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Zollner L, Boekstegers F, Barahona Ponce C, Scherer D, Marcelain K, Gárate-Calderón V, Waldenberger M, Morales E, Rojas A, Munoz C, Retamales J, De Toro G, Kortmann AV, Barajas O, Rivera MT, Cortés A, Loader D, Saavedra J, Gutiérrez L, Ortega A, Bertrán ME, Bartolotti L, Gabler F, Campos M, Alvarado J, Moisán F, Spencer L, Nervi B, Carvajal D, Losada H, Almau M, Fernández P, Olloquequi J, Carter AR, Miquel Poblete JF, Bustos BI, Fuentes Guajardo M, Gonzalez-Jose R, Bortolini MC, Acuña-Alonzo V, Gallo C, Ruiz Linares A, Rothhammer F, Lorenzo Bermejo J. Gallbladder Cancer Risk and Indigenous South American Mapuche Ancestry: Instrumental Variable Analysis Using Ancestry-Informative Markers. Cancers (Basel) 2023; 15:4033. [PMID: 37627062 PMCID: PMC10452561 DOI: 10.3390/cancers15164033] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
A strong association between the proportion of indigenous South American Mapuche ancestry and the risk of gallbladder cancer (GBC) has been reported in observational studies. Chileans show the highest incidence of GBC worldwide, and the Mapuche are the largest indigenous people in Chile. We set out to assess the confounding-free effect of the individual proportion of Mapuche ancestry on GBC risk and to investigate the mediating effects of gallstone disease and body mass index (BMI) on this association. Genetic markers of Mapuche ancestry were selected based on the informativeness for assignment measure, and then used as instrumental variables in two-sample Mendelian randomization analyses and complementary sensitivity analyses. Results suggested a putatively causal effect of Mapuche ancestry on GBC risk (inverse variance-weighted (IVW) risk increase of 0.8% per 1% increase in Mapuche ancestry proportion, 95% CI 0.4% to 1.2%, p = 6.7 × 10-5) and also on gallstone disease (3.6% IVW risk increase, 95% CI 3.1% to 4.0%), pointing to a mediating effect of gallstones on the association between Mapuche ancestry and GBC. In contrast, the proportion of Mapuche ancestry showed a negative effect on BMI (IVW estimate -0.006 kg/m2, 95% CI -0.009 to -0.003). The results presented here may have significant implications for GBC prevention and are important for future admixture mapping studies. Given that the association between the individual proportion of Mapuche ancestry and GBC risk previously noted in observational studies appears to be free of confounding, primary and secondary prevention strategies that consider genetic ancestry could be particularly efficient.
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Affiliation(s)
- Linda Zollner
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (L.Z.); (F.B.); (C.B.P.); (D.S.); (V.G.-C.)
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Felix Boekstegers
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (L.Z.); (F.B.); (C.B.P.); (D.S.); (V.G.-C.)
| | - Carol Barahona Ponce
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (L.Z.); (F.B.); (C.B.P.); (D.S.); (V.G.-C.)
| | - Dominique Scherer
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (L.Z.); (F.B.); (C.B.P.); (D.S.); (V.G.-C.)
| | - Katherine Marcelain
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago 8380000, Chile; (K.M.); (O.B.)
| | - Valentina Gárate-Calderón
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (L.Z.); (F.B.); (C.B.P.); (D.S.); (V.G.-C.)
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago 8380000, Chile; (K.M.); (O.B.)
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany;
| | - Erik Morales
- Hospital Regional de Talca, Talca 3460000, Chile; (E.M.); (C.M.)
- Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile;
| | - Armando Rojas
- Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile;
| | - César Munoz
- Hospital Regional de Talca, Talca 3460000, Chile; (E.M.); (C.M.)
- Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile;
| | | | - Gonzalo De Toro
- Hospital de Puerto Montt, Puerto Montt 5480000, Chile; (G.D.T.); (A.V.K.)
- Escuela de Tecnología Médica, Universidad Austral de Chile sede Puerto Montt, Puerto Montt 5480000, Chile
| | | | - Olga Barajas
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago 8380000, Chile; (K.M.); (O.B.)
- Hospital Clínico Universidad de Chile, Santiago 8380456, Chile
| | | | - Analía Cortés
- Hospital del Salvador, Santiago 7500922, Chile; (M.T.R.); (A.C.)
| | - Denisse Loader
- Hospital Padre Hurtado, Santiago 8880456, Chile; (D.L.); (J.S.)
| | | | | | | | | | | | - Fernando Gabler
- Hospital San Borja Arriarán, Santiago 8320000, Chile; (F.G.); (M.C.)
| | - Mónica Campos
- Hospital San Borja Arriarán, Santiago 8320000, Chile; (F.G.); (M.C.)
| | - Juan Alvarado
- Hospital Regional Guillermo Grant Benavente, Concepción 4070386, Chile; (J.A.); (F.M.); (L.S.)
| | - Fabricio Moisán
- Hospital Regional Guillermo Grant Benavente, Concepción 4070386, Chile; (J.A.); (F.M.); (L.S.)
| | - Loreto Spencer
- Hospital Regional Guillermo Grant Benavente, Concepción 4070386, Chile; (J.A.); (F.M.); (L.S.)
| | - Bruno Nervi
- Departamento de Hematología y Oncología, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago 8330077, Chile;
| | - Daniel Carvajal
- Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7650568, Chile;
| | - Héctor Losada
- Departamento de Cirugía, Universidad de la Frontera, Temuco 4780000, Chile;
| | - Mauricio Almau
- Hospital de Rancagua, Rancagua 2820000, Chile; (M.A.); (P.F.)
| | | | - Jordi Olloquequi
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain;
- Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca 3460000, Chile
| | - Alice R. Carter
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK;
| | - Juan Francisco Miquel Poblete
- Departamento de Gastroenterología, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile;
| | - Bernabe Ignacio Bustos
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA;
| | - Macarena Fuentes Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Tarapacá University, Arica 1000815, Chile;
| | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9120ACD, Argentina;
| | - Maria Cátira Bortolini
- Instituto de Biociências, Universidad Federal do Rio Grande do Sul, Puerto Alegre 15053, Brazil;
| | | | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru;
| | - Andres Ruiz Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200434, China;
- ADES (Anthropologie Bio-Culturelle, Droit, Éthique et Santé), UFR de Médecine, Aix-Marseille University, 13007 Marseille, France
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Justo Lorenzo Bermejo
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (L.Z.); (F.B.); (C.B.P.); (D.S.); (V.G.-C.)
