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10 results on '"Macarena Fuentes-Guajardo"'

1. A genome‐wide association study identifies novel gene associations with facial skin wrinkling and mole count in Latin Americans

Author

Valeria Villegas, Tábita Hünemeier, Javier Mendoza-Revilla, Samuel Canizales-Quinteros, Jorge Gómez-Valdés, Vanessa Granja, Lavinia Schuler-Faccini, Rodrigo Barquera Lozano, M. Blin, Rolando González-José, Sagnik Palmal, Betty Bonfante, David J. Balding, G. Poletti, Gabriel Bedoya, Juan Camilo Chacón-Duque, Francisco Rothhammer, Macarena Fuentes-Guajardo, C.C.S. de Cerqueira, Virginia Ramallo, Paola Everardo-Martínez, Claudia Jaramillo, Malena Hurtado, M. André, Kaustubh Adhikari, Sijia Wang, Williams Arias, Yee-Chun Chen, Victor Acuña-Alonzo, Pierre Faux, Hugo Villamil-Ramírez, Carla Gallo, Desmond J. Tobin, Maria Cátira Bortolini, and Andres Ruiz-Linares

Subjects
Genetics, 0303 health sciences, Candidate gene, education.field_of_study, SLC45A2, Population, Single-nucleotide polymorphism, Genome-wide association study, Dermatology, purl.org/pe-repo/ocde/ford#3.02.15 [https], Biology, Heritability, Genome, Latin Americans, 3. Good health, mole count, 03 medical and health sciences, 0302 clinical medicine, facial skin wrinkling, 030220 oncology & carcinogenesis, biology.protein, novel gene associations, education, 030304 developmental biology, Genetic association
Abstract

Background: Genome-wide association studies (GWASs) have identified genes influencing skin ageing and mole count in Europeans, but little is known about the relevance of these (or other genes) in non-Europeans. - Objectives: To conduct a GWAS for facial skin ageing and mole count in adults

Published
2021

2. Prediction of eye, hair and skin colour in Latin Americans

Author

Maria Cátira Bortolini, Jorge Gómez-Valdés, Francisco Rothhammer, Andres Ruiz-Linares, Anood Sohail, Caio Cesar Silva de Cerqueira, Giovanni Poletti, Carla Gallo, William Arias, Paola Everardo-Martínez, Rodrigo Barquera Lozano, Javier Mendoza-Revilla, Rolando González-José, Tábita Hünemeier, Maria-Laura Parolin, Samuel Canizales-Quinteros, Sagnik Palmal, Claudia Jaramillo, Betty Bonfante, David J. Balding, Valeria Villegas, Victor Acuña-Alonzo, Pierre Faux, Virginia Ramallo, Hugo Villamil-Ramírez, Malena Hurtado, Kaustubh Adhikari, Lavinia Schuler-Faccini, Gabriel Bedoya, Vanessa Granja, Macarena Fuentes-Guajardo, Juan Camilo Chacón-Duque, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), and Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Genotype, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Datasets as Topic, Skin Pigmentation, Quantitative trait locus, Biology, GENOMAS, Polymorphism, Single Nucleotide, Pathology and Forensic Medicine, purl.org/becyt/ford/1 [https], 03 medical and health sciences, 0302 clinical medicine, DNA PHENOTYPING, Statistics, Genetics, Eye color, PIGMENTATION PREDICTION, Humans, 030216 legal & forensic medicine, education, Hair Color, purl.org/becyt/ford/1.6 [https], Categorical variable, EYE-COLOUR, ComputingMilieux_MISCELLANEOUS, education.field_of_study, Eye Color, integumentary system, Contrast (statistics), Genetic architecture, Random forest, LATIN AMERICANS, ADMIXTURE, purl.org/pe-repo/ocde/ford#3.01.02 [https], 030104 developmental biology, Genetics, Population, Latin America, Logistic Models, Phenotype, HAIR-COLOUR, sense organs, SKIN-COLOUR, DNA phenotyping
Abstract

Here we evaluate the accuracy of prediction for eye, hair and skin pigmentation in a dataset of > 6500 individuals from Mexico, Colombia, Peru, Chile and Brazil (including genome-wide SNP data and quantitative/categorical pigmentation phenotypes - the CANDELA dataset CAN). We evaluated accuracy in relation to different analytical methods and various phenotypic predictors. As expected from statistical principles, we observe that quantitative traits are more sensitive to changes in the prediction models than categorical traits. We find that Random Forest or Linear Regression are generally the best performing methods. We also compare the prediction accuracy of SNP sets defined in the CAN dataset (including 56, 101 and 120 SNPs for eye, hair and skin colour prediction, respectively) to the well-established HIrisPlex-S SNP set (including 6, 22 and 36 SNPs for eye, hair and skin colour prediction respectively). When training prediction models on the CAN data, we observe remarkably similar performances for HIrisPlex-S and the larger CAN SNP sets for the prediction of hair (categorical) and eye (both categorical and quantitative), while the CAN sets outperform HIrisPlex-S for quantitative, but not for categorical skin pigmentation prediction. The performance of HIrisPlex-S, when models are trained in a world-wide sample (although consisting of 80% Europeans, https://hirisplex.erasmusmc.nl), is lower relative to training in the CAN data (particularly for hair and skin colour). Altogether, our observations are consistent with common variation of eye and hair colour having a relatively simple genetic architecture, which is well captured by HIrisPlex-S, even in admixed Latin Americans (with partial European ancestry). By contrast, since skin pigmentation is a more polygenic trait, accuracy is more sensitive to prediction SNP set size, although here this effect was only apparent for a quantitative measure of skin pigmentation. Our results support the use of HIrisPlex-S in the prediction of categorical pigmentation traits for forensic purposes in Latin America, while illustrating the impact of training datasets on its accuracy. Fil: Palmal, Sagnik. Centre National de la Recherche Scientifique; Francia. Aix-Marseille Université; Francia Fil: Kaustubh Adhikari. The Open University; