Gene expression and splicing QTL analysis of blood cells in African American participants from the Jackson Heart Study.
Jia WenQuan SunLe HuangLingbo ZhouMargaret F DoyleLynette EkunwePeter DurdaNels C OlsonAlexander P ReinerYun LiLaura M RaffieldPublished in: Genetics (2024)
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.
Keyphrases
- african american
- gene expression
- genome wide
- dna methylation
- electronic health record
- single cell
- emergency department
- high density
- big data
- atrial fibrillation
- machine learning
- cell cycle arrest
- high resolution
- health information
- artificial intelligence
- room temperature
- adverse drug
- transcription factor
- bioinformatics analysis