ArticleScience advances2021
A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation.
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Article in Science advances, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
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45citing papers in PubMed, 1 pooled it
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Who cites it
45 citing papers in PubMed, 1 synthesis or guideline pooled it, 72 citations in OpenAlex.
- Advancement in Human Face Prediction Using DNA.Genes · 2023Pooled it
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- Insights into the genetic basis of bilateral head asymmetry in a scale-eating cichlid fish.Science advances · 2025Article
- Forensic skeletal and molecular anthropology face to face: Combining expertise for identification of human remains.Annals of the New York Academy of Sciences · 2025Review
- Combined genome-wide association study of facial traits in Europeans increases explained variance and improves prediction.Nature communications · 2025Article
- 3D facial imaging: a novel approach for metabolic abnormalities risk profiling.Science China. Life sciences · 2025Article
- Exploring the association between SNPs and facial morphology in a Spanish population.Scientific reports · 2025Article
- Enhanced insights into the genetic architecture of 3D cranial vault shape using pleiotropy-informed GWAS.Communications biology · 2025Article
- Optimized phenotyping of complex morphological traits: enhancing discovery of common and rare genetic variants.Briefings in bioinformatics · 2025Article
- Human dispersal into East Eurasia: ancient genome insights and the need for research on physiological adaptations.Journal of physiological anthropology · 2025Review
- Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk.bioRxiv : the preprint server for biology · 2025Article
- Loss ofJBMR plus · 2025Article
- Archaic hominin admixture and its consequences for modern humans.Current opinion in genetics & development · 2025Review
- PITX2 expression and Neanderthal introgression in HS3ST3A1 contribute to variation in tooth dimensions in modern humans.Current biology : CB · 2025Article
- Mapping genes for human face shape: Exploration of univariate phenotyping strategies.PLoS computational biology · 2024Article
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Authors and funding
54 authors at 20 institutions in 14 countries.
Betty BonfanteAix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France.ORCID 0000-0001-6226-080X
Pierre FauxAix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France.ORCID 0000-0003-4486-6327
Nicolas NavarroBiogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France.ORCID 0000-0001-5694-4201
Javier Mendoza-RevillaLaboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú.
Morgane DubiedBiogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France.ORCID 0000-0002-9304-2714
Charlotte MontillotINSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France.
Emma WentworthDepartment of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06030, USA.
Lauriane PoloniBiogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France.
Ceferino Varón-GonzálezInstitut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, UA, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris 75005, France.ORCID 0000-0002-4577-4187
Philip JonesDepartment of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK.
Ziyi XiongDepartment of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands.
Macarena Fuentes-GuajardoDepartamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile.
Sagnik PalmalAix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France.
Juan Camilo Chacón-DuqueDivision of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK.
Malena HurtadoLaboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú.
Valeria VillegasLaboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú.
Vanessa GranjaLaboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú.
Claudia JaramilloGENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia.
William AriasGENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia.
Rodrigo BarqueraMolecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico.ORCID 0000-0003-0518-4518
Paola Everardo-MartínezMolecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico.
Mirsha Sánchez-QuintoForensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), Mexico City 06320, Mexico.
Jorge Gómez-ValdésMolecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico.
Hugo Villamil-RamírezUnidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico.
Caio C Silva de CerqueiraScientific Police of São Paulo State, Ourinhos-SP 19900-109, Brazil.
Tábita HünemeierDepartamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil.
Virginia RamalloDepartamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil.
Fan LiuDepartment of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands.ORCID 0000-0001-9241-8161
Seth M WeinbergDepartment of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA.ORCID 0000-0001-9467-4556
John R ShafferDepartment of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA.
Evie StergiakouliMedical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS1 2LY, UK.
Laurence J HoweMedical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS1 2LY, UK.
Pirro G HysiDepartment of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK.ORCID 0000-0001-5752-2510
Timothy D SpectorDepartment of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK.ORCID 0000-0002-9795-0365
Rolando Gonzalez-JoséInstituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina.
Lavinia Schüler-FacciniDepartamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil.
Maria-Cátira BortoliniDepartamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil.
Victor Acuña-AlonzoMolecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico.
Samuel Canizales-QuinterosUnidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico.
Carla GalloLaboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú.
Giovanni PolettiLaboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú.
Gabriel BedoyaGENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia.
Francisco RothhammerInstituto de Alta Investigación, Universidad de Tarapacá, Arica, Arica 1000000, Chile.
Christel Thauvin-RobinetINSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France.
Laurence FaivreINSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France.
Caroline CostedoatAix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France.
David BaldingDepartment of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK.
Timothy CoxDepartment of Oral and Craniofacial Sciences, School of Dentistry and Department of Pediatrics, School of Medicine, University of Missouri, Kansas City, MO 64108, USA.
Manfred KayserDepartment of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands.
Laurence DuplombINSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France.
Binnaz YalcinINSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France.ORCID 0000-0002-1924-6807
Justin CotneyDepartment of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06030, USA.
Kaustubh AdhikariSchool of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK. andresruiz@fudan.edu.cn kaustubh.adhikari@open.ac.uk.ORCID 0000-0001-5825-4191
Andrés Ruiz-LinaresAix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France. andresruiz@fudan.edu.cn kaustubh.adhikari@open.ac.uk.ORCID 0000-0001-8372-1011
Centre National de la Recherche Scientifique · FRInserm · FRUniversidad Peruana Cayetano Heredia · PELaboratory of Molecular Genetics · PLUniversidad de Antioquia · COUniversidade Federal do Rio Grande do Sul · BRErasmus MC · NLKing's College London · GBNational Institute of Genomic Medicine · MXUConn Health · USUniversity of Pittsburgh · USUniversity of Tarapacá · CLBeijing Institute of Genomics · CNBristol City Council · GBCentro Científico Tecnológico Patagónico · ARFederal Police of Brazil · BRInstitut Pasteur · FRNatural History Museum · GBThe Open University · GBThe University of Melbourne · AU
Funding
Extending the Phenotype of Nonsyndromic Orofacial CleftsR01DE016148 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI MARAZITA, MARY L., WEINBERG, SETH M · 2004 to 2018
$19.7MThe Genetic Architecture of Human Facial MorphologyR01DE027023 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI CLAES, PETER, SHAFFER, JOHN R · 2017 to 2024
$5.2MSkeletal, Craniofacial and Oral Biology Training GrantT90DE021989 · NIDCR · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI MINA, MINA · 2011 to 2022
$4.5MUnraveling mechanisms of genome regulation to understand and improvehuman healthR35GM119465 · NIGMS · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI COTNEY, JUSTIN LEE · 2016 to 2025
$3.9M3D Analysis of Normal Facial Variation: Data Repository and Genetics (Research)U01DE020078 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI MARAZITA, MARY L., WEINBERG, SETH M · 2009 to 2013
$2.0MSkeletal, Craniofacial and Oral Biology Training GrantT90DE033006 · NIDCR · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI FRANK C NICHOLS · 2023 to 2026
$2.0MFunctional characterization of craniofacial enhancers at single cell and single base pair resolutionR01DE028945 · NIDCR · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI COTNEY, JUSTIN LEE · 2019 to 2023
$1.9MIdentification of human orofacial enhancers and their role in orofacial cleftsR00DE024194 · NIDCR · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI COTNEY, JUSTIN LEE · 2015 to 2017
$732kNIDCR NIH HHS R00 DE024194NIDCR NIH HHS R01 DE016148NIDCR NIH HHS R01 DE027023NIDCR NIH HHS T90 DE021989NIDCR NIH HHS T90 DE033006NIDCR NIH HHS U01 DE020078
Abstract
To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.
Indexed as
FacePolymorphism, Single NucleotideVesicular Transport ProteinsAnimalsGenome-Wide Association StudyGenotypeHispanic or LatinoHumansMicePhenotypeVesicular Transport ProteinsVPS13B protein, human
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