- Department of Biostatistics for Precision Oncology, Institut de Cancérologie Strasbourg Europe, 67200 Strasbourg, France
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Li Y, Xiong Z, Zhang M, Hysi PG, Qian Y, Adhikari K, Weng J, Wu S, Du S, Gonzalez-Jose R, Schuler-Faccini L, Bortolini MC, Acuna-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Wang J, Tan J, Yuan Z, Jin L, Uitterlinden AG, Ghanbari M, Ikram MA, Nijsten T, Zhu X, Lei Z, Jia P, Ruiz-Linares A, Spector TD, Wang S, Kayser M, Liu F. Combined genome-wide association study of 136 quantitative ear morphology traits in multiple populations reveal 8 novel loci. PLoS Genet 2023; 19:e1010786. [PMID: 37459304 PMCID: PMC10351707 DOI: 10.1371/journal.pgen.1010786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 05/16/2023] [Indexed: 07/20/2023] Open
Abstract
Human ear morphology, a complex anatomical structure represented by a multidimensional set of correlated and heritable phenotypes, has a poorly understood genetic architecture. In this study, we quantitatively assessed 136 ear morphology traits using deep learning analysis of digital face images in 14,921 individuals from five different cohorts in Europe, Asia, and Latin America. Through GWAS meta-analysis and C-GWASs, a recently introduced method to effectively combine GWASs of many traits, we identified 16 genetic loci involved in various ear phenotypes, eight of which have not been previously associated with human ear features. Our findings suggest that ear morphology shares genetic determinants with other surface ectoderm-derived traits such as facial variation, mono eyebrow, and male pattern baldness. Our results enhance the genetic understanding of human ear morphology and shed light on the shared genetic contributors of different surface ectoderm-derived phenotypes. Additionally, gene editing experiments in mice have demonstrated that knocking out the newly ear-associated gene (Intu) and a previously ear-associated gene (Tbx15) causes deviating mouse ear morphology.
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Affiliation(s)
- Yi Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
| | - Ziyi Xiong
- Department of Genetic Identification, Erasmus MC, University Medical Center, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
| | - Manfei Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London, United Kingdom
| | - Yu Qian
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
- Beijing No.8 High School, Beijing, China
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, United Kingdom
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, United Kingdom
| | - Jun Weng
- Center for Biometrics and Security Research & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, China
| | - Sijie Wu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- University of Chinese Academy of Sciences, China
| | - Rolando Gonzalez-Jose
- Instituto Patagonico de Ciencias Sociales y Humanas, Centro Nacional Patagonico, CONICET, Argentina
| | | | | | - Victor Acuna-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Quimica, UNAM-Instituto Nacional de Medicina Genomica, Mexico
| | - Carla Gallo
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Peru
| | - Giovanni Poletti
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Peru
| | - Gabriel Bedoya
- GENMOL (Genetica Molecular), Universidad de Antioquia, Medellin, Colombia
| | | | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, China
| | - Li Jin
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
- Fudan-Taizhou Institute of Health Sciences, China
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, the Netherlands
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC, University Medical Center, the Netherlands
| | - Xiangyu Zhu
- Center for Biometrics and Security Research & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, China
| | - Zhen Lei
- Center for Biometrics and Security Research & National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, United Kingdom
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, China
- Aix-Marseille Universite, CNRS, EFS, ADES, France
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, United Kingdom
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, China
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center, the Netherlands
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
- Department of Genetic Identification, Erasmus MC, University Medical Center, the Netherlands
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Boekstegers F, Scherer D, Barahona Ponce C, Marcelain K, Gárate-Calderón V, Waldenberger M, Morales E, Rojas A, Munoz C, Retamales J, de Toro G, Barajas O, Rivera MT, Cortés A, Loader D, Saavedra J, Gutiérrez L, Ortega A, Bertrán ME, Bartolotti L, Gabler F, Campos M, Alvarado J, Moisán F, Spencer L, Nervi B, Carvajal-Hausdorf D, Losada H, Almau M, Fernández P, Olloquequi J, Fuentes-Guajardo M, Gonzalez-Jose R, Bortolini MC, Acuña-Alonzo V, Gallo C, Linares AR, Rothhammer F, Lorenzo Bermejo J. Development and internal validation of a multifactorial risk prediction model for gallbladder cancer in a high-incidence country. Int J Cancer 2023. [PMID: 37260300 DOI: 10.1002/ijc.34607] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/04/2023] [Accepted: 05/04/2023] [Indexed: 06/02/2023]
Abstract
Since 2006, Chile has been implementing a gallbladder cancer (GBC) prevention program based on prophylactic cholecystectomy for gallstone patients aged 35 to 49 years. The effectiveness of this prevention program has not yet been comprehensively evaluated. We conducted a retrospective study of 473 Chilean GBC patients and 2137 population-based controls to develop and internally validate three GBC risk prediction models. The Baseline Model accounted for gallstones while adjusting for sex and birth year. Enhanced Model I also included the non-genetic risk factors: body mass index, educational level, Mapuche surnames, number of children and family history of GBC. Enhanced Model II further included Mapuche ancestry and the genotype for rs17209837. Multiple Cox regression was applied to assess the predictive performance, quantified by the area under the precision-recall curve (AUC-PRC) and the number of cholecystectomies needed (NCN) to prevent one case of GBC at age 70 years. The AUC-PRC for the Baseline Model (0.44%, 95%CI 0.42-0.46) increased by 0.22 (95%CI 0.15-0.29) when non-genetic factors were included, and by 0.25 (95%CI 0.20-0.30) when incorporating non-genetic and genetic factors. The overall NCN for Chileans with gallstones (115, 95%CI 104-131) decreased to 92 (95%CI 60-128) for Chileans with a higher risk than the median according to Enhanced Model I, and to 80 (95%CI 59-110) according to Enhanced Model II. In conclusion, age, sex and gallstones are strong risk factors for GBC, but consideration of other non-genetic factors and individual genotype data improves risk prediction and may optimize allocation of financial resources and surgical capacity.
