Systematic identification of trans eQTLs as putative drivers of known disease associations

Lude Franke and colleagues report the results of a large expression QTL study performed on peripheral blood samples from 5,311 individuals. They identify trans -eQTL effects for 103 independent loci that were previously associated with complex traits at genome-wide significance, suggesting that this...

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Veröffentlicht in:Nature genetics 2013-10, Vol.45 (10), p.1238-1243
Hauptverfasser: Westra, Harm-Jan, Peters, Marjolein J, Esko, Tõnu, Yaghootkar, Hanieh, Schurmann, Claudia, Kettunen, Johannes, Christiansen, Mark W, Fairfax, Benjamin P, Schramm, Katharina, Powell, Joseph E, Zhernakova, Alexandra, Zhernakova, Daria V, Veldink, Jan H, Van den Berg, Leonard H, Karjalainen, Juha, Withoff, Sebo, Uitterlinden, André G, Hofman, Albert, Rivadeneira, Fernando, 't Hoen, Peter A C, Reinmaa, Eva, Fischer, Krista, Nelis, Mari, Milani, Lili, Melzer, David, Ferrucci, Luigi, Singleton, Andrew B, Hernandez, Dena G, Nalls, Michael A, Homuth, Georg, Nauck, Matthias, Radke, Dörte, Völker, Uwe, Perola, Markus, Salomaa, Veikko, Brody, Jennifer, Suchy-Dicey, Astrid, Gharib, Sina A, Enquobahrie, Daniel A, Lumley, Thomas, Montgomery, Grant W, Makino, Seiko, Prokisch, Holger, Herder, Christian, Roden, Michael, Grallert, Harald, Meitinger, Thomas, Strauch, Konstantin, Li, Yang, Jansen, Ritsert C, Visscher, Peter M, Knight, Julian C, Psaty, Bruce M, Ripatti, Samuli, Teumer, Alexander, Frayling, Timothy M, Metspalu, Andres, van Meurs, Joyce B J, Franke, Lude
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container_end_page 1243
container_issue 10
container_start_page 1238
container_title Nature genetics
container_volume 45
creator Westra, Harm-Jan
Peters, Marjolein J
Esko, Tõnu
Yaghootkar, Hanieh
Schurmann, Claudia
Kettunen, Johannes
Christiansen, Mark W
Fairfax, Benjamin P
Schramm, Katharina
Powell, Joseph E
Zhernakova, Alexandra
Zhernakova, Daria V
Veldink, Jan H
Van den Berg, Leonard H
Karjalainen, Juha
Withoff, Sebo
Uitterlinden, André G
Hofman, Albert
Rivadeneira, Fernando
't Hoen, Peter A C
Reinmaa, Eva
Fischer, Krista
Nelis, Mari
Milani, Lili
Melzer, David
Ferrucci, Luigi
Singleton, Andrew B
Hernandez, Dena G
Nalls, Michael A
Homuth, Georg
Nauck, Matthias
Radke, Dörte
Völker, Uwe
Perola, Markus
Salomaa, Veikko
Brody, Jennifer
Suchy-Dicey, Astrid
Gharib, Sina A
Enquobahrie, Daniel A
Lumley, Thomas
Montgomery, Grant W
Makino, Seiko
Prokisch, Holger
Herder, Christian
Roden, Michael
Grallert, Harald
Meitinger, Thomas
Strauch, Konstantin
Li, Yang
Jansen, Ritsert C
Visscher, Peter M
Knight, Julian C
Psaty, Bruce M
Ripatti, Samuli
Teumer, Alexander
Frayling, Timothy M
Metspalu, Andres
van Meurs, Joyce B J
Franke, Lude
description Lude Franke and colleagues report the results of a large expression QTL study performed on peripheral blood samples from 5,311 individuals. They identify trans -eQTL effects for 103 independent loci that were previously associated with complex traits at genome-wide significance, suggesting that this approach can provide insights into the downstream effects of many trait-associated variants. Identifying the downstream effects of disease-associated SNPs is challenging. To help overcome this problem, we performed expression quantitative trait locus (eQTL) meta-analysis in non-transformed peripheral blood samples from 5,311 individuals with replication in 2,775 individuals. We identified and replicated trans eQTLs for 233 SNPs (reflecting 103 independent loci) that were previously associated with complex traits at genome-wide significance. Some of these SNPs affect multiple genes in trans that are known to be altered in individuals with disease: rs4917014, previously associated with systemic lupus erythematosus (SLE) 1 , altered gene expression of C1QB and five type I interferon response genes, both hallmarks of SLE 2 , 3 , 4 . DeepSAGE RNA sequencing showed that rs4917014 strongly alters the 3′ UTR levels of IKZF1 in cis , and chromatin immunoprecipitation and sequencing analysis of the trans -regulated genes implicated IKZF1 as the causal gene. Variants associated with cholesterol metabolism and type 1 diabetes showed similar phenomena, indicating that large-scale eQTL mapping provides insight into the downstream effects of many trait-associated variants.
