are employees and stockholders of Biogen. Y.X. is supported by the UK Economic and Social Research Council (ES/T013192/1). C.D.W. is an employee and stockholder of Johnson & Johnson. S.P. and D.S.P. are employees and stockholders of AstraZeneca. D.J.G. is an employee and stockholder of BioMarin Pharmaceutical. D.J.R. is an employee of NHS Blood and Transplant. J.E.P. is supported by a Medical Research Foundation Fellowship (MRF-057-0003-RG-PETE-C0799) and has received hospitality and travel expenses to speak at Olink-sponsored academic meetings (none within the past 5 years). J.D. holds a British Heart Foundation Professorship and a NIHR Senior Investigator Award [*]. A.S.B. has received grants outside of this work from AstraZeneca, Bayer, Biogen, BioMarin and Sanofi. M.I. is supported by the Munz Chair of Cardiovascular Prediction and Prevention and the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014; NIHR203312) [*]. M.I. is also supported by the UK Economic and Social Research Council (ES/T013192/1). M.I. is a trustee of the Public Health Genomics (PHG) Foundation, a member of the Scientific Advisory Board of Open Targets, and has a research collaboration with AstraZeneca that is unrelated to this study. ### Funding Statement Participants in the INTERVAL randomized controlled trial were recruited with the active collaboration of NHS Blood and Transplant England (https://www.nhsbt.nhs.uk/), which has supported field work and other elements of the trial. DNA extraction and genotyping were co-funded by the National Institute for Health and Care Research (NIHR), the NIHR BioResource (https://bioresource.nihr.ac.uk/) and the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014) [*]. RNA-seq was funded as part of an alliance between the University of Cambridge and the AstraZeneca Centre for Genomics Research, and by the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014) [*]. Olink Target assays (Neurology panel) were funded by Biogen, Inc. SomaLogic assays were funded by Merck & Co, Inc and the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014) [*]. Metabolon HD4 assays were funded by the NIHR BioResource; NIHR Cambridge Biomedical Research Centre (BRC-1215-20014) [*]; Wellcome Trust grant number 206194; and BioMarin Pharmaceutical, Inc. Nightingale Health assays were funded by the European Commission Framework Programme 7 (HEALTH-F2-2012-279233). The academic coordinating center for INTERVAL was supported by core funding from the NIHR Blood and Transplant Research Unit (BTRU) in Donor Health and Genomics (NIHR BTRU-2014-10024); NIHR BTRU in Donor Health and Behaviour (NIHR203337); UK Medical Research Council (MR/L003120/1); British Heart Foundation (SP/09/002; RG/13/13/30194; RG/18/13/33946); and NIHR Cambridge BRC (BRC-1215-20014; NIHR203312) [*]. A complete list of the investigators and contributors to the INTERVAL trial is provided in Di Angelantonio et al.16 The academic coordinating center would like to thank blood donor center staff and blood donors for participating in the INTERVAL trial. This work was supported by Health Data Research UK, which is funded by the UK Medical Research Council, Engineering and Physical Sciences Research Council, Economic and Social Research Council, Department of Health and Social Care (England), Chief Scientist Office of the Scottish Government Health and Social Care Directorates, Health and Social Care Research and Development Division (Welsh Government), Public Health Agency (Northern Ireland), British Heart Foundation and Wellcome. *The views expressed are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care. The Wellcome Sanger Institute is supported by core funding from the Wellcome Trust (206194 and 220540/Z/20/A). We thank the Wellcome Sanger Institute's Scientific Operations team for their contribution to sequencing data generation. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. This work was performed using resources provided by the Cambridge Service for Data Driven Discovery (CSD3) operated by the University of Cambridge Research Computing Service (https://www.csd3.cam.ac.uk/), provided by Dell EMC and Intel using Tier-2 funding from the Engineering and Physical Sciences Research Council (capital grant EP/P020259/1), and DiRAC funding from the Science and Technology Facilities Council (https://dirac.ac.uk/). We thank the participants and investigators of the UK Biobank study who made this work possible (Resource Application Numbers 26041 and 65851). A.T. is supported by the Wellcome Trust (PhD studentship 222548/Z/21/Z). E.P. was funded by the EU/EFPIA Innovative Medicines Initiative Joint Undertaking BigData@Heart grant 116074 and is funded by the NIHR BTRU in Donor Health and Behaviour (NIHR203337) [*]. M.A.Q. is on the KOL panel for New England Biolabs. S.C.R was funded by a BHF Programme Grant (RG/18/13/33946) and the NIHR Cambridge BRC (BRC-1215-20014; NIHR203312). B.B.S. and H.R. are employees and stockholders of Biogen. Y.X. is supported by the UK Economic and Social Research Council (ES/T013192/1). C.D.W. is an employee and stockholder of Johnson & Johnson. S.P. and D.S.P. are employees and stockholders of AstraZeneca. D.J.G. is an employee and stockholder of BioMarin Pharmaceutical. D.J.R. is an employee of NHS Blood and Transplant. J.E.P. is supported by a Medical Research Foundation Fellowship (MRF-057-0003-RG-PETE-C0799) and has received hospitality and travel expenses to speak at Olink-sponsored academic meetings (none within the past 5 years). J.D. holds a British Heart Foundation Professorship and a NIHR Senior Investigator Award [*]. A.S.B. has received grants outside of this work from AstraZeneca, Bayer, Biogen, BioMarin and Sanofi. M.I. is supported by the Munz Chair of Cardiovascular Prediction and Prevention and the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014; NIHR203312) [*]. M.I. is also supported by the UK Economic and Social Research Council (ES/T013192/1). M.I. is a trustee of the Public Health Genomics (PHG) Foundation, a member of the Scientific Advisory Board of Open Targets, and has a research collaboration with AstraZeneca that is unrelated to this study. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The National Research Ethics Service of the Health Research Authority gave ethical approval for this work. (11/EE/0538) I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The INTERVAL study data used in this paper are available to bona fide researchers from ceu-dataaccess@medschl.cam.ac.uk. The data access policy for the data is available at http://www.donorhealth-btru.nihr.ac.uk/project/bioresource. The newly generated RNA-sequencing data (n=4,732 INTERVAL participants) have been deposited at the European Genome-phenome Archive (EGA) under the accession number EGAD00001008015. The results from the genetic association, colocalization and mediation analyses are available at https://IntervalRNA.org.uk. All original code has been deposited at GitHub at https://github.com/INTERVAL-RNAseq/manuscript-scripts.