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Affiliation(s)
- Felix Boekstegers
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
| | - Dominique Scherer
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
| | - Carol Barahona Ponce
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
| | - Katherine Marcelain
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago, Chile
| | - Valentina Gárate-Calderón
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago, Chile
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology and Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Erik Morales
- Hospital Regional de Talca, Talca, Chile
- Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - Armando Rojas
- Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - César Munoz
- Hospital Regional de Talca, Talca, Chile
- Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | | | - Gonzalo de Toro
- Hospital de Puerto Montt, Puerto Montt, Chile
- Escuela de Tecnología Médica, Universidad Austral de Chile sede Puerto Montt, Puerto Montt, Chile
| | - Olga Barajas
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago, Chile
- Hospital Clínico Universidad de Chile, Santiago, Chile
| | | | | | | | | | | | | | | | | | | | | | - Juan Alvarado
- Hospital Regional Guillermo Grant Benavente, Concepción, Chile
| | - Fabricio Moisán
- Hospital Regional Guillermo Grant Benavente, Concepción, Chile
| | - Loreto Spencer
- Hospital Regional Guillermo Grant Benavente, Concepción, Chile
| | - Bruno Nervi
- Departamento de Hematología y Oncología, Escuela de Medicina Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Héctor Losada
- Departamento de Cirugía, Universidad de La Frontera, Temuco, Chile
| | | | | | - Jordi Olloquequi
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Tarapacá University, Arica, Chile
| | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidad Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Andres 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, China
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, France
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
| | | | - Justo Lorenzo Bermejo
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
- Department of Biostatistics for Precision Oncology, Institut de Cancérologie Strasbourg Europe, Strasbourg, France
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Morales L, Navarro P, Cintas C, Gonzalez-Jose R, Ramallo V, Delrieux C. Bulsarapp: Interactive Visual Analysis for Surname Trend Exploration. IEEE Comput Graph Appl 2022; 42:28-39. [PMID: 34559640 DOI: 10.1109/mcg.2021.3115052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The study of surnames for a given population, together with their distribution and spatial patterns identification, has been a long-standing problem in the fields of human biology, public health, and social sciences. The ancestry inferred from surname information can be a useful means to understand the dynamics of human populations. This knowledge allows us to characterize geographically the ethnicity of populations, and to understand the complex relationships between identity, migration, and health issues in a demographic view. However, in most cases, a detailed geolocalization of this data can be a daunting task. We propose a visual analytic tool that summarizes the heterogeneous surname and geographic information collected from Argentinean electoral rolls. This tool allows a massive data analysis, and facilitates interdisciplinary studies about population dynamics related to ancestry, migration, and health. It also offers an easy-to-use interface that allows interactive exploration of isonymy and surname origins, their distribution, and spatial trends in a high population density context.
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Blandino A, Scherer D, Rounge TB, Umu SU, Boekstegers F, Barahona Ponce C, Marcelain K, Gárate-Calderón V, Waldenberger M, Morales E, Rojas A, Munoz C, Retamales J, de Toro G, Barajas O, Rivera MT, Cortés A, Loader D, Saavedra J, Gutiérrez L, Ortega A, Bertrán ME, Gabler F, Campos M, Alvarado J, Moisán F, Spencer L, Nervi B, Carvajal-Hausdorf DE, Losada H, Almau M, Fernández P, Gallegos I, Olloquequi J, Fuentes-Guajardo M, Gonzalez-Jose R, Bortolini MC, Gallo C, Linares AR, Rothhammer F, Lorenzo Bermejo J. Identification of Circulating lncRNAs Associated with Gallbladder Cancer Risk by Tissue-Based Preselection, Cis-eQTL Validation, and Analysis of Association with Genotype-Based Expression. Cancers (Basel) 2022; 14:cancers14030634. [PMID: 35158906 PMCID: PMC8833674 DOI: 10.3390/cancers14030634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Received: 11/19/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play key roles in cell processes and are good candidates for cancer risk prediction. Few studies have investigated the association between individual genotypes and lncRNA expression. Here we integrate three separate datasets with information on lncRNA expression only, both lncRNA expression and genotype, and genotype information only to identify circulating lncRNAs associated with the risk of gallbladder cancer (GBC) using robust linear and logistic regression techniques. In the first dataset, we preselect lncRNAs based on expression changes along the sequence "gallstones → dysplasia → GBC". In the second dataset, we validate associations between genetic variants and serum expression levels of the preselected lncRNAs (cis-lncRNA-eQTLs) and build lncRNA expression prediction models. In the third dataset, we predict serum lncRNA expression based on individual genotypes and assess the association between genotype-based expression and GBC risk. AC084082.3 and LINC00662 showed increasing expression levels (p-value = 0.009), while C22orf34 expression decreased in the sequence from gallstones to GBC (p-value = 0.04). We identified and validated two cis-LINC00662-eQTLs (r2 = 0.26) and three cis-C22orf34-eQTLs (r2 = 0.24). Only LINC00662 showed a genotyped-based serum expression associated with GBC risk (OR = 1.25 per log2 expression unit, 95% CI 1.04-1.52, p-value = 0.02). Our results suggest that preselection of lncRNAs based on tissue samples and exploitation of cis-lncRNA-eQTLs may facilitate the identification of circulating noncoding RNAs linked to cancer risk.