doi_str_mv 10.1038/ng.2756
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They identify trans -eQTL effects for 103 independent loci that were previously associated with complex traits at genome-wide significance, suggesting that this approach can provide insights into the downstream effects of many trait-associated variants. Identifying the downstream effects of disease-associated SNPs is challenging. To help overcome this problem, we performed expression quantitative trait locus (eQTL) meta-analysis in non-transformed peripheral blood samples from 5,311 individuals with replication in 2,775 individuals. We identified and replicated trans eQTLs for 233 SNPs (reflecting 103 independent loci) that were previously associated with complex traits at genome-wide significance. Some of these SNPs affect multiple genes in trans that are known to be altered in individuals with disease: rs4917014, previously associated with systemic lupus erythematosus (SLE) 1 , altered gene expression of C1QB and five type I interferon response genes, both hallmarks of SLE 2 , 3 , 4 . DeepSAGE RNA sequencing showed that rs4917014 strongly alters the 3′ UTR levels of IKZF1 in cis , and chromatin immunoprecipitation and sequencing analysis of the trans -regulated genes implicated IKZF1 as the causal gene. Variants associated with cholesterol metabolism and type 1 diabetes showed similar phenomena, indicating that large-scale eQTL mapping provides insight into the downstream effects of many trait-associated variants.</description><identifier>ISSN: 1061-4036</identifier><identifier>EISSN: 1546-1718</identifier><identifier>DOI: 10.1038/ng.2756</identifier><identifier>PMID: 24013639</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>631/208/191/2018 ; 631/208/200 ; 631/208/205 ; Agriculture ; Animal Genetics and Genomics ; Binding sites ; Biomedicine ; Cancer Research ; Diabetes Mellitus, Type 1 - genetics ; Disease ; Gene expression ; Gene Function ; Gene mapping ; Genetic aspects ; Genetic Predisposition to Disease ; Genomes ; Human Genetics ; Humans ; Identification and classification ; letter ; Lupus Erythematosus, Systemic - genetics ; Meta-analysis ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Single nucleotide polymorphisms ; 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They identify trans -eQTL effects for 103 independent loci that were previously associated with complex traits at genome-wide significance, suggesting that this approach can provide insights into the downstream effects of many trait-associated variants. Identifying the downstream effects of disease-associated SNPs is challenging. To help overcome this problem, we performed expression quantitative trait locus (eQTL) meta-analysis in non-transformed peripheral blood samples from 5,311 individuals with replication in 2,775 individuals. We identified and replicated trans eQTLs for 233 SNPs (reflecting 103 independent loci) that were previously associated with complex traits at genome-wide significance. Some of these SNPs affect multiple genes in trans that are known to be altered in individuals with disease: rs4917014, previously associated with systemic lupus erythematosus (SLE) 1 , altered gene expression of C1QB and five type I interferon response genes, both hallmarks of SLE 2 , 3 , 4 . DeepSAGE RNA sequencing showed that rs4917014 strongly alters the 3′ UTR levels of IKZF1 in cis , and chromatin immunoprecipitation and sequencing analysis of the trans -regulated genes implicated IKZF1 as the causal gene. Variants associated with cholesterol metabolism and type 1 diabetes showed similar phenomena, indicating that large-scale eQTL mapping provides insight into the downstream effects of many trait-associated variants.