ArticleAmerican journal of human genetics2016
REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.
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Article in American journal of human genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT07396285 (UCSF Center for Genome Surgery Biobank and Registry), which is not on this map. Cited by 1,834 papers, 2 of them syntheses that pooled it.
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1,834citing papers in PubMed, 2 pooled it
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
UCSF Center for Genome Surgery Biobank and Registry
Who cites it
1,834 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Predicting Oncogenic Mutants of Epidermal Growth Factor Receptor in Lung Cancer by Molecular Dynamics Simulation with Machine Learning.ACS omega · 2026Article
- Interpreting human genetic variation at atomic resolution.Nature genetics · 2026Review
- TNFα-dependent modulation of WT1-MMP9 regulatory axis links developmental and inflammatory pathways in glaucoma.iScience · 2026Article
1,774 more citing papers are in PubMed but not listed here.
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Authors and funding
41 authors.
Nilah M IoannidisDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA.
Joseph H RothsteinDepartment of Health Research and Policy, Stanford University, Stanford, CA 94305, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Vikas PejaverDepartment of Computer Science and Informatics, Indiana University, Bloomington, IN 47405, USA.
Sumit MiddhaDepartment of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Shannon K McDonnellDepartment of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.
Saurabh BahetiDepartment of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.
Anthony MusolfComputational and Statistical Genomics Branch, National Human Genome Research Institute, Baltimore, MD 21224, USA.
Qing LiComputational and Statistical Genomics Branch, National Human Genome Research Institute, Baltimore, MD 21224, USA.
Emily HolzingerComputational and Statistical Genomics Branch, National Human Genome Research Institute, Baltimore, MD 21224, USA.
Danielle KaryadiCancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA.
Lisa A Cannon-AlbrightDepartment of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84108, USA.
Craig C TeerlinkDepartment of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84108, USA.
Janet L StanfordPublic Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
William B IsaacsBrady Urological Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
Jianfeng XuNorthShore University HealthSystem Research Institute, Evanston, IL 60201, USA.
Kathleen A CooneyDepartment of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84108, USA; Departments of Internal Medicine and Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
Ethan M LangeDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Johanna SchleutkerDepartment of Medical Biochemistry and Genetics, University of Turku, Turku 20014, Finland; Department of Medical Genetics, Tyks Microbiology and Genetics, Turku University Hospital, Turku 20520, Finland.
John D CarptenIntegrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA.
Isaac J PowellDepartment of Urology, Wayne State University, Detroit, MI 48201, USA.
Olivier CussenotCentre de Recherche sur les Pathologies Prostatiques et Urologiques, Universite Paris, Paris, 75013, France.
Geraldine Cancel-TassinCentre de Recherche sur les Pathologies Prostatiques et Urologiques, Universite Paris, Paris, 75013, France.
Graham G GilesCancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3004, Australia; Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC 3010, Australia.
Robert J MacInnisCancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3004, Australia; Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC 3010, Australia.
Christiane MaierInstitute of Human Genetics, University Hospital of Ulm, Ulm 89075, Germany; Department of Urology, University Hospital of Ulm, Ulm 89075, Germany.
Chih-Lin HsiehDepartment of Urology, University of Southern California, Los Angeles, CA 90033, USA.
Fredrik WiklundDepartment of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 171 77, Sweden.
William J CatalonaDepartment of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
William D FoulkesDepartments of Oncology and Human Genetics, Montreal General Hospital, Montreal, QC H3G 1A4, Canada.
Diptasri MandalDepartment of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA.
Rosalind A EelesDivision of Genetics and Epidemiology, Institute of Cancer Research, London SM2 5NG, UK.
Zsofia Kote-JaraiDivision of Genetics and Epidemiology, Institute of Cancer Research, London SM2 5NG, UK.
Carlos D BustamanteDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
Daniel J SchaidDepartment of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA.
