Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease

Matteo D’Antonio (), Jennifer P. Nguyen, Timothy D. Arthur, Hiroko Matsui, Agnieszka D’Antonio-Chronowska and Kelly A. Frazer ()
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Matteo D’Antonio: University of California San Diego
Jennifer P. Nguyen: University of California, San Diego
Timothy D. Arthur: University of California, San Diego
Hiroko Matsui: University of California San Diego
Agnieszka D’Antonio-Chronowska: University of California San Diego
Kelly A. Frazer: University of California San Diego

Nature Communications, 2023, vol. 14, issue 1, 1-18

Abstract: Abstract The causal variants and genes underlying thousands of cardiac GWAS signals have yet to be identified. Here, we leverage spatiotemporal information on 966 RNA-seq cardiac samples and perform an expression quantitative trait locus (eQTL) analysis detecting eQTLs considering both eGenes and eIsoforms. We identify 2,578 eQTLs associated with a specific developmental stage-, tissue- and/or cell type. Colocalization between eQTL and GWAS signals of five cardiac traits identified variants with high posterior probabilities for being causal in 210 GWAS loci. Pulse pressure GWAS loci are enriched for colocalization with fetal- and smooth muscle- eQTLs; pulse rate with adult- and cardiac muscle- eQTLs; and atrial fibrillation with cardiac muscle- eQTLs. Fine mapping identifies 79 credible sets with five or fewer SNPs, of which 15 were associated with spatiotemporal eQTLs. Our study shows that many cardiac GWAS variants impact traits and disease in a developmental stage-, tissue- and/or cell type-specific fashion.

Date: 2023
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DOI: 10.1038/s41467-023-36638-2

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