ArticleGenome biology2021
Exploiting the GTEx resources to decipher the mechanisms at GWAS loci.
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Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 207 papers, 13 of them syntheses that pooled it.
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207citing papers in PubMed, 13 pooled it
20.3field-weighted citation impact, top 1% of its field
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Who cites it
207 citing papers in PubMed, 13 syntheses or guidelines pooled it, 323 citations in OpenAlex.
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- Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data.Genome biology · 2023Pooled it
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- Cross-ancestry meta-analysis of opioid use disorder uncovers novel loci with predominant effects in brain regions associated with addiction.Nature neuroscience · 2022Pooled it
- Advancing our understanding of genetic risk factors and potential personalized strategies for pelvic organ prolapse.Nature communications · 2022Pooled it
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- Genetically regulated expression in late-onset Alzheimer's disease implicates risk genes within known and novel loci.Translational psychiatry · 2021Pooled it
- OmicsPred as a centralized resource for genetic prediction of multi-omic traits.Nature genetics · 2026Article
- Genetically Predicted Blood DNA Methylation Reveals Putative Regulatory Signals Associated with ALS Risk.medRxiv : the preprint server for health sciences · 2026Article
- Overlapping genetic etiology of pediatric and adult germ cell tumors.Journal of the National Cancer Institute · 2026Article
- Tissue-resident immune cells drive genetic risk in autoimmune and lung diseases.Nature immunology · 2026Article
- AI-based multimodal integration of genomics and electronic health records.Nature reviews. Genetics · 2026Review
- Integrative exome sequencing and multi-omics analysis elucidates the regulatory role of rare variants in metabolic syndrome.Functional & integrative genomics · 2026Article
- BMI-genome interactions regulate global gene expression with emphasis in brain and gut.Cell genomics · 2026Article
147 more citing papers are in PubMed but not listed here.
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Authors and funding
30 authors at 12 institutions in 4 countries.
Alvaro N Barbeira *Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA.
Rodrigo Bonazzola *Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA.
Eric R Gamazon *Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
Yanyu Liang *Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA.
YoSon Park *Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
Sarah Kim-HellmuthStatistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany.
Gao WangDepartment of Human Genetics, University of Chicago, Chicago, IL, USA.
Zhuoxun JiangSection of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA.
Dan ZhouDivision of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
Farhad HormozdiariThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Boxiang LiuDepartment of Biology, Stanford University, Stanford, 94305, CA, USA.
Abhiram RaoDepartment of Biology, Stanford University, Stanford, 94305, CA, USA.
Andrew R HamelThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Milton D PividoriSection of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA.
François AguetThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
GTEx GWAS Working Group
Lisa BastaracheDepartment of Biomedical Informatics, Department of Medicine, Vanderbilt University, Nashville, TN, USA.
Daniel M JordanDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Marie VerbanckDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Ron DoDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
GTEx Consortium
Matthew StephensDepartment of Human Genetics, University of Chicago, Chicago, IL, USA.
Kristin ArdlieThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Mark McCarthyUniversity of Oxford, Oxford, UK.
Stephen B MontgomeryDepartment of Genetics, Stanford University, Stanford, CA, USA.
Ayellet V SegrèThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Christopher D BrownDepartment of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
Tuuli LappalainenNew York Genome Center, New York, NY, USA.