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Affiliation(s)
- Alice Blandino
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (A.B.); (D.S.); (F.B.); (C.B.P.); (V.G.-C.)
| | - Dominique Scherer
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (A.B.); (D.S.); (F.B.); (C.B.P.); (V.G.-C.)
| | - Trine B. Rounge
- Department of Research, Cancer Registry of Norway, 0379 Oslo, Norway; (T.B.R.); (S.U.U.)
- Department of Informatics, University of Oslo, 0304 Oslo, Norway
| | - Sinan U. Umu
- Department of Research, Cancer Registry of Norway, 0379 Oslo, Norway; (T.B.R.); (S.U.U.)
| | - Felix Boekstegers
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (A.B.); (D.S.); (F.B.); (C.B.P.); (V.G.-C.)
| | - Carol Barahona Ponce
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (A.B.); (D.S.); (F.B.); (C.B.P.); (V.G.-C.)
| | - Katherine Marcelain
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago 8380000, Chile; (K.M.); (O.B.); (I.G.)
| | - Valentina Gárate-Calderón
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (A.B.); (D.S.); (F.B.); (C.B.P.); (V.G.-C.)
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago 8380000, Chile; (K.M.); (O.B.); (I.G.)
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology and Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany;
| | - Erik Morales
- Hospital Regional de Talca, Talca 3460000, Chile; (E.M.); (C.M.)
- Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile;
| | - Armando Rojas
- Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile;
| | - César Munoz
- Hospital Regional de Talca, Talca 3460000, Chile; (E.M.); (C.M.)
- Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile;
| | | | - Gonzalo de Toro
- Hospital de Puerto Montt, Puerto Montt 5480000, Chile;
- Escuela de Tecnología Médica, Universidad Austral de Chile sede Puerto Montt, Puerto Montt 5480000, Chile
| | - Olga Barajas
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago 8380000, Chile; (K.M.); (O.B.); (I.G.)
- Hospital Clínico Universidad de Chile, Santiago 8380456, Chile
| | | | - Analía Cortés
- Hospital del Salvador, Santiago 7500922, Chile; (M.T.R.); (A.C.)
| | - Denisse Loader
- Hospital Padre Hurtado, Santiago 8880456, Chile; (D.L.); (J.S.)
| | | | | | | | | | - Fernando Gabler
- Hospital San Borja Arriarán, Santiago 8320000, Chile; (F.G.); (M.C.)
| | - Mónica Campos
- Hospital San Borja Arriarán, Santiago 8320000, Chile; (F.G.); (M.C.)
| | - Juan Alvarado
- Hospital Regional Guillermo Grant Benavente, Concepcion 4070386, Chile; (J.A.); (F.M.); (L.S.)
| | - Fabrizio Moisán
- Hospital Regional Guillermo Grant Benavente, Concepcion 4070386, Chile; (J.A.); (F.M.); (L.S.)
| | - Loreto Spencer
- Hospital Regional Guillermo Grant Benavente, Concepcion 4070386, Chile; (J.A.); (F.M.); (L.S.)
| | - Bruno Nervi
- Departamento de Hematología y Oncología, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago 8330077, Chile; or
| | | | | | - Mauricio Almau
- Hospital de Rancagua, Rancagua 2820000, Chile; (M.A.); (P.F.)
| | | | - Ivan Gallegos
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago 8380000, Chile; (K.M.); (O.B.); (I.G.)
- Hospital Clínico Universidad de Chile, Santiago 8380456, Chile
| | - Jordi Olloquequi
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain;
- Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca 3460000, Chile
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Tarapacá University, Arica 1000815, Chile;
| | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9120ACD, Argentina;
| | - Maria Cátira Bortolini
- Instituto de Biociências, Universidad Federal do Rio Grande do Sul, Puerto Alegre 15053, Brazil;
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru;
| | - Andres Ruiz Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200434, China;
- ADES (Anthropologie Bio-Culturelle, Droit, Éthique et Santé), UFR de Médecine, Aix-Marseille University, 13007 Marseille, France
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Justo Lorenzo Bermejo
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, 69120 Heidelberg, Germany; (A.B.); (D.S.); (F.B.); (C.B.P.); (V.G.-C.)
- Correspondence: ; Tel.: +49-062-2156-4180
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6
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Koenigstein F, Boekstegers F, Wilson JF, Fuentes-Guajardo M, Gonzalez-Jose R, Bedoya G, Bortolini MC, Acuña-Alonzo V, Gallo C, Linares AR, Rothhammer F, Bermejo JL. Inbreeding, native American ancestry and child mortality: Linking human selection and paediatric medicine. Hum Mol Genet 2021; 31:975-984. [PMID: 34673976 PMCID: PMC8947305 DOI: 10.1093/hmg/ddab302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/23/2021] [Revised: 10/07/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
The children of related parents show increased risk of early mortality. The Native American genome typically exhibits long stretches of homozygosity, and Latin Americans are highly heterogeneous regarding the individual burden of homozygosity, the proportion, and the type of Native American ancestry. We analysed nationwide mortality and genome-wide genotype data from admixed Chileans to investigate the relationship between common causes of child mortality, homozygosity and Native American ancestry. Results from two-stage linear-Poisson regression revealed a strong association between the sum length of runs of homozygosity (SROH) above 1.5 Megabases (Mb) in each genome and mortality due to intracranial non-traumatic haemorrhage of foetus and new-born (5% increased risk of death per Mb in SROH, P = 1 × 10-3) and disorders related to short gestation and low birth weight (P = 3 × 10-4). The major indigenous populations in Chile are Aymara-Quechua in the north of the country, and the Mapuche-Huilliche in the south. The individual proportion of Aymara-Quechua ancestry was associated with an increased risk of death due to anencephaly and similar malformations (P = 4 × 10-5), and the risk of death due to Edwards and Patau trisomy syndromes decreased 4% per 1% Aymara-Quechua ancestry proportion (P = 4 × 10-4) and 5% per 1% Mapuche-Huilliche ancestry proportion (P = 2 × 10-3). The present results suggest that short gestation, low birth weight and intracranial non-traumatic haemorrhage mediate the negative effect of inbreeding on human selection. Independent validation of the identified associations between common causes of child death, homozygosity and fine-scale ancestry proportions may inform paediatric medicine.