Trevor HastieDepartment of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Statistics, Stanford University, Stanford, CA 94305, USA.
Elaine A OstranderCancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA.
Joan E Bailey-WilsonComputational and Statistical Genomics Branch, National Human Genome Research Institute, Baltimore, MD 21224, USA.
Predrag RadivojacDepartment of Computer Science and Informatics, Indiana University, Bloomington, IN 47405, USA.
Stephen N ThibodeauDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA.
Alice S WhittemoreDepartment of Health Research and Policy, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
Weiva SiehDepartment of Health Research and Policy, Stanford University, Stanford, CA 94305, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: weiva.sieh@mssm.edu.
Funding
Tumor Environment and Metastasis (TEAM) Research ProgramP30CA060553 · NCI · NORTHWESTERN UNIVERSITY AT CHICAGO · PI Daniela E Matei · 1993 to 2026
$153.9MProstate Cancer Susceptibility: The ICPCG StudyU01CA089600 · NCI · MAYO CLINIC ROCHESTER · PI THIBODEAU, STEPHEN NORMAN · 2002 to 2016
$27.3MTargeting FOXA1-downstream pathways: a novel therapeutic strategy for castration-resistant prostate cancerP50CA180995 · NCI · NORTHWESTERN UNIVERSITY AT CHICAGO · PI ABDULKADIR, SARKI A., HUSSAIN, MAHA H · 2015 to 2025
$19.9MFinding Genes for Human Prostate CancerZIAHG200325 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI OSTRANDER, ELAINE · 2009 to 2021
$17.7MStatistical Methods for Genetic EpidemiologyR01CA094069 · NCI · STANFORD UNIVERSITY · PI WHITTEMORE, ALICE · 2002 to 2016
$7.7MDevelopment of statistical genetics methodologyZIAHG000153 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI BAILEY-WILSON, JOAN ELLEN · 2009 to 2022
$5.0MInformatic Profiling of Clinically Relevant MutationR01LM009722 · NLM · UNIVERSITY OF WASHINGTON · PI MOONEY, SEAN DAVID · 2007 to 2014
$3.5MA computational framework for predicting the impact of mutations in autismR01MH105524 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IAKOUCHEVA, LILIA M, RADIVOJAC, PREDRAG · 2014 to 2016
$1.4MGenetic Epidemiology of Ovarian and Prostate CancerK07CA143047 · NCI · STANFORD UNIVERSITY · PI SIEH, WEIVA · 2010 to 2014
$867kInferring the effects of genetic variants on gene expression and splicingF32HG008330 · NHGRI · STANFORD UNIVERSITY · PI IOANNIDIS, NILAH MONNIER · 2015 to 2017
$155kNCI NIH HHS K07 CA143047NCI NIH HHS P30 CA060553NCI NIH HHS P50 CA180995NCI NIH HHS R01 CA094069NCI NIH HHS U01 CA089600NHGRI NIH HHS F32 HG008330NIMH NIH HHS R01 MH105524NLM NIH HHS R01 LM009722
Abstract
The vast majority of coding variants are rare, and assessment of the contribution of rare variants to complex traits is hampered by low statistical power and limited functional data. Improved methods for predicting the pathogenicity of rare coding variants are needed to facilitate the discovery of disease variants from exome sequencing studies. We developed REVEL (rare exome variant ensemble learner), an ensemble method for predicting the pathogenicity of missense variants on the basis of individual tools: MutPred, FATHMM, VEST, PolyPhen, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP, SiPhy, phyloP, and phastCons. REVEL was trained with recently discovered pathogenic and rare neutral missense variants, excluding those previously used to train its constituent tools. When applied to two independent test sets, REVEL had the best overall performance (p < 10
Indexed as
SoftwareArea Under CurveDiseaseDNA Mutational AnalysisExomeGene FrequencyHumansMutation, MissenseROC Curve
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NCT07396285ClinicalTrials.gov
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.