Xiaoquan WenDepartment of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
Hae Kyung ImSection of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA. haky@uchicago.edu.ORCID 0000-0003-0333-5685
University of Chicago · USBroad Institute · USVanderbilt University · USStanford University · USUniversity of Michigan · USIcahn School of Medicine at Mount Sinai · USMax Planck Institute of Psychiatry · DENew York Genome Center · USTranslational Therapeutics (United States) · USUniversité Sorbonne Paris Nord · FRUniversity of Oxford · GBVanderbilt University Medical Center · US
Funding
Pilot and Feasibility ProgramP30DK020595 · NIDDK · UNIVERSITY OF CHICAGO · PI RONALD N COHEN · 2013 to 2026
$20.9MRe-Engineering Translational Research at the University of ChicagoUL1TR000430 · NCATS · UNIVERSITY OF CHICAGO · PI SOLWAY, JULIAN · 2012 to 2016
$20.2MTRAINING PROGRAM IN MOLECULAR AND CELLULAR CARDIOLOGYT32HL007824 · NHLBI · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI GELB, BRUCE D · 1995 to 2022
$8.6MA portal and integrative collaborative analysis platform for GTExU41HG009494 · NHGRI · BROAD INSTITUTE, INC. · PI ARDLIE, KRISTIN, GETZ, GAD A · 2017 to 2021
$5.2MUncovering novel biological processes and pathogenic mechanisms for glaucomaR01EY031424 · NEI · MASSACHUSETTS EYE AND EAR INFIRMARY · PI Ayellet Vered Segre · 2020 to 2026
$4.5MTowards an integrated map of causal connections for common, complex diseasesR35GM124836 · NIGMS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Ron Do · 2017 to 2026
$3.9MEpigenetic fine-mapping of cardiometabolic disease loci in the human liverR01HL133218 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI BROWN, CHRISTOPHER DAVID, ENGELHARDT, BARBARA · 2017 to 2020
$3.1MIntegrated target discovery in Alzheimer's diseaseRF1AG055477 · NIA · UNIVERSITY OF PENNSYLVANIA · PI BROWN, CHRISTOPHER DAVID · 2017 to 2017
$2.9MResolving Methodological Challenges in Genomics Research: Causality, Risk Prediction, and Reproducibility: Administrative SupplementR35GM138121 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Xiaoquan Wen · 2020 to 2026
$2.4MMethods for high-resolution analysis of genetic effects on gene expressionR01MH101814 · NIMH · UNIVERSITY OF GENEVA · PI BUSTAMANTE, CARLOS DANIEL, DERMITZAKIS, EMMANOUIL · 2013 to 2016
$2.3MFunctional Genomics: A Phenome-wide SurveyR35HG010718 · NHGRI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI GAMAZON, ERIC R · 2019 to 2023
$2.2MIdentification and validation of cell specific eQTLs by Bayesian modelingR01MH101822 · NIMH · UNIVERSITY OF PENNSYLVANIA · PI BROWN, CHRISTOPHER DAVID, ENGELHARDT, BARBARA · 2013 to 2016
$1.9MNational Institute of Diabetes and Digestive and Kidney Diseases (US) P30DK20595National Institute of Health R01MH107666NCATS NIH HHS UL1 TR000430NEI NIH HHS R01 EY031424NHGRI NIH HHS R01 HG011138NHGRI NIH HHS R35 HG010718NHGRI NIH HHS U01 HG007593NHGRI NIH HHS U01 HG007598NHGRI NIH HHS U41 HG009494NHLBI NIH HHS HHSN268201000029CNHLBI NIH HHS R01 HL133218NHLBI NIH HHS R01 HL133559NHLBI NIH HHS R01 HL139865NHLBI NIH HHS T32 HL007824NIA NIH HHS RF1 AG055477NIDDK NIH HHS P30 DK020595NIGMS NIH HHS R35 GM124836NIGMS NIH HHS R35 GM138121NIMH NIH HHS R01 MH101814NIMH NIH HHS R01 MH101822NIMH NIH HHS R01 MH107666
Abstract
The resources generated by the GTEx consortium offer unprecedented opportunities to advance our understanding of the biology of human diseases. Here, we present an in-depth examination of the phenotypic consequences of transcriptome regulation and a blueprint for the functional interpretation of genome-wide association study-discovered loci. Across a broad set of complex traits and diseases, we demonstrate widespread dose-dependent effects of RNA expression and splicing. We develop a data-driven framework to benchmark methods that prioritize causal genes and find no single approach outperforms the combination of multiple approaches. Using colocalization and association approaches that take into account the observed allelic heterogeneity of gene expression, we propose potential target genes for 47% (2519 out of 5385) of the GWAS loci examined.
Indexed as
Gene ExpressionGenotypeGenesGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansMultifactorial InheritanceTranscriptome
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