1
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Faux P, Ding L, Ramirez-Aristeguieta LM, Chacón-Duque JC, Comini M, Mendoza-Revilla J, Fuentes-Guajardo M, Jaramillo C, Arias W, Hurtado M, Villegas V, Granja V, Barquera R, Everardo-Martínez P, Quinto-Sánchez M, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hünemeier T, Ramallo V, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Poletti G, Gallo C, Rothhammer F, Rojas W, Schmid AB, Adhikari K, Bennett DL, Ruiz-Linares A. Neanderthal introgression in SCN9A impacts mechanical pain sensitivity. Commun Biol 2023; 6:958. [PMID: 37816865 PMCID: PMC10564861 DOI: 10.1038/s42003-023-05286-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/25/2023] [Indexed: 10/12/2023] Open
Abstract
The Nav1.7 voltage-gated sodium channel plays a key role in nociception. Three functional variants in the SCN9A gene (encoding M932L, V991L, and D1908G in Nav1.7), have recently been identified as stemming from Neanderthal introgression and to associate with pain symptomatology in UK BioBank data. In 1000 genomes data, these variants are absent in Europeans but common in Latin Americans. Analysing high-density genotype data from 7594 Latin Americans, we characterized Neanderthal introgression in SCN9A. We find that tracts of introgression occur on a Native American genomic background, have an average length of ~123 kb and overlap the M932L, V991L, and D1908G coding positions. Furthermore, we measured experimentally six pain thresholds in 1623 healthy Colombians. We found that Neanderthal ancestry in SCN9A is significantly associated with a lower mechanical pain threshold after sensitization with mustard oil and evidence of additivity of effects across Nav1.7 variants. Our findings support the reported association of Neanderthal Nav1.7 variants with clinical pain, define a specific sensory modality affected by archaic introgression in SCN9A and are consistent with independent effects of the Neanderthal variants on Nav1.7 function.
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Affiliation(s)
- Pierre Faux
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, 200438, Shanghai, China
- UMR ADES, Aix-Marseille Université, CNRS, EFS, 13005, Marseille, France
- UMR GenPhySE, INRAE, INP, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Li Ding
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, 200438, Shanghai, China
| | | | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, SE-1069, Stockholm, Sweden
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Maddalena Comini
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, OX3 9DU, UK
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015, Paris, France
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, 1000000, Arica, Chile
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, 5001000, Medellín, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, 5001000, Medellín, Colombia
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, 6600, Mexico, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), 07745, Jena, Germany
| | - Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, 6600, Mexico, Mexico
| | - Mirsha Quinto-Sánchez
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), 06320, Mexico City, Mexico
| | - Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, 6600, Mexico, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, 4510, Mexico City, Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, 90040-060, Porto Alegre, Brasil
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, U9129ACD, Puerto Madryn, Argentina
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, U9129ACD, Puerto Madryn, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, 90040-060, Porto Alegre, Brasil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, 90040-060, Porto Alegre, Brasil
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, 6600, Mexico, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, 4510, Mexico City, Mexico
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 31, Lima, Perú
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, 1000000, Arica, Chile
| | - Winston Rojas
- GENMOL (Genética Molecular), Universidad de Antioquia, 5001000, Medellín, Colombia
| | - Annina B Schmid
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, OX3 9DU, UK
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, UK.
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
| | - David L Bennett
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, OX3 9DU, UK.
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, 200438, Shanghai, China.
- UMR ADES, Aix-Marseille Université, CNRS, EFS, 13005, Marseille, France.
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
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2
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Li Q, Chen J, Faux P, Delgado ME, Bonfante B, Fuentes-Guajardo M, Mendoza-Revilla J, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Barquera R, Everardo-Martínez P, Sánchez-Quinto M, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hünemeier T, Ramallo V, Wu S, Du S, Giardina A, Paria SS, Khokan MR, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Rojas W, Rothhammer F, Navarro N, Wang S, Adhikari K, Ruiz-Linares A. Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape. Commun Biol 2023; 6:481. [PMID: 37156940 PMCID: PMC10167347 DOI: 10.1038/s42003-023-04838-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10-8) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.
