Yu Chen, Sihan Liu, Zongyao Ren, Feiran Wang, Qiuman Liang, Yi Jiang, Rujia Dai, Fangyuan Duan, Cong Han, Zhilin Ning, Yan Xia, Miao Li, Kai Yuan, Wenying Qiu, Xiao-Xin Yan, Jiapei Dai, Richard F Kopp, Jufang Huang, Shuhua Xu, Beisha Tang, Lingqian Wu, Eric R Gamazon, Tim Bigdeli, Elliot Gershon, Hailiang Huang, Chao Ma, Chunyu Liu, Chao Chen
{"title":"Cross-ancestry analysis of brain QTLs enhances interpretation of schizophrenia genome-wide association studies.","authors":"Yu Chen, Sihan Liu, Zongyao Ren, Feiran Wang, Qiuman Liang, Yi Jiang, Rujia Dai, Fangyuan Duan, Cong Han, Zhilin Ning, Yan Xia, Miao Li, Kai Yuan, Wenying Qiu, Xiao-Xin Yan, Jiapei Dai, Richard F Kopp, Jufang Huang, Shuhua Xu, Beisha Tang, Lingqian Wu, Eric R Gamazon, Tim Bigdeli, Elliot Gershon, Hailiang Huang, Chao Ma, Chunyu Liu, Chao Chen","doi":"10.1016/j.ajhg.2024.09.001","DOIUrl":null,"url":null,"abstract":"<p><p>Research on brain expression quantitative trait loci (eQTLs) has illuminated the genetic underpinnings of schizophrenia (SCZ). Yet most of these studies have been centered on European populations, leading to a constrained understanding of population diversities and disease risks. To address this gap, we examined genotype and RNA-seq data from African Americans (AA, n = 158), Europeans (EUR, n = 408), and East Asians (EAS, n = 217). When comparing eQTLs between EUR and non-EUR populations, we observed concordant patterns of genetic regulatory effect, particularly in terms of the effect sizes of the eQTLs. However, 343,737 cis-eQTLs linked to 1,276 genes and 198,769 SNPs were found to be specific to non-EUR populations. Over 90% of observed population differences in eQTLs could be traced back to differences in allele frequency. Furthermore, 35% of these eQTLs were notably rare in the EUR population. Integrating brain eQTLs with SCZ signals from diverse populations, we observed a higher disease heritability enrichment of brain eQTLs in matched populations compared to mismatched ones. Prioritization analysis identified five risk genes (SFXN2, VPS37B, DENR, FTCDNL1, and NT5DC2) and three potential regulatory variants in known risk genes (CNNM2, MTRFR, and MPHOSPH9) that were missed in the EUR dataset. Our findings underscore that increasing genetic ancestral diversity is more efficient for power improvement than merely increasing the sample size within single-ancestry eQTLs datasets. Such a strategy will not only improve our understanding of the biological underpinnings of population structures but also pave the way for the identification of risk genes in SCZ.</p>","PeriodicalId":7659,"journal":{"name":"American journal of human genetics","volume":null,"pages":null},"PeriodicalIF":8.1000,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"American journal of human genetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1016/j.ajhg.2024.09.001","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/10/2 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0
Abstract
Research on brain expression quantitative trait loci (eQTLs) has illuminated the genetic underpinnings of schizophrenia (SCZ). Yet most of these studies have been centered on European populations, leading to a constrained understanding of population diversities and disease risks. To address this gap, we examined genotype and RNA-seq data from African Americans (AA, n = 158), Europeans (EUR, n = 408), and East Asians (EAS, n = 217). When comparing eQTLs between EUR and non-EUR populations, we observed concordant patterns of genetic regulatory effect, particularly in terms of the effect sizes of the eQTLs. However, 343,737 cis-eQTLs linked to 1,276 genes and 198,769 SNPs were found to be specific to non-EUR populations. Over 90% of observed population differences in eQTLs could be traced back to differences in allele frequency. Furthermore, 35% of these eQTLs were notably rare in the EUR population. Integrating brain eQTLs with SCZ signals from diverse populations, we observed a higher disease heritability enrichment of brain eQTLs in matched populations compared to mismatched ones. Prioritization analysis identified five risk genes (SFXN2, VPS37B, DENR, FTCDNL1, and NT5DC2) and three potential regulatory variants in known risk genes (CNNM2, MTRFR, and MPHOSPH9) that were missed in the EUR dataset. Our findings underscore that increasing genetic ancestral diversity is more efficient for power improvement than merely increasing the sample size within single-ancestry eQTLs datasets. Such a strategy will not only improve our understanding of the biological underpinnings of population structures but also pave the way for the identification of risk genes in SCZ.
期刊介绍:
The American Journal of Human Genetics (AJHG) is a monthly journal published by Cell Press, chosen by The American Society of Human Genetics (ASHG) as its premier publication starting from January 2008. AJHG represents Cell Press's first society-owned journal, and both ASHG and Cell Press anticipate significant synergies between AJHG content and that of other Cell Press titles.