ArticleCell2021
Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease.
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Article in Cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers, 2 of them syntheses that pooled it.
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124citing papers in PubMed, 2 pooled it
14.7field-weighted citation impact, top 1% of its field
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Who cites it
124 citing papers in PubMed, 2 syntheses or guidelines pooled it, 206 citations in OpenAlex.
- Multi-ancestry GWAS meta-analyses of lung cancer reveal susceptibility loci and elucidate smoking-independent genetic risk.Nature communications · 2024Pooled it
- Advancements and trends in exosome research in lung cancer from a bibliometric analysis (2004-2023).Frontiers in oncology · 2024Pooled it
- Genotype-driven variations in lncRNA expression underlie predisposition to high-grade serous ovarian cancer.Journal of advanced research · 2026Article
- Genome-wide identification of long non-coding RNAs in pigs and their roles in muscle development.Animal bioscience · 2026Article
- SNHG family lncRNAs promote Ewing sarcoma cell fitness through intronic snoRNA-guided rRNA modifications.NAR cancer · 2026Article
- Differential expression of long non-coding RNAs can effectively distinguish monozygotic twins.International journal of legal medicine · 2026Article
- Mapping genetic regulation of gene expression to cellular contexts identifies long non-coding RNAs associated with brain disorders.Nature communications · 2026Article
- AI-Guided Long Non-Coding RNA Target Discovery for Precision Medicine: Integrating GWAS, Multi-Omics, Experimental Validation, and RNA Therapeutics.Biomedicines · 2026Review
- Vein graft failure: Pathophysiology, detection, prevention and emerging therapeutic strategies.Pharmacological reviews · 2026Review
- Population-scale multi-omics analysis reveals diverse phenotypic impacts of lncRNAs in rice.Cell research · 2026Article
- The long non-coding RNA landscape of endurance exercise training.Molecular metabolism · 2026Article
- Multivariable genome-wide analysis elucidates the shared genetic architecture, immunosenescence features, and gut-origin therapeutic targets of ulcerative colitis-associated multisystem inflammation.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026Article
- Non-coding RNAs in lipid metabolism and their roles in atherosclerosis.Nature reviews. Cardiology · 2026Review
- A novel deep learning-driven framework for improving lncRNA comprehensive annotation with LncADeep 2.0.Bioinformatics (Oxford, England) · 2026Article
- Long non-coding RNA C20orf56 as a predictor of response to neoadjuvant CCRT and survival rates of rectal cancers.Histology and histopathology · 2026Article
- Leveraging extracellular vesicle biology for novel tests and therapeutics for kidney fibrosis.Clinical and translational medicine · 2026Review
- Multi-layered gene regulation by long non-coding RNAs: from chromatin to genome architecture.BMB reports · 2026Review
- Genetic and non-genetic factors distinctly shape the variation of the immune response in cattle.Nature communications · 2026Article
- LncRNA Wee1-AS coordinates oxidative fatty acid metabolism through the activation of mitochondrial CDK1/CYCLIN B1.Signal transduction and targeted therapy · 2026Article
- Genetic control of non-coding RNAs in the human brain and their implications for complex traits.American journal of human genetics · 2026Article
64 more citing papers are in PubMed but not listed here.
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Authors and funding
28 authors at 15 institutions in 3 countries.
Olivia M de GoedeDepartment of Genetics, Stanford University, Stanford, CA 94305, USA. Electronic address: odegoede@stanford.edu.
Daniel C NachunDepartment of Pathology, Stanford University, Stanford, CA 94305, USA.
Nicole M FerraroBiomedical Informatics Training Program, Stanford University, Stanford, CA 94305, USA.
Michael J GloudemansBiomedical Informatics Training Program, Stanford University, Stanford, CA 94305, USA.
Abhiram S RaoDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Craig SmailBiomedical Informatics Training Program, Stanford University, Stanford, CA 94305, USA; Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO 64108, USA.
Tiffany Y EulalioBiomedical Informatics Training Program, Stanford University, Stanford, CA 94305, USA.
François AguetThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Bernard NgDepartment of Statistics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, BC V5Z 4H4, Canada.
Jishu XuRush Alzheimer's Disease Center, Rush University, Chicago, Illinois 60612, USA.
Alvaro N BarbeiraSection of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
Stephane E CastelNew York Genome Center, New York, NY 10013, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA.
Sarah Kim-HellmuthNew York Genome Center, New York, NY 10013, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich 80337, Germany.
YoSon ParkDepartment of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
Alexandra J ScottMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA.
Benjamin J StroberDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
GTEx Consortium
Christopher D BrownDepartment of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
Xiaoquan WenDepartment of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.
Ira M HallDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
Alexis BattleDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
Tuuli LappalainenNew York Genome Center, New York, NY 10013, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA.
Hae Kyung ImSection of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
Kristin G ArdlieThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Sara MostafaviPaul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA.
Thomas QuertermousDivision of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA.
Karla KirkegaardDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
Stephen B MontgomeryDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA. Electronic address: smontgom@stanford.edu.