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Affiliation(s)
- Fabienne Koenigstein
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
| | - Felix Boekstegers
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Tarapacá University, Arica, Chile
| | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Gabriel Bedoya
- Instituto de Biología, Grupo Genmol, Universidad de Antioquía, Medellín, Colombia
| | - Maria Cátira Bortolini
- Instituto de Biociências, Universidad Federal do Rio Grande do Sul, Puerto Alegre, Brazil
| | | | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Andres 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, China.,Aix-Marseille Université, CNRS, EFS, ADES, Marseille, France.,Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
| | | | - Justo Lorenzo Bermejo
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
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7
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Barahona Ponce C, Scherer D, Brinster R, Boekstegers F, Marcelain K, Gárate-Calderón V, Müller B, de Toro G, Retamales J, Barajas O, Ahumada M, Morales E, Rojas A, Sanhueza V, Loader D, Rivera MT, Gutiérrez L, Bernal G, Ortega A, Montalvo D, Portiño S, Bertrán ME, Gabler F, Spencer L, Olloquequi J, Fischer C, Jenab M, Aleksandrova K, Katzke V, Weiderpass E, Bonet C, Moradi T, Fischer K, Bossers W, Brenner H, Hveem K, Eklund N, Völker U, Waldenberger M, Fuentes Guajardo M, Gonzalez-Jose R, Bedoya G, Bortolini MC, Canizales-Quinteros S, Gallo C, Ruiz-Linares A, Rothhammer F, Lorenzo Bermejo J. Gallstones, Body Mass Index, C-Reactive Protein, and Gallbladder Cancer: Mendelian Randomization Analysis of Chilean and European Genotype Data. Hepatology 2021; 73:1783-1796. [PMID: 32893372 DOI: 10.1002/hep.31537] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 07/10/2020] [Accepted: 07/31/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND AND AIMS Gallbladder cancer (GBC) is a neglected disease with substantial geographical variability: Chile shows the highest incidence worldwide, while GBC is relatively rare in Europe. Here, we investigate the causal effects of risk factors considered in current GBC prevention programs as well as C-reactive protein (CRP) level as a marker of chronic inflammation. APPROACH AND RESULTS We applied two-sample Mendelian randomization (MR) using publicly available data and our own data from a retrospective Chilean and a prospective European study. Causality was assessed by inverse variance weighted (IVW), MR-Egger regression, and weighted median estimates complemented with sensitivity analyses on potential heterogeneity and pleiotropy, two-step MR, and mediation analysis. We found evidence for a causal effect of gallstone disease on GBC risk in Chileans (P = 9 × 10-5 ) and Europeans (P = 9 × 10-5 ). A genetically elevated body mass index (BMI) increased GBC risk in Chileans (P = 0.03), while higher CRP concentrations increased GBC risk in Europeans (P = 4.1 × 10-6 ). European results suggest causal effects of BMI on gallstone disease (P = 0.008); public Chilean data were not, however, available to enable assessment of the mediation effects among causal GBC risk factors. CONCLUSIONS Two risk factors considered in the current Chilean program for GBC prevention are causally linked to GBC risk: gallstones and BMI. For Europeans, BMI showed a causal effect on gallstone risk, which was itself causally linked to GBC risk.