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Affiliation(s)
- Qing Li
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
| | - Jieyi Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Pierre Faux
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France
| | - Miguel Eduardo Delgado
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, República Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Buenos Aires, República Argentina
| | - Betty Bonfante
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000000, Chile
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, 75015, France
| | - J Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, 07745, Germany
| | - Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
| | - Mirsha Sánchez-Quinto
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), Mexico City, 06320, Mexico
| | - Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90040-060, Brazil
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Sijie Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andrea Giardina
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Soumya Subhra Paria
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Mahfuzur Rahman Khokan
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90040-060, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90040-060, Brazil
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, 14050, Mexico, 6600, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Winston Rojas
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Arica, 1000000, Chile
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, Université de Bourgogne, Dijon, 21000, France
- EPHE, PSL University, Paris, 75014, France
| | - Sijia Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, MK7 6AA, United Kingdom.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, 200438, China.
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
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3
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Mendoza-Revilla J, Chacón-Duque JC, Fuentes-Guajardo M, Ormond L, Wang K, Hurtado M, Villegas V, Granja V, Acuña-Alonzo V, Jaramillo C, Arias W, Barquera R, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Badillo Rivera KM, Nieves-Colón MA, Gignoux CR, Wojcik GL, Moreno-Estrada A, Hünemeier T, Ramallo V, Schuler-Faccini L, Gonzalez-José R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Balding D, Fumagalli M, Adhikari K, Ruiz-Linares A, Hellenthal G. Disentangling Signatures of Selection Before and After European Colonization in Latin Americans. Mol Biol Evol 2022; 39:6565306. [PMID: 35460423 PMCID: PMC9034689 DOI: 10.1093/molbev/msac076] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.
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Affiliation(s)
- Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Louise Ormond
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom
| | - Ke Wang
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,National School of Anthropology and History, Mexico City, Mexico
| | | | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | | | - Maria A Nieves-Colón
- Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Christopher R Gignoux
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Genevieve L Wojcik
- Bloomberg School of Public Health, John Hopkins University, Baltimore, MD, USA
| | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Tábita Hünemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | | | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | | | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, Australia
| | - Matteo Fumagalli
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom.,Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China.,Aix-Marseille Université, CNRS, EFS, ADES, Marseille, France
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, United Kingdom
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4
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Bonfante B, Faux P, Navarro N, Mendoza-Revilla J, Dubied M, Montillot C, Wentworth E, Poloni L, Varón-González C, Jones P, Xiong Z, Fuentes-Guajardo M, Palmal S, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Barquera R, Everardo-Martínez P, Sánchez-Quinto M, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hünemeier T, Ramallo V, Liu F, Weinberg SM, Shaffer JR, Stergiakouli E, Howe LJ, Hysi PG, Spector TD, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Thauvin-Robinet C, Faivre L, Costedoat C, Balding D, Cox T, Kayser M, Duplomb L, Yalcin B, Cotney J, Adhikari K, Ruiz-Linares A. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation. Sci Adv 2021; 7:eabc6160. [PMID: 33547071 PMCID: PMC7864580 DOI: 10.1126/sciadv.abc6160] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/17/2020] [Indexed: 05/25/2023]
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.
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Affiliation(s)
- Betty Bonfante
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Pierre Faux
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
- EPHE, PSL University, Paris 75014, France
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris 75015, France
| | - Morgane Dubied
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
| | - Charlotte Montillot
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Emma Wentworth
- Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06030, USA
| | - Lauriane Poloni
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
- EPHE, PSL University, Paris 75014, France
| | - Ceferino Varón-González
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, UA, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris 75005, France
| | - Philip Jones
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Ziyi Xiong
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | - Sagnik Palmal
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Juan Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena 07745, Germany
| | - Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Mirsha Sánchez-Quinto
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), Mexico City 06320, Mexico
| | - Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100864, China