</description><subject>631/208/191/2018</subject><subject>631/208/200</subject><subject>631/208/205</subject><subject>Agriculture</subject><subject>Animal Genetics and Genomics</subject><subject>Binding sites</subject><subject>Biomedicine</subject><subject>Cancer Research</subject><subject>Diabetes Mellitus, Type 1 - genetics</subject><subject>Disease</subject><subject>Gene expression</subject><subject>Gene Function</subject><subject>Gene mapping</subject><subject>Genetic aspects</subject><subject>Genetic Predisposition to Disease</subject><subject>Genomes</subject><subject>Human Genetics</subject><subject>Humans</subject><subject>Identification and classification</subject><subject>letter</subject><subject>Lupus Erythematosus, Systemic - 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identification of trans eQTLs as putative drivers of known disease associations</title><author>Westra, Harm-Jan ; Peters, Marjolein J ; Esko, Tõnu ; Yaghootkar, Hanieh ; Schurmann, Claudia ; Kettunen, Johannes ; Christiansen, Mark W ; Fairfax, Benjamin P ; Schramm, Katharina ; Powell, Joseph E ; Zhernakova, Alexandra ; Zhernakova, Daria V ; Veldink, Jan H ; Van den Berg, Leonard H ; Karjalainen, Juha ; Withoff, Sebo ; Uitterlinden, André G ; Hofman, Albert ; Rivadeneira, Fernando ; 't Hoen, Peter A C ; Reinmaa, Eva ; Fischer, Krista ; Nelis, Mari ; Milani, Lili ; Melzer, David ; Ferrucci, Luigi ; Singleton, Andrew B ; Hernandez, Dena G ; Nalls, Michael A ; Homuth, Georg ; Nauck, Matthias ; Radke, Dörte ; Völker, Uwe ; Perola, Markus ; Salomaa, Veikko ; Brody, Jennifer ; Suchy-Dicey, Astrid ; Gharib, Sina A ; Enquobahrie, Daniel A ; Lumley, Thomas ; Montgomery, Grant W ; Makino, Seiko ; Prokisch, Holger ; Herder, Christian ; Roden, Michael ; Grallert, Harald ; Meitinger, Thomas ; Strauch, Konstantin ; Li, Yang ; Jansen, Ritsert C ; Visscher, Peter M ; Knight, Julian C ; Psaty, Bruce M ; Ripatti, Samuli ; Teumer, Alexander ; Frayling, Timothy M ; Metspalu, Andres ; van Meurs, Joyce B J ; Franke, Lude</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c631t-b45d628068454ff9cfed35e359a96dfce2fce8929182a2bf2f3de3fa4c275b323</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>631/208/191/2018</topic><topic>631/208/200</topic><topic>631/208/205</topic><topic>Agriculture</topic><topic>Animal Genetics and Genomics</topic><topic>Binding sites</topic><topic>Biomedicine</topic><topic>Cancer Research</topic><topic>Diabetes Mellitus, Type 1 - genetics</topic><topic>Disease</topic><topic>Gene expression</topic><topic>Gene Function</topic><topic>Gene mapping</topic><topic>Genetic aspects</topic><topic>Genetic Predisposition to Disease</topic><topic>Genomes</topic><topic>Human Genetics</topic><topic>Humans</topic><topic>Identification and classification</topic><topic>letter</topic><topic>Lupus Erythematosus, Systemic - genetics</topic><topic>Meta-analysis</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Quantitative Trait Loci</topic><topic>Single nucleotide polymorphisms</topic><topic>Studies</topic><topic>Systemic lupus erythematosus</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Westra, Harm-Jan</creatorcontrib><creatorcontrib>Peters, Marjolein J</creatorcontrib><creatorcontrib>Esko, Tõnu</creatorcontrib><creatorcontrib>Yaghootkar, Hanieh</creatorcontrib><creatorcontrib>Schurmann, Claudia</creatorcontrib><creatorcontrib>Kettunen, Johannes</creatorcontrib><creatorcontrib>Christiansen, Mark W</creatorcontrib><creatorcontrib>Fairfax, Benjamin