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bioRxiv · 10.1101/2023.04.26.538455

Gene Expression and Splicing QTL Analysis of Blood Cells in African American Participants from the Jackson Heart Study

Wen, J.·Sun, Q.·Huang, L.·Zhou, L.·Doyle, M. F.·Ekunwe, L.·Olson, N. C.·Reiner, A. P.·Li, Y.·Raffield, L. M.
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Abstract

Most gene expression and alternative splicing quantitative trait loci (eQTL/sQTL) studies have been biased toward European ancestry individuals. Here, we performed eQTL and sQTL analysis using TOPMed whole genome sequencing-derived genotype data and RNA sequencing data from stored peripheral blood mononuclear cells in 1,012 African American participants from the Jackson Heart Study (JHS). At a false discovery rate (FDR) of 5%, we identified 4,798,604 significant eQTL-gene pairs, covering 16,538 unique genes; and 5,921,368 sQTL-gene-cluster pairs, covering 9,605 unique genes. About 31% of detected eQTL and sQTL variants with a minor allele frequency (MAF) > 1% in JHS were rare (MAF < 0.1%), and therefore unlikely to be detected, in European ancestry individuals. We also generated 17,630 eQTL credible sets and 24,525 sQTL credible sets for genes (gene-clusters) with lead QTL p < 5e-8. Finally, we created an open database, which is freely available online, allowing fast query and bulk download of our QTL results.

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Wen, J., Sun, Q., Huang, L., Zhou, L., Doyle, M. F., Ekunwe, L., Olson, N. C., Reiner, A. P., Li, Y., Raffield, L. M.. 2023-04-29. Gene Expression and Splicing QTL Analysis of Blood Cells in African American Participants from the Jackson Heart Study. https://doi.org/10.1101/2023.04.26.538455

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