- University of Chinese Academy of Sciences, Beijing 100864, China
| | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - John R Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS1 2LY, UK
- School of Oral and Dental Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Arica 1000000, Chile
| | - Christel Thauvin-Robinet
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
- Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs" de l'Est, Centre de Génétique, FHU TRANSLAD, CHU Dijon, Dijon 21000, France
| | - Laurence Faivre
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
- Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs" de l'Est, Centre de Génétique, FHU TRANSLAD, CHU Dijon, Dijon 21000, France
| | | | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Timothy Cox
- Department of Oral and Craniofacial Sciences, School of Dentistry and Department of Pediatrics, School of Medicine, University of Missouri, Kansas City, MO 64108, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
| | - Laurence Duplomb
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Binnaz Yalcin
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06030, USA
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Andrés Ruiz-Linares
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China
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5
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Adhikari K, Mendoza-Revilla J, Sohail A, Fuentes-Guajardo M, Lampert J, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Acuña-Alonzo V, Jaramillo C, Arias W, Lozano RB, Everardo P, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hunemeier T, Ramallo V, Schuler-Faccini L, Salzano FM, Gonzalez-José R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Tobin DJ, Fumagalli M, Balding D, Ruiz-Linares A. A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia. Nat Commun 2019; 10:358. [PMID: 30664655 PMCID: PMC6341102 DOI: 10.1038/s41467-018-08147-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/20/2018] [Indexed: 12/17/2022] Open
Abstract
We report a genome-wide association scan in >6,000 Latin Americans for pigmentation of skin and eyes. We found eighteen signals of association at twelve genomic regions. These include one novel locus for skin pigmentation (in 10q26) and three novel loci for eye pigmentation (in 1q32, 20q13 and 22q12). We demonstrate the presence of multiple independent signals of association in the 11q14 and 15q13 regions (comprising the GRM5/TYR and HERC2/OCA2 genes, respectively) and several epistatic interactions among independently associated alleles. Strongest association with skin pigmentation at 19p13 was observed for an Y182H missense variant (common only in East Asians and Native Americans) in MFSD12, a gene recently associated with skin pigmentation in Africans. We show that the frequency of the derived allele at Y182H is significantly correlated with lower solar radiation intensity in East Asia and infer that MFSD12 was under selection in East Asians, probably after their split from Europeans. Pigmentation variation in humans is influenced by complex genetic architecture in different populations. Here, the authors perform a genome-wide association analysis involving > 6,000 Latin Americans for pigmentation of skin and eyes, and identify known and novel genetic associations.
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Affiliation(s)
- Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Anood Sohail
- Department of Genetics, Cambridge University, Cambridge, CB2 3EH, UK
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000000, Chile
| | - Jodie Lampert
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Juan Camilo Chacón-Duque
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,National Institute of Anthropology and History, Mexico City, 4510, Mexico
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Rodrigo Barquera Lozano
- National Institute of Anthropology and History, Mexico City, 4510, Mexico.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Paola Everardo
- National Institute of Anthropology and History, Mexico City, 4510, Mexico
| | - Jorge Gómez-Valdés
- National Institute of Anthropology and History, Mexico City, 4510, Mexico
| | - Hugo Villamil-Ramírez
- Unidad 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 Cerqueira
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Tábita Hunemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil.,Instituto Patagonico de Ciencias Sociales y Humanas, Centro Nacional Patagonico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Rolando Gonzalez-José
- Instituto Patagonico de Ciencias Sociales y Humanas, Centro Nacional Patagonico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapaca, Arica, 1000000, Chile.,Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8320000, Chile
| | - Desmond J Tobin
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, BD7 1DP, West Yorkshire, UK.,The Charles Institute of Dermatology, University College Dublin, Dublin, D4, Ireland
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park campus, Imperial College London, Ascot, SL5 7PY, UK
| | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China. .,Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France.
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6
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Chacón-Duque JC, Adhikari K, Fuentes-Guajardo M, Mendoza-Revilla J, Acuña-Alonzo V, Barquera R, Quinto-Sánchez M, Gómez-Valdés J, Everardo Martínez P, Villamil-Ramírez H, Hünemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Villena M, Vásquez R, Llop E, Sandoval JR, Salazar-Granara AA, Parolin ML, Sandoval K, Peñaloza-Espinosa RI, Rangel-Villalobos H, Winkler CA, Klitz W, Bravi C, Molina J, Corach D, Barrantes R, Gomes V, Resende C, Gusmão L, Amorim A, Xue Y, Dugoujon JM, Moral P, González-José R, Schuler-Faccini L, Salzano FM, Bortolini MC, Canizales-Quinteros S, Poletti G, Gallo C, Bedoya G, Rothhammer F, Balding D, Hellenthal G, Ruiz-Linares A. Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance. Nat Commun 2018; 9:5388. [PMID: 30568240 PMCID: PMC6300600 DOI: 10.1038/s41467-018-07748-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample.