P</creatorcontrib><creatorcontrib>Schramm, Katharina</creatorcontrib><creatorcontrib>Powell, Joseph E</creatorcontrib><creatorcontrib>Zhernakova, Alexandra</creatorcontrib><creatorcontrib>Zhernakova, Daria V</creatorcontrib><creatorcontrib>Veldink, Jan H</creatorcontrib><creatorcontrib>Van den Berg, Leonard H</creatorcontrib><creatorcontrib>Karjalainen, Juha</creatorcontrib><creatorcontrib>Withoff, Sebo</creatorcontrib><creatorcontrib>Uitterlinden, André G</creatorcontrib><creatorcontrib>Hofman, Albert</creatorcontrib><creatorcontrib>Rivadeneira, Fernando</creatorcontrib><creatorcontrib>'t Hoen, Peter A C</creatorcontrib><creatorcontrib>Reinmaa, Eva</creatorcontrib><creatorcontrib>Fischer, Krista</creatorcontrib><creatorcontrib>Nelis, Mari</creatorcontrib><creatorcontrib>Milani, Lili</creatorcontrib><creatorcontrib>Melzer, David</creatorcontrib><creatorcontrib>Ferrucci, Luigi</creatorcontrib><creatorcontrib>Singleton, Andrew B</creatorcontrib><creatorcontrib>Hernandez, Dena G</creatorcontrib><creatorcontrib>Nalls, Michael A</creatorcontrib><creatorcontrib>Homuth, Georg</creatorcontrib><creatorcontrib>Nauck, Matthias</creatorcontrib><creatorcontrib>Radke, Dörte</creatorcontrib><creatorcontrib>Völker, Uwe</creatorcontrib><creatorcontrib>Perola, Markus</creatorcontrib><creatorcontrib>Salomaa, Veikko</creatorcontrib><creatorcontrib>Brody, Jennifer</creatorcontrib><creatorcontrib>Suchy-Dicey, Astrid</creatorcontrib><creatorcontrib>Gharib, Sina A</creatorcontrib><creatorcontrib>Enquobahrie, Daniel A</creatorcontrib><creatorcontrib>Lumley, Thomas</creatorcontrib><creatorcontrib>Montgomery, Grant W</creatorcontrib><creatorcontrib>Makino, Seiko</creatorcontrib><creatorcontrib>Prokisch, Holger</creatorcontrib><creatorcontrib>Herder, Christian</creatorcontrib><creatorcontrib>Roden, Michael</creatorcontrib><creatorcontrib>Grallert, Harald</creatorcontrib><creatorcontrib>Meitinger, Thomas</creatorcontrib><creatorcontrib>Strauch, Konstantin</creatorcontrib><creatorcontrib>Li, Yang</creatorcontrib><creatorcontrib>Jansen, Ritsert C</creatorcontrib><creatorcontrib>Visscher, Peter M</creatorcontrib><creatorcontrib>Knight, Julian C</creatorcontrib><creatorcontrib>Psaty, Bruce M</creatorcontrib><creatorcontrib>Ripatti, Samuli</creatorcontrib><creatorcontrib>Teumer, Alexander</creatorcontrib><creatorcontrib>Frayling, Timothy M</creatorcontrib><creatorcontrib>Metspalu, Andres</creatorcontrib><creatorcontrib>van Meurs, Joyce B J</creatorcontrib><creatorcontrib>Franke, Lude</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium &amp; Calcified Tissue 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genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Westra, Harm-Jan</au><au>Peters, Marjolein J</au><au>Esko, Tõnu</au><au>Yaghootkar, Hanieh</au><au>Schurmann, Claudia</au><au>Kettunen, Johannes</au><au>Christiansen, Mark W</au><au>Fairfax, Benjamin P</au><au>Schramm, Katharina</au><au>Powell, Joseph E</au><au>Zhernakova, Alexandra</au><au>Zhernakova, Daria V</au><au>Veldink, Jan H</au><au>Van den Berg, Leonard H</au><au>Karjalainen, Juha</au><au>Withoff, Sebo</au><au>Uitterlinden, André G</au><au>Hofman, Albert</au><au>Rivadeneira, Fernando</au><au>'t Hoen, Peter A C</au><au>Reinmaa, Eva</au><au>Fischer, Krista</au><au>Nelis, Mari</au><au>Milani, Lili</au><au>Melzer, David</au><au>Ferrucci, Luigi</au><au>Singleton, Andrew B</au><au>Hernandez, Dena G</au><au>Nalls, Michael A</au><au>Homuth, Georg</au><au>Nauck, Matthias</au><au>Radke, Dörte</au><au>Völker, Uwe</au><au>Perola, Markus</au><au>Salomaa, Veikko</au><au>Brody, Jennifer</au><au>Suchy-Dicey, Astrid</au><au>Gharib, Sina A</au><au>Enquobahrie, Daniel A</au><au>Lumley, Thomas</au><au>Montgomery, Grant