Stanford University · USBroad Institute · USCardiovascular Institute of the South · USNew York Genome Center · USUniversity of Pennsylvania · USJohns Hopkins University · USTranslational Therapeutics (United States) · USUniversity of Chicago · USUniversity of Michigan · USUniversity of Washington · USYale University · USJames S. McDonnell Foundation · USMercy Research · USRush University · USUniversity of British Columbia · CA
Funding
New York Center for Collaborative Research In Common Disease Genomics: Genome Aggregation and Joint Variant Calling for CCDG Freeze2UM1HG008901 · NHGRI · NEW YORK GENOME CENTER · PI MANIATIS, THOMAS P, WIGLER, MICHAEL H · 2016 to 2020
$56.6MPOSTDOCTORAL TRAINING IN MEDICAL INFORMATION SCIENCEST15LM007033 · NLM · STANFORD UNIVERSITY · PI SYLVIA KATINA PLEVRITIS · 1985 to 2026
$25.5MPilot and Feasibility ProgramP30DK020595 · NIDDK · UNIVERSITY OF CHICAGO · PI Raghavendra G Mirmira · 2013 to 2026
$20.9MBIOMEDICAL ENGINEERING TRAINING PROGRAMT32GM007057 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI KANOLD, PATRICK O, KARCHIN, RACHEL · 1985 to 2023
$10.4MCausal variant association mechanisms in TCF21 binding coronary disease lociR01HL134817 · NHLBI · STANFORD UNIVERSITY · PI THOMAS QUERTERMOUS · 2017 to 2026
$6.2MMechanism of the Coronary Heart Disease Association at Chromosome 6q23.2R01HL109512 · NHLBI · STANFORD UNIVERSITY · PI QUERTERMOUS, THOMAS · 2011 to 2019
$6.1MOptimizing imputation for diverse populations in a distributed frameworkU01HG009080 · NHGRI · STANFORD UNIVERSITY · PI KENNY, EIMEAR ELIZABETH · 2016 to 2020
$5.2MA portal and integrative collaborative analysis platform for GTExU41HG009494 · NHGRI · BROAD INSTITUTE, INC. · PI ARDLIE, KRISTIN · 2017 to 2021
$5.2MStatistical models for fine-mapping and interpretation of schizophrenia-associated lociR01MH106842 · NIMH · NEW YORK GENOME CENTER · PI BUSSEMAKER, HARMEN J, LAPPALAINEN, TUULI · 2015 to 2024
$5.0MThe SMAD3 signaling network in coronary artery disease riskR01HL139478 · NHLBI · STANFORD UNIVERSITY · PI THOMAS QUERTERMOUS · 2018 to 2026
$3.7MMapping Molecular and Phenotypic Interactions in Alzheimers DiseaseR01AG066490 · NIA · STANFORD UNIVERSITY · PI MONTGOMERY, STEPHEN · 2020 to 2024
$3.6MPredoctoral Training of NeuroscientistsT32NS105604 · NINDS · UNIVERSITY OF MINNESOTA · PI A DAVID REDISH · 2018 to 2026
$3.5MNHGRI NIH HHS K99 HG009916NHGRI NIH HHS R01 HG008150NHGRI NIH HHS R01 HG010067NHGRI NIH HHS U01 HG009080NHGRI NIH HHS U01 HG009431NHGRI NIH HHS U41 HG009494NHGRI NIH HHS UM1 HG008901NHLBI NIH HHS HHSN268201000029CNHLBI NIH HHS R01 HL109512NHLBI NIH HHS R01 HL134817NHLBI NIH HHS R01 HL135313NHLBI NIH HHS R01 HL139478NHLBI NIH HHS R01 HL142015NHLBI NIH HHS R01 HL142028NHLBI NIH HHS R33 HL120757NIA NIH HHS R01 AG066490NIDDK NIH HHS P30 DK020595NIGMS NIH HHS R01 GM122924NIGMS NIH HHS R01 GM124486NIGMS NIH HHS T32 GM007057NIMH NIH HHS R01 MH101814NIMH NIH HHS R01 MH101822NIMH NIH HHS R01 MH106842NIMH NIH HHS R01 MH107666NIMH NIH HHS R01 MH109905NIMH NIH HHS R01 MH125244NINDS NIH HHS T32 NS105604NLM NIH HHS T15 LM007033
Abstract
Long non-coding RNA (lncRNA) genes have well-established and important impacts on molecular and cellular functions. However, among the thousands of lncRNA genes, it is still a major challenge to identify the subset with disease or trait relevance. To systematically characterize these lncRNA genes, we used Genotype Tissue Expression (GTEx) project v8 genetic and multi-tissue transcriptomic data to profile the expression, genetic regulation, cellular contexts, and trait associations of 14,100 lncRNA genes across 49 tissues for 101 distinct complex genetic traits. Using these approaches, we identified 1,432 lncRNA gene-trait associations, 800 of which were not explained by stronger effects of neighboring protein-coding genes. This included associations between lncRNA quantitative trait loci and inflammatory bowel disease, type 1 and type 2 diabetes, and coronary artery disease, as well as rare variant associations to body mass index.
Indexed as
TranscriptomeCoronary Artery DiseaseDiabetes Mellitus, Type 1Diabetes Mellitus, Type 2DiseaseGene Expression ProfilingGenetic VariationHumansInflammatory Bowel DiseasesMultifactorial InheritanceOrgan SpecificityPopulationQuantitative Trait LociRNA, Long NoncodingRNA, Long Noncodingco-expressioncolocalizationcomplex traitdiseaseeQTLexpression quantitative trait lociGTExlncRNAlong non-coding RNA
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