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Affiliation(s)
- Juan-Camilo Chacón-Duque
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000009, Chile
| | - Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Mirsha Quinto-Sánchez
- Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Jorge Gómez-Valdés
- Posgrado en Antropología Física, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
| | - Paola Everardo Martínez
- Posgrado en Antropología, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, 04510, Mexico
| | - Tábita Hünemeier
- Departamento de Genética e Biología Evolutiva, Instituto de Biociências, Universidade de São Paulo, Sao Paulo, 05508-090, Brazil
| | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Caio C Silva de Cerqueira
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Mercedes Villena
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Mayor de San Andrés (UMSA), La Paz, 2070, Bolivia
| | - René Vásquez
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Autónoma Tomás Frías, Potosí, 53820, Bolivia
| | - Elena Llop
- Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 1027, Chile
| | - José R Sandoval
- Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, 12, Peru
| | | | - Maria-Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
| | - Karla Sandoval
- National Laboratory of Genomics and Biodiversity (LANGEBIO), CINVESTAV, Irapuato, 36821, Mexico
| | - Rosenda I Peñaloza-Espinosa
- Department of Biological Systems, Division of Biological and Health Sciences, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, 04960, Mexico
| | - Hector Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara, Ocotlán, 1115, Mexico
| | - Cheryl A Winkler
- Basic Research Laboratory, National Cancer Institute, Frederick National Laboratory, Frederick, MD, 21702, USA
| | - William Klitz
- Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Claudio Bravi
- Instituto Multidisciplinario de Biología Celular, CONICET, La Plata, B1906APO, Argentina
| | - Julio Molina
- Centro de Investigaciones Biomédicas de Guatemala, Ciudad de Guatemala, 01011, Guatemala
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas and CONICET, Universidad de Buenos Aires, Buenos Aires, C1113AAD, Argentina
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Verónica Gomes
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
| | - Carlos Resende
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
| | - Leonor Gusmão
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
- DNA Diagnostic Laboratory (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, 23968-000, Brazil
| | - Antonio Amorim
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, 4169-007, Portugal
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jean-Michel Dugoujon
- Centre National de la Recherche Scientifique, Université Toulouse 3 Paul Sabatier, Toulouse, 31330, France
| | - Pedro Moral
- Departamento de Biología Evolutiva, Ecología y Ciencias Ambientales, Universitat de Barcelona, Barcelona, 08007, Spain
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, 04510, Mexico
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Gabriel Bedoya
- Genética Molecular (GENMOL), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Francisco Rothhammer
- Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 1027, Chile
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, 1000009, Chile
| | - David Balding
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200433, China.
- Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, 13007, France.
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7
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Adhikari K, Fuentes-Guajardo M, Quinto-Sánchez M, Mendoza-Revilla J, Camilo Chacón-Duque J, Acuña-Alonzo V, Jaramillo C, Arias W, Lozano RB, Pérez GM, Gómez-Valdés J, Villamil-Ramírez H, Hunemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Gallo C, Poletti G, Schuler-Faccini L, Salzano FM, Bortolini MC, Canizales-Quinteros S, Cheeseman M, Rosique J, Bedoya G, Rothhammer F, Headon D, González-José R, Balding D, Ruiz-Linares A. A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation. Nat Commun 2016; 7:11616. [PMID: 27193062 PMCID: PMC4874031 DOI: 10.1038/ncomms11616] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 04/14/2016] [Indexed: 12/28/2022] Open
Abstract
We report a genome-wide association scan for facial features in ∼6,000 Latin Americans. We evaluated 14 traits on an ordinal scale and found significant association (P values<5 × 10−8) at single-nucleotide polymorphisms (SNPs) in four genomic regions for three nose-related traits: columella inclination (4q31), nose bridge breadth (6p21) and nose wing breadth (7p13 and 20p11). In a subsample of ∼3,000 individuals we obtained quantitative traits related to 9 of the ordinal phenotypes and, also, a measure of nasion position. Quantitative analyses confirmed the ordinal-based associations, identified SNPs in 2q12 associated to chin protrusion, and replicated the reported association of nasion position with SNPs in PAX3. Strongest association in 2q12, 4q31, 6p21 and 7p13 was observed for SNPs in the EDAR, DCHS2, RUNX2 and GLI3 genes, respectively. Associated SNPs in 20p11 extend to PAX1. Consistent with the effect of EDAR on chin protrusion, we documented alterations of mandible length in mice with modified Edar funtion. Humans show great diversity in facial appearance and this variation is highly heritable. Here, Andres Ruiz-Linares and colleagues examined facial features in admixed Latin Americans and identify genome-wide associations for 14 facial traits, including four gene loci (RUNX2, GLI3, DCHS2 and PAX1) influencing nose morphology.