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Affiliation(s)
- Carol Barahona Ponce
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago de Chile, Chile
| | - Dominique Scherer
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Regina Brinster
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Felix Boekstegers
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Katherine Marcelain
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago de Chile, Chile
| | - Valentina Gárate-Calderón
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago de Chile, Chile
| | - Bettina Müller
- Servicio de Oncología Médica, Instituto Nacional del Cáncer, Santiago, Chile
| | - Gonzalo de Toro
- Escuela de Tecnologia Medica, Universidad Austral de Chile sede Puerto Montt, Puerto Montt, Chile
- Servicio de Anatomía Patológica, Hospital de Puerto Montt, Puerto Montt, Chile
| | - Javier Retamales
- Servicio de Oncología Médica, Instituto Nacional del Cáncer, Santiago, Chile
| | - Olga Barajas
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago de Chile, Chile
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago, Chile
- Oncology Department, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Monica Ahumada
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago de Chile, Chile
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago, Chile
- Oncology Department, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Erik Morales
- Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
- Unidad de Anatomía Patológica del Hospital Regional de Talca, Talca, Chile
| | - Armando Rojas
- Laboratorio de Investigaciones Biomédicas en la Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - Verónica Sanhueza
- Servicio de Anatomía Patológica, Hospital Padre Hurtado, Santiago, Chile
| | - Denisse Loader
- Servicio de Anatomía Patológica, Hospital Padre Hurtado, Santiago, Chile
| | | | - Lorena Gutiérrez
- Servicio de Anatomía Patológica, Hospital San Juan de Dios, Santiago, Chile
| | - Giuliano Bernal
- Laboratory of Molecular and Cellular Biology of Cancer (CancerLab), Department of Biomedical Sciences, Faculty of Medicine, Universidad Católica del Norte, Coquimbo, Chile
| | - Alejandro Ortega
- Servicio de Anatomía Patológica, Hospital Regional, Arica, Chile
| | | | - Sergio Portiño
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago, Chile
- Oncology Department, Hospital Clínico Universidad de Chile, Santiago, Chile
| | | | - Fernando Gabler
- Servicio de Anatomía Patológica, Hospital San Borja Arriarán, Santiago, Chile
| | - Loreto Spencer
- Servicio de Anatomía Patológica, Hospital Regional Guillermo Grant Benavente, Concepción, Chile
| | - Jordi Olloquequi
- Laboratory of Cellular and Molecular Pathology, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
| | - Christine Fischer
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Mazda Jenab
- International Agency for Research on Cancer, Lyon, France
| | - Krasimira Aleksandrova
- Department of Epidemiology, German Institute of Human Nutrition, Potsdam-Rehbrücke, Germany
| | - Verena Katzke
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Elisabete Weiderpass
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Catalina Bonet
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Programme, Catalan Institute of Oncology, Barcelona, Spain
| | - Tahereh Moradi
- Division of Epidemiology, Department of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Krista Fischer
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center, National Center for Tumor Diseases, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Kristian Hveem
- The Nord-Trøndelag Health Research Centre, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Public Health and Nursing, K.G. Jebsen Centre for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Niina Eklund
- Genomics and Biobank, National Institute for Health and Welfare, Helsinki, Finland
| | - Uwe Völker
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Universitätsmedizin Greifswald, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology and Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Rolando Gonzalez-Jose
- Centro Nacional Patagónico, Instituto Patagónico de Ciencias Sociales y Humanas, CONICET, Puerto Madryn, Argentina
| | - Gabriel Bedoya
- Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Maria C Bortolini
- Instituto de Biociências, Universidad Federal do Rio Grande do Sul, Puerto Alegre, Brazil
| | | | - Carla Gallo
- Unidad de Neurobiología Molecular y Genética, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Andres 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, China
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille, France
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
| | | | - Justo Lorenzo Bermejo
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
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8
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Boekstegers F, Marcelain K, Barahona Ponce C, Baez Benavides PF, Müller B, de Toro G, Retamales J, Barajas O, Ahumada M, Morales E, Rojas A, Sanhueza V, Loader D, Rivera MT, Gutiérrez L, Bernal G, Ortega A, Montalvo D, Portiño S, Bertrán ME, Gabler F, Spencer L, Olloquequi J, González Silos R, Fischer C, Scherer D, Jenab M, Aleksandrova K, Katzke V, Weiderpass E, Moradi T, Fischer K, Bossers W, Brenner H, Hveem K, Eklund N, Völker U, Waldenberger M, Fuentes Guajardo M, Gonzalez-Jose R, Bedoya G, Bortolini MC, Canizales S, Gallo C, Ruiz Linares A, Rothhammer F, Lorenzo Bermejo J. ABCB1/4 gallbladder cancer risk variants identified in India also show strong effects in Chileans. Cancer Epidemiol 2020; 65:101643. [PMID: 32058310 DOI: 10.1016/j.canep.2019.101643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 09/20/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The first large-scale genome-wide association study of gallbladder cancer (GBC) recently identified and validated three susceptibility variants in the ABCB1 and ABCB4 genes for individuals of Indian descent. We investigated whether these variants were also associated with GBC risk in Chileans, who show the highest incidence of GBC worldwide, and in Europeans with a low GBC incidence. METHODS This population-based study analysed genotype data from retrospective Chilean case-control (255 cases, 2042 controls) and prospective European cohort (108 cases, 181 controls) samples consistently with the original publication. RESULTS Our results confirmed the reported associations for Chileans with similar risk effects. Particularly strong associations (per-allele odds ratios close to 2) were observed for Chileans with high Native American (=Mapuche) ancestry. No associations were noticed for Europeans, but the statistical power was low. CONCLUSION Taking full advantage of genetic and ethnic differences in GBC risk may improve the efficiency of current prevention programs.
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Affiliation(s)
- Felix Boekstegers
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Germany
| | - Katherine Marcelain
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Chile
| | - Carol Barahona Ponce
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Germany; Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Chile
| | | | - Bettina Müller
- Servicio de Oncología Médica, Instituto Nacional del Cáncer, Santiago, Chile
| | - Gonzalo de Toro
- Servicio de Anatomía Patológica, Hospital de Puerto Montt, Puerto Montt, Chile
| | - Javier Retamales
- Servicio de Oncología Médica, Instituto Nacional del Cáncer, Santiago, Chile
| | - Olga Barajas
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Chile; Oncology, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Monica Ahumada
- Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Chile; Oncology, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Erik Morales
- Servicio de Anatomía Patológica, Hospital Regional, Talca, Chile
| | - Armando Rojas
- Biomedical Research Labs, Medicine Faculty, Catholic University of Maule, Talca, Chile
| | - Verónica Sanhueza
- Servicio de Anatomía Patológica, Hospital Padre Hurtado, Santiago, Chile
| | - Denisse Loader
- Servicio de Anatomía Patológica, Hospital Padre Hurtado, Santiago, Chile
| | | | - Lorena Gutiérrez
- Servicio de Anatomía Patológica, Hospital San Juan de Dios, Santiago, Chile
| | - Giuliano Bernal
- Laboratory of Molecular and Cellular Biology of Cancer (CancerLab), Department of Biomedical Sciences, Faculty of Medicine, Universidad Católica del Norte, Coquimbo, Chile
| | - Alejandro Ortega
- Servicio de Anatomía Patológica, Hospital Regional, Arica, Chile
| | | | - Sergio Portiño
- Oncology, Hospital Clínico Universidad de Chile, Santiago, Chile
| | | | - Fernando Gabler
- Servicio de Anatomía Patológica, Hospital San Borja Arriarán, Santiago, Chile
| | - Loreto Spencer
- Servicio de Anatomía Patológica, Hospital Regional Guillermo Grant Benavente, Concepción, Chile
| | - Jordi Olloquequi
- Laboratory of Cellular and Molecular Pathology, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
| | - Rosa González Silos
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Germany
| | | | - Dominique Scherer
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Germany
| | - Mazda Jenab
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Krasimira Aleksandrova
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany; University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Verena Katzke
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elisabete Weiderpass
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Tahereh Moradi
- Division of Epidemiology, Department of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Krista Fischer
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kristian Hveem
- The Nord-Trøndelag Health (HUNT) Research Centre, Norwegian University of Science and Technology (NTNU), Trondheim, K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Norway
| | - Niina Eklund
- Genomics and biobank, National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Uwe Völker
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Universitätsmedizin Greifswald, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology and Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Gabriel Bedoya
- Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Maria C Bortolini
- Instituto de Biociências, Universidad Federal do Rio Grande do Sul, Puerto Alegre, Brazil
| | - Samuel Canizales
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Carla Gallo
- Unidad de Neurobiología Molecular y Genética, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Andres 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
| | | | - Justo Lorenzo Bermejo
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Germany.
