Multi-ancestry GWAS for venous thromboembolism identifies novel loci followed by experimental validation in zebrafish

Genome wide association study (GWAS) results for Venous Thromboembolism (VTE) across 9 international cohorts of the Global Biobank Meta-analysis Initiative (GBMI), with representation across six ancestry groups (cases=27,987, controls=1,035,290), were combined using inverse-variance weighted meta-analysis. This multi-ancestry GWAS resulted in 38 genome-wide significant loci, 9 of which are potentially novel. For each autosomal locus we performed gene prioritization using seven independent, yet converging, lines of evidence. Through prioritization we identified genes known for VTE (e.g., F5, F11, VWF ), genes known to modify blood coagulation (e.g., STAB2 ), and genes without known coagulation mechanisms from functional studies (e.g., PLCG2, TC2N ). We evaluated the function of six prioritized genes, including F7 as a positive control, using laser mediated endothelial injury to induce thrombosis in zebrafish. We used CRISPR/Cas9 to knock down these potentially causal genes and measured time to occlusion after laser injury. From this assay we have supportive evidence for a role of RASIP1 and TC2N in the modification of human VTE, and suggestive evidence for STAB2 and TSPAN15 . This study expands the currently identified genomic architecture of VTE through biobank-based multi-ancestry GWAS, in silico candidate gene predictions, and in vivo functional follow-up of novel candidate genes. ### Competing Interest Statement The spouse of CJW works at Regeneron pharmaceuticals. SMD receives research support from RenalytixAI and personal consulting fees from Calico Labs, outside the scope of the current research. SMD is named as a co-inventor on a Government-owned US Patent application related to the use of genetic risk prediction for venous thromboembolic disease filed by the US Department of Veterans Affairs in accordance with Federal regulatory requirements. ### Funding Statement JS was supported by R35 HL150784. D-AT was supported by the EPIDEMIOM-VT Senior Chair from the University of Bordeaux initiative of excellence (IdEX) and the GENMED Laboratory of Excellence on Medical Genomics [ANR-10-LABX-0013], a research program managed by the National Research Agency (ANR) as part of the French Investment for the Future. CJW, IS, KHW, and BNW were supported by R35-HL135824 (Willer, PI). SMD is supported by IK2-CX001780. This research is based on data from the Million Veteran Program, Office of Research and Development, Veterans Health Administration, and was supported by award # BX003362. This publication does not represent the views of the Department of Veteran Affairs or the United States Government. This work was supported by funding from the Department of Veterans Affairs Office of Research and Development, Million Veteran Program Grant MVP000; Department of Veterans. The views expressed in this manuscript are those of the authors and do not necessarily represent the views of the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the U.S. Department of Health and Human Services. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. The data used for the analyses described in this manuscript were obtained from GTEx Analysis v8 on the GTEx Portal on 05/01/2021. ### 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: Please refer to Supplementary Note of https://doi.org/10.1101/2021.11.19.21266436 for information regarding individual studies involved in the Global Biobank Meta-analysis Initiative. Zebrafish were maintained according to protocols approved by the University of Michigan Animal Care and Use Committee. 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 and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All summary statistics will be released with the GBMI flagship paper. All functional data in the present study are available upon request. Code used is available on github.