Multi-population GWAS for venous thromboembolism identifies novel loci followed by experimental validation in zebrafish Open Access

• We identified 38 significant loci associated with VTE through GWAS meta-analysis and prioritized causal genes through an integrative method

• Functional confirmatory studies of GWAS hits via genome editing in zebrafish showed a novel role in thrombosis for genes TC2N and RASIP1.

Venous thromboembolism (VTE) is a leading cause of morbidity and mortality. Although many genetic risk factors have been identified, a substantial portion of the heritability remains unexplained. Here we employ genome wide association study (GWAS) VTE across 9 international cohorts of the Global Biobank Meta-analysis Initiative (GBMI) to address this question, along with in vivo functional validation. The multi-population GWAS (VTE cases=27,987, controls=1,035,290) resulted in 38 genome-wide significant loci, 4 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 associated with VTE through GWAS and/or functional studies (e.g., F5, F11, VWF, STAB2, PLCG2, TC2N), functionally validated those that did not have evidence other than GWAS (TC2N, TSPAN15), and discovered one not previously associated with coagulation (RASIP1). We evaluated the function of six prioritized genes with strong genetic evidence, including F7 as a positive control, using laser-mediated endothelial injury to induce thrombosis in zebrafish after CRISPR/Cas9 knockdown. 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-population GWAS, in silico candidate gene predictions, and in vivo functional follow-up of candidate genes.