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

IF 3.3 3区生物学 Q2 GENETICS & HEREDITY

Genetics Pub Date : 2024-09-04 DOI:10.1093/genetics/iyae098

Jia Wen, Quan Sun, Le Huang, Lingbo Zhou, Margaret F Doyle, Lynette Ekunwe, Peter Durda, Nels C Olson, Alexander P Reiner, Yun Li, Laura M Raffield

{"title":"Gene expression and splicing QTL analysis of blood cells in African American participants from the Jackson Heart Study.","authors":"Jia Wen, Quan Sun, Le Huang, Lingbo Zhou, Margaret F Doyle, Lynette Ekunwe, Peter Durda, Nels C Olson, Alexander P Reiner, Yun Li, Laura M Raffield","doi":"10.1093/genetics/iyae098","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":null,"pages":null},"PeriodicalIF":3.3000,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373511/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/genetics/iyae098","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}

引用次数: 0

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.

查看原文本刊更多论文

杰克逊心脏研究非裔美国人血细胞基因表达和剪接 QTL 分析。

大多数基因表达和替代剪接定量性状位点（eQTL/sQTL）研究都偏重于欧洲血统的个体。在这里，我们使用 TOPMed 全基因组测序得出的基因型数据和来自杰克逊心脏病研究（JHS）的 1,012 名非洲裔美国人储存的外周血单核细胞的 RNA 测序数据，进行了 eQTL 和 sQTL 分析。在5%的错误发现率下，我们发现了17,630个独特的eQTL可信集，涵盖16,538个独特的基因；以及24,525个独特的sQTL可信集，涵盖9,605个独特的基因，主导QTL的P < 5e-8。在JHS中，小等位基因频率大于1%的独立eQTL和独立sQTL中约有24%是罕见的（小等位基因频率小于0.1%），因此在欧洲血统的个体中不太可能被检测到。最后，我们创建了一个开放式数据库，可免费在线使用，允许快速查询和批量下载我们的 QTL 结果。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Genetics GENETICS & HEREDITY-

CiteScore

6.90

自引率

6.10%

发文量

177

审稿时长

1.5 months

期刊介绍： GENETICS is published by the Genetics Society of America, a scholarly society that seeks to deepen our understanding of the living world by advancing our understanding of genetics. Since 1916, GENETICS has published high-quality, original research presenting novel findings bearing on genetics and genomics. The journal publishes empirical studies of organisms ranging from microbes to humans, as well as theoretical work. While it has an illustrious history, GENETICS has changed along with the communities it serves: it is not your mentor''s journal. The editors make decisions quickly – in around 30 days – without sacrificing the excellence and scholarship for which the journal has long been known. GENETICS is a peer reviewed, peer-edited journal, with an international reach and increasing visibility and impact. All editorial decisions are made through collaboration of at least two editors who are practicing scientists. GENETICS is constantly innovating: expanded types of content include Reviews, Commentary (current issues of interest to geneticists), Perspectives (historical), Primers (to introduce primary literature into the classroom), Toolbox Reviews, plus YeastBook, FlyBook, and WormBook (coming spring 2016). For particularly time-sensitive results, we publish Communications. As part of our mission to serve our communities, we''ve published thematic collections, including Genomic Selection, Multiparental Populations, Mouse Collaborative Cross, and the Genetics of Sex.