W</au><au>Makino, Seiko</au><au>Prokisch, Holger</au><au>Herder, Christian</au><au>Roden, Michael</au><au>Grallert, Harald</au><au>Meitinger, Thomas</au><au>Strauch, Konstantin</au><au>Li, Yang</au><au>Jansen, Ritsert C</au><au>Visscher, Peter M</au><au>Knight, Julian C</au><au>Psaty, Bruce M</au><au>Ripatti, Samuli</au><au>Teumer, Alexander</au><au>Frayling, Timothy M</au><au>Metspalu, Andres</au><au>van Meurs, Joyce B J</au><au>Franke, Lude</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Systematic identification of trans eQTLs as putative drivers of known disease associations</atitle><jtitle>Nature genetics</jtitle><stitle>Nat Genet</stitle><addtitle>Nat Genet</addtitle><date>2013-10-01</date><risdate>2013</risdate><volume>45</volume><issue>10</issue><spage>1238</spage><epage>1243</epage><pages>1238-1243</pages><issn>1061-4036</issn><eissn>1546-1718</eissn><abstract>Lude Franke and colleagues report the results of a large expression QTL study performed on peripheral blood samples from 5,311 individuals. They identify trans -eQTL effects for 103 independent loci that were previously associated with complex traits at genome-wide significance, suggesting that this approach can provide insights into the downstream effects of many trait-associated variants. Identifying the downstream effects of disease-associated SNPs is challenging. To help overcome this problem, we performed expression quantitative trait locus (eQTL) meta-analysis in non-transformed peripheral blood samples from 5,311 individuals with replication in 2,775 individuals. We identified and replicated trans eQTLs for 233 SNPs (reflecting 103 independent loci) that were previously associated with complex traits at genome-wide significance. Some of these SNPs affect multiple genes in trans that are known to be altered in individuals with disease: rs4917014, previously associated with systemic lupus erythematosus (SLE) 1 , altered gene expression of C1QB and five type I interferon response genes, both hallmarks of SLE 2 , 3 , 4 . DeepSAGE RNA sequencing showed that rs4917014 strongly alters the 3′ UTR levels of IKZF1 in cis , and chromatin immunoprecipitation and sequencing analysis of the trans -regulated genes implicated IKZF1 as the causal gene. Variants associated with cholesterol metabolism and type 1 diabetes showed similar phenomena, indicating that large-scale eQTL mapping provides insight into the downstream effects of many trait-associated variants.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>24013639</pmid><doi>10.1038/ng.2756</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0001-7038-567X</orcidid><oa>free_for_read</oa></addata></record>
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identifier ISSN: 1061-4036
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issn 1061-4036
1546-1718
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3991562
source MEDLINE; SpringerLink Journals; Nature Journals Online
subjects 631/208/191/2018
631/208/200
631/208/205
Agriculture
Animal Genetics and Genomics
Binding sites
Biomedicine
Cancer Research
Diabetes Mellitus, Type 1 - genetics
Disease
Gene expression
Gene Function
Gene mapping
Genetic aspects
Genetic Predisposition to Disease
Genomes
Human Genetics
Humans
Identification and classification
letter
Lupus Erythematosus, Systemic - genetics
Meta-analysis
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Single nucleotide polymorphisms
Studies
Systemic lupus erythematosus
title Systematic identification of trans eQTLs as putative drivers of known disease associations
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