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9
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Xiong Z, Dankova G, Howe LJ, Lee MK, Hysi PG, de Jong MA, Zhu G, Adhikari K, Li D, Li Y, Pan B, Feingold E, Marazita ML, Shaffer JR, McAloney K, Xu SH, Jin L, Wang S, de Vrij FMS, Lendemeijer B, Richmond S, Zhurov A, Lewis S, Sharp GC, Paternoster L, Thompson H, Gonzalez-Jose R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Uitterlinden AG, Ikram MA, Wolvius E, Kushner SA, Nijsten TEC, Palstra RJTS, Boehringer S, Medland SE, Tang K, Ruiz-Linares A, Martin NG, Spector TD, Stergiakouli E, Weinberg SM, Liu F, Kayser M. Novel genetic loci affecting facial shape variation in humans. eLife 2019; 8:e49898. [PMID: 31763980 PMCID: PMC6905649 DOI: 10.7554/elife.49898] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022] Open
Abstract
The human face represents a combined set of highly heritable phenotypes, but knowledge on its genetic architecture remains limited, despite the relevance for various fields. A series of genome-wide association studies on 78 facial shape phenotypes quantified from 3-dimensional facial images of 10,115 Europeans identified 24 genetic loci reaching study-wide suggestive association (p < 5 × 10-8), among which 17 were previously unreported. A follow-up multi-ethnic study in additional 7917 individuals confirmed 10 loci including six unreported ones (padjusted < 2.1 × 10-3). A global map of derived polygenic face scores assembled facial features in major continental groups consistent with anthropological knowledge. Analyses of epigenomic datasets from cranial neural crest cells revealed abundant cis-regulatory activities at the face-associated genetic loci. Luciferase reporter assays in neural crest progenitor cells highlighted enhancer activities of several face-associated DNA variants. These results substantially advance our understanding of the genetic basis underlying human facial variation and provide candidates for future in-vivo functional studies.
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Affiliation(s)
- Ziyi Xiong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Gabriela Dankova
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Pirro G Hysi
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Markus A de Jong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | - Gu Zhu
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Kaustubh Adhikari
- Department of Genetics, Evolution, and EnvironmentUniversity College LondonLondonUnited Kingdom
| | - Dan Li
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Yi Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Bo Pan
- Department of Auricular ReconstructionPlastic Surgery HospitalBeijingChina
| | - Eleanor Feingold
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | | | - Shu-Hua Xu
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Li Jin
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
| | - Sijia Wang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Femke MS de Vrij
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Bas Lendemeijer
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stephen Richmond
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Alexei Zhurov
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Sarah Lewis
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Holly Thompson
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Rolando Gonzalez-Jose
- Instituto Patagonico de Ciencias Sociales y Humanas, CENPAT-CONICETPuerto MadrynArgentina
| | | | - Samuel Canizales-Quinteros
- UNAM-Instituto Nacional de Medicina Genomica, Facultad de QuımicaUnidad de Genomica de Poblaciones Aplicada a la SaludMexico CityMexico
| | - Carla Gallo
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Giovanni Poletti
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Gabriel Bedoya
- GENMOL (Genetica Molecular)Universidad de AntioquiaMedellınColombia
| | | | - André G Uitterlinden
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Internal MedicineErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - M Arfan Ikram
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Eppo Wolvius
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Steven A Kushner
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Tamar EC Nijsten
- Department of DermatologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Robert-Jan TS Palstra
- Department of BiochemistryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stefan Boehringer
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | | | - Kun Tang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Andres Ruiz-Linares
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
- Aix-Marseille Université, CNRS, EFS, ADESMarseilleFrance
| | | | - Timothy D Spector
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
- Department of AnthropologyUniversity of PittsburghPittsburghUnited States
| | - Fan Liu
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
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10
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Liu F, Chen Y, Zhu G, Hysi PG, Wu S, Adhikari K, Breslin K, Pospiech E, Hamer MA, Peng F, Muralidharan C, Acuna-Alonzo V, Canizales-Quinteros S, Bedoya G, Gallo C, Poletti G, Rothhammer F, Bortolini MC, Gonzalez-Jose R, Zeng C, Xu S, Jin L, Uitterlinden AG, Ikram MA, van Duijn CM, Nijsten T, Walsh S, Branicki W, Wang S, Ruiz-Linares A, Spector TD, Martin NG, Medland SE, Kayser M. Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair. Hum Mol Genet 2019; 27:559-575. [PMID: 29220522 PMCID: PMC5886212 DOI: 10.1093/hmg/ddx416] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [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: 09/05/2017] [Accepted: 11/29/2017] [Indexed: 01/18/2023] Open
Abstract
Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P < 5e-8). All except one (1p36.22 PEX14) were replicated with nominal significance in at least one of the 6 additional cohorts of European, Native American and East Asian origins. Three additional previously known genes (EDAR, OFCC1, and PRSS53) were confirmed at the nominal significance level. A multivariable regression model revealed that 14 SNPs from different genes significantly and independently contribute to hair shape variation, reaching a cross-validated AUC value of 0.66 (95% CI: 0.62–0.70) and an AUC value of 0.64 in an independent validation cohort, providing an improved accuracy compared with a previous model. Prediction outcomes of 2504 individuals from a multiethnic sample were largely consistent with general knowledge on the global distribution of hair shape variation. Our study thus delivers target genes and DNA variants for future functional studies to further evaluate the molecular basis of hair shape in humans.