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Affiliation(s)
- Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK.,Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000009, Chile
| | - Mirsha Quinto-Sánchez
- Centro Nacional Patagónico, CONICET, Unidad de Diversidad, Sistematica y Evolucion, Puerto Madryn U912OACD, Argentina
| | - Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK.,Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Juan Camilo Chacón-Duque
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK.,Laboratorio de Genética Molecular, Escuela Nacional de Antropologia e Historia, México City 14030, México
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera Lozano
- Laboratorio de Genética Molecular, Escuela Nacional de Antropologia e Historia, México City 14030, México.,Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México City 4510, México
| | - Gastón Macín Pérez
- Laboratorio de Genética Molecular, Escuela Nacional de Antropologia e Historia, México City 14030, México.,Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México City 4510, México
| | - Jorge Gómez-Valdés
- Departamento de Anatomía, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), México City 04510, México
| | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México City 4510, México
| | - Tábita Hunemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Virginia Ramallo
- Centro Nacional Patagónico, CONICET, Unidad de Diversidad, Sistematica y Evolucion, Puerto Madryn U912OACD, Argentina.,Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Caio C Silva de Cerqueira
- Centro Nacional Patagónico, CONICET, Unidad de Diversidad, Sistematica y Evolucion, Puerto Madryn U912OACD, Argentina.,Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México City 4510, México
| | - Michael Cheeseman
- Division of Developmental Biology, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Javier Rosique
- Departamento de Antropología, Universidad de Antioquia, Medellín 5001000, Colombia
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | | | - Denis Headon
- Division of Developmental Biology, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Rolando González-José
- Centro Nacional Patagónico, CONICET, Unidad de Diversidad, Sistematica y Evolucion, Puerto Madryn U912OACD, Argentina
| | - David Balding
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK.,Schools of BioSciences and Mathematics and Statistics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
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8
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Adhikari K, Fontanil T, Cal S, Mendoza-Revilla J, Fuentes-Guajardo M, Chacón-Duque JC, Al-Saadi F, Johansson JA, Quinto-Sanchez M, Acuña-Alonzo V, Jaramillo C, Arias W, Barquera Lozano R, Macín Pérez G, Gómez-Valdés J, Villamil-Ramírez H, Hunemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Gallo C, Poletti G, Schuler-Faccini L, Salzano FM, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Bedoya G, Gonzalez-José R, Headon D, López-Otín C, Tobin DJ, Balding D, Ruiz-Linares A. A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features. Nat Commun 2016; 7:10815. [PMID: 26926045 PMCID: PMC4773514 DOI: 10.1038/ncomms10815] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 01/25/2016] [Indexed: 12/20/2022] Open
Abstract
We report a genome-wide association scan in over 6,000 Latin Americans for features of scalp hair (shape, colour, greying, balding) and facial hair (beard thickness, monobrow, eyebrow thickness). We found 18 signals of association reaching genome-wide significance (P values 5 × 10(-8) to 3 × 10(-119)), including 10 novel associations. These include novel loci for scalp hair shape and balding, and the first reported loci for hair greying, monobrow, eyebrow and beard thickness. A newly identified locus influencing hair shape includes a Q30R substitution in the Protease Serine S1 family member 53 (PRSS53). We demonstrate that this enzyme is highly expressed in the hair follicle, especially the inner root sheath, and that the Q30R substitution affects enzyme processing and secretion. The genome regions associated with hair features are enriched for signals of selection, consistent with proposals regarding the evolution of human hair.
