Gene expression and splicing QTL analysis of blood cells in African American participants from the Jackson Heart Study

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 analyses using TOPMed whole-genome sequencing-derived genotype data and RNA-sequencing data from stored periphera...

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Bibliographic Details
Published in:Genetics (Austin) 2024-09, Vol.228 (1)
Main Authors: Wen, Jia, Sun, Quan, Huang, Le, Zhou, Lingbo, Doyle, Margaret F, Ekunwe, Lynette, Durda, Peter, Olson, Nels C, Reiner, Alexander P, Li, Yun, Raffield, Laura M
Format: Article
Language:English
Subjects:
Alleles
Alternative splicing
Blood cells
Data analysis
Gene expression
Gene frequency
Gene mapping
Gene sequencing
Genes
Genotypes
Heart rate
Leukocytes (mononuclear)
Peripheral blood mononuclear cells
Quantitative trait loci
Uniqueness
Whole genome sequencing
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Summary: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 analyses 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 of 5%, we identified 17,630 unique eQTL credible sets covering 16,538 unique genes; and 24,525 unique sQTL credible sets covering 9,605 unique genes, with lead QTL at P < 5e−8. About 24% of independent eQTLs and independent sQTLs with a minor allele frequency > 1% in JHS were rare (minor allele frequency < 0.1%), and therefore unlikely to be detected, in European ancestry individuals. Finally, we created an open database, which is freely available online, allowing fast query and bulk download of our QTL results.
ISSN:1943-2631
0016-6731
1943-2631
DOI:10.1093/genetics/iyae098