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dc.contributor.authorYao, Chen
dc.contributor.authorJoehanes, Roby
dc.contributor.authorJohnson, Andrew D.
dc.contributor.authorHuan, Tianxiao
dc.contributor.authorLiu, Chunyu
dc.contributor.authorFreedman, Jane E.
dc.contributor.authorMunson, Peter J.
dc.contributor.authorHill, David A
dc.contributor.authorVidal, Marc
dc.contributor.authorLevy, Daniel
dc.date2022-08-11T08:09:20.000
dc.date.accessioned2022-08-23T16:27:06Z
dc.date.available2022-08-23T16:27:06Z
dc.date.issued2017-04-06
dc.date.submitted2017-05-25
dc.identifier.citationAm J Hum Genet. 2017 Apr 6;100(4):571-580. Epub 2017 Mar 9. <a href="https://doi.org/10.1016/j.ajhg.2017.02.003">Link to article on publisher's site</a>
dc.identifier.issn0002-9297 (Linking)
dc.identifier.doi10.1016/j.ajhg.2017.02.003
dc.identifier.pmid28285768
dc.identifier.urihttp://hdl.handle.net/20.500.14038/36705
dc.description.abstractIdentifying causal genetic variants and understanding their mechanisms of effect on traits remains a challenge in genome-wide association studies (GWASs). In particular, how genetic variants (i.e., trans-eQTLs) affect expression of remote genes (i.e., trans-eGenes) remains unknown. We hypothesized that some trans-eQTLs regulate expression of distant genes by altering the expression of nearby genes (cis-eGenes). Using published GWAS datasets with 39,165 single-nucleotide polymorphisms (SNPs) associated with 1,960 traits, we explored whole blood gene expression associations of trait-associated SNPs in 5,257 individuals from the Framingham Heart Study. We identified 2,350 trans-eQTLs (at p < 10-7); more than 80% of them were found to have cis-associated eGenes. Mediation testing suggested that for 35% of trans-eQTL-trans-eGene pairs in different chromosomes and 90% pairs in the same chromosome, the disease-associated SNP may alter expression of the trans-eGene via cis-eGene expression. In addition, we identified 13 trans-eQTL hotspots, affecting from ten to hundreds of genes, suggesting the existence of master genetic regulators. Using causal inference testing, we searched causal variants across eight cardiometabolic traits (BMI, systolic and diastolic blood pressure, LDL cholesterol, HDL cholesterol, total cholesterol, triglycerides, and fasting blood glucose) and identified several cis-eGenes (ALDH2 for systolic and diastolic blood pressure, MCM6 and DARS for total cholesterol, and TRIB1 for triglycerides) that were causal mediators for the corresponding traits, as well as examples of trans-mediators (TAGAP for LDL cholesterol). The finding of extensive evidence of genome-wide mediation effects suggests a critical role of cryptic gene regulation underlying many disease traits.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=28285768&dopt=Abstract">Link to Article in PubMed</a>
dc.relation.urlhttps://doi.org/10.1016/j.ajhg.2017.02.003
dc.subjectGWAS
dc.subjectcardiometabolic traits
dc.subjectcausal variants
dc.subjecteQTLs
dc.subjecthotspots
dc.subjectmediation
dc.subjecttrans
dc.subjectCellular and Molecular Physiology
dc.subjectGenetics and Genomics
dc.subjectMolecular Biology
dc.titleDynamic Role of trans Regulation of Gene Expression in Relation to Complex Traits
dc.typeJournal Article
dc.source.journaltitleAmerican journal of human genetics
dc.source.volume100
dc.source.issue4
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/metnet_pubs/73
dc.identifier.contextkey10212134
html.description.abstract<p>Identifying causal genetic variants and understanding their mechanisms of effect on traits remains a challenge in genome-wide association studies (GWASs). In particular, how genetic variants (i.e., trans-eQTLs) affect expression of remote genes (i.e., trans-eGenes) remains unknown. We hypothesized that some trans-eQTLs regulate expression of distant genes by altering the expression of nearby genes (cis-eGenes). Using published GWAS datasets with 39,165 single-nucleotide polymorphisms (SNPs) associated with 1,960 traits, we explored whole blood gene expression associations of trait-associated SNPs in 5,257 individuals from the Framingham Heart Study. We identified 2,350 trans-eQTLs (at p < 10-7); more than 80% of them were found to have cis-associated eGenes. Mediation testing suggested that for 35% of trans-eQTL-trans-eGene pairs in different chromosomes and 90% pairs in the same chromosome, the disease-associated SNP may alter expression of the trans-eGene via cis-eGene expression. In addition, we identified 13 trans-eQTL hotspots, affecting from ten to hundreds of genes, suggesting the existence of master genetic regulators. Using causal inference testing, we searched causal variants across eight cardiometabolic traits (BMI, systolic and diastolic blood pressure, LDL cholesterol, HDL cholesterol, total cholesterol, triglycerides, and fasting blood glucose) and identified several cis-eGenes (ALDH2 for systolic and diastolic blood pressure, MCM6 and DARS for total cholesterol, and TRIB1 for triglycerides) that were causal mediators for the corresponding traits, as well as examples of trans-mediators (TAGAP for LDL cholesterol). The finding of extensive evidence of genome-wide mediation effects suggests a critical role of cryptic gene regulation underlying many disease traits.</p>
dc.identifier.submissionpathmetnet_pubs/73
dc.contributor.departmentDepartment of Medicine, Division of Cardiovascular Medicine
dc.contributor.departmentUMass Metabolic Network
dc.source.pages571-580


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