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Affiliation(s)
- Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Tania Fontanil
- Departamento de Bioquímica y Biología Molecular, IUOPA, Universidad de Oviedo, Oviedo 33006, Spain
| | - Santiago Cal
- Departamento de Bioquímica y Biología Molecular, IUOPA, Universidad de Oviedo, Oviedo 33006, Spain
| | - Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000009, Chile
| | - Juan-Camilo Chacón-Duque
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Farah Al-Saadi
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Jeanette A. Johansson
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | | | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- National Institute of Anthropology and History, México 4510, México
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera Lozano
- National Institute of Anthropology and History, México 4510, México
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México 4510, México
| | - Gastón Macín Pérez
- National Institute of Anthropology and History, México 4510, México
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México 4510, México
| | | | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México 4510, México
| | - Tábita Hunemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Virginia Ramallo
- Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Caio C. Silva de Cerqueira
- Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Francisco M. Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México 4510, México
| | | | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | | | - Denis Headon
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, IUOPA, Universidad de Oviedo, Oviedo 33006, Spain
| | - Desmond J. Tobin
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, Victoria, UK
| | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Schools of BioSciences and Mathematics and Statistics, University of Melbourne, Melbourne 3010, Australia
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
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9
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Adhikari K, Reales G, Smith AJP, Konka E, Palmen J, Quinto-Sanchez M, Acuña-Alonzo V, Jaramillo C, Arias W, Fuentes M, Pizarro M, Barquera Lozano R, Macín Pérez G, Gómez-Valdés J, Villamil-Ramírez H, Hunemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Gallo C, Poletti G, Schuler-Faccini L, Salzano FM, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Bedoya G, Calderón R, Rosique J, Cheeseman M, Bhutta MF, Humphries SE, Gonzalez-José R, Headon D, Balding D, Ruiz-Linares A. A genome-wide association study identifies multiple loci for variation in human ear morphology. Nat Commun 2015; 6:7500. [PMID: 26105758 PMCID: PMC4491814 DOI: 10.1038/ncomms8500] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 05/14/2015] [Indexed: 11/09/2022] Open
Abstract
Here we report a genome-wide association study for non-pathological pinna morphology in over 5,000 Latin Americans. We find genome-wide significant association at seven genomic regions affecting: lobe size and attachment, folding of antihelix, helix rolling, ear protrusion and antitragus size (linear regression P values 2 × 10(-8) to 3 × 10(-14)). Four traits are associated with a functional variant in the Ectodysplasin A receptor (EDAR) gene, a key regulator of embryonic skin appendage development. We confirm expression of Edar in the developing mouse ear and that Edar-deficient mice have an abnormally shaped pinna. Two traits are associated with SNPs in a region overlapping the T-Box Protein 15 (TBX15) gene, a major determinant of mouse skeletal development. Strongest association in this region is observed for SNP rs17023457 located in an evolutionarily conserved binding site for the transcription factor Cartilage paired-class homeoprotein 1 (CART1), and we confirm that rs17023457 alters in vitro binding of CART1.
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Affiliation(s)
- Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Guillermo Reales
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Andrew J P Smith
- Centre for Cardiovascular Genetics, BHF Laboratories, Institute Cardiovascular Sciences, University College London, Rayne Building, London WC1E 6JF, UK
| | - Esra Konka
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Jutta Palmen
- Centre for Cardiovascular Genetics, BHF Laboratories, Institute Cardiovascular Sciences, University College London, Rayne Building, London WC1E 6JF, UK
| | | | - Victor Acuña-Alonzo
- 1] Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK [2] National Institute of Anthropology and History, Mexico City 4510, Mexico
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Macarena Fuentes
- Instituto de Alta Investigación, Universidad de Tarapacá, Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile and Centro de Investigaciones del Hombre en el Desierto, Arica 1000000, Chile
| | - María Pizarro
- Instituto de Alta Investigación, Universidad de Tarapacá, Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile and Centro de Investigaciones del Hombre en el Desierto, Arica 1000000, Chile
| | - Rodrigo Barquera Lozano
- 1] National Institute of Anthropology and History, Mexico City 4510, Mexico [2] Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Gastón Macín Pérez
- 1] National Institute of Anthropology and History, Mexico City 4510, Mexico [2] Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | | | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Tábita Hunemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Virginia Ramallo
- 1] Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina [2] Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | | | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Peru
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Peru
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Peru
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Peru
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Peru
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile and Centro de Investigaciones del Hombre en el Desierto, Arica 1000000, Chile
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rosario Calderón
- Departamento de Zoología y Antropología Física, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Javier Rosique
- Departamento de Antropología, Facultad de Ciencias Sociales y Humanas, Universidad de Antioquia, Medellín 5001000, Colombia
| | - Michael Cheeseman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Mahmood F Bhutta
- 1] UCL Ear Institute, University College London, London WC1X 8EE, UK [2] Royal National Throat Nose and Ear Hospital, London WC1X 8EE, UK
| | - Steve E Humphries
- 1] Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK [2] Centre for Cardiovascular Genetics, BHF Laboratories, Institute Cardiovascular Sciences, University College London, Rayne Building, London WC1E 6JF, UK
| | | | - Denis Headon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - David Balding
- 1] Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK [2] Schools of BioSciences and Mathematics &Statistics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
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