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Affiliation(s)
- Fan Liu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gu Zhu
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sijie Wu
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kaustubh Adhikari
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Krystal Breslin
- Department of Biology, Indiana-University-Purdue-University-Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Ewelina Pospiech
- Institute of Zoology and Biomedical Research, Faculty of Biology and Earth Sciences, Jagiellonian University, Kraków, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Merel A Hamer
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Fuduan Peng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Charanya Muralidharan
- Department of Biology, Indiana-University-Purdue-University-Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Victor Acuna-Alonzo
- Laboratorio de Genética Molecular, Escuela Nacional de Antropologia e Historia, México City, México
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México City, México
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, Colombia
| | - 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
| | | | - Maria Catira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
| | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas, CENPAT-CONICET, Puerto Madryn, Argentina
| | - Changqing Zeng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Shuhua Xu
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Li Jin
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Susan Walsh
- Department of Biology, Indiana-University-Purdue-University-Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.,Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Sijia Wang
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK.,Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China.,Laboratory of Biocultural Anthropology, Law, Ethics, and Health (Centre National de la Recherche Scientifique and Etablissement Français du Sang), Aix-Marseille Université, Marseille, France
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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11
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Quinto-Sánchez M, Muñoz-Muñoz F, Gomez-Valdes J, Cintas C, Navarro P, Cerqueira CCSD, Paschetta C, de Azevedo S, Ramallo V, Acuña-Alonzo V, Adhikari K, Fuentes-Guajardo M, Hünemeier T, Everardo P, de Avila F, Jaramillo C, Arias W, Gallo C, Poletti G, Bedoya G, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Rosique J, Ruiz-Linares A, Gonzalez-Jose R. Developmental pathways inferred from modularity, morphological integration and fluctuating asymmetry patterns in the human face. Sci Rep 2018; 8:963. [PMID: 29343858 PMCID: PMC5772513 DOI: 10.1038/s41598-018-19324-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/15/2017] [Indexed: 01/25/2023] Open
Abstract
Facial asymmetries are usually measured and interpreted as proxies to developmental noise. However, analyses focused on its developmental and genetic architecture are scarce. To advance on this topic, studies based on a comprehensive and simultaneous analysis of modularity, morphological integration and facial asymmetries including both phenotypic and genomic information are needed. Here we explore several modularity hypotheses on a sample of Latin American mestizos, in order to test if modularity and integration patterns differ across several genomic ancestry backgrounds. To do so, 4104 individuals were analyzed using 3D photogrammetry reconstructions and a set of 34 facial landmarks placed on each individual. We found a pattern of modularity and integration that is conserved across sub-samples differing in their genomic ancestry background. Specifically, a signal of modularity based on functional demands and organization of the face is regularly observed across the whole sample. Our results shed more light on previous evidence obtained from Genome Wide Association Studies performed on the same samples, indicating the action of different genomic regions contributing to the expression of the nose and mouth facial phenotypes. Our results also indicate that large samples including phenotypic and genomic metadata enable a better understanding of the developmental and genetic architecture of craniofacial phenotypes.
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Affiliation(s)
- Mirsha Quinto-Sánchez
- Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Francesc Muñoz-Muñoz
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Avinguda de l'Eix Central, Edifici C, E-08193, Bellaterra (Cerdanyola del Vallès), Spain
| | - Jorge Gomez-Valdes
- Posgrado en Antropología Física, Escuela Nacional de Antropología e Historia, Ciudad de México, Mexico
| | - Celia Cintas
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Pablo Navarro
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Caio Cesar Silva de Cerqueira
- Superintendência da Polícia Técnico-Científica do Estado de São Paulo. Equipe de Perícias Criminalísticas de Ourinhos, São Paulo, Brazil
| | - Carolina Paschetta
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Soledad de Azevedo
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
- Licenciatura en Antropología Física, Escuela Nacional de Antropología e Historia, Ciudad de México, Mexico
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, Chile
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Paola Everardo
- Licenciatura en Antropología Física, Escuela Nacional de Antropología e Historia, Ciudad de México, Mexico
- Posgrado en Antropología, Instituto de Investigaciones Antropológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Francisco de Avila
- Licenciatura en Antropología Física, Escuela Nacional de Antropología e Historia, Ciudad de México, Mexico
| | | | | | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Giovani Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Francisco Rothhammer
- Facultad Instituto de Alta Investigación Universidad de Tarapacá, Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile y Centro de Investigaciones del Hombre en el Desierto, Arica, Chile
| | - Javier Rosique
- Departamento de Antropología, Facultad de Ciencias Sociales y Humanas. Universidad de Antioquia, Medellín, Colombia
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
- MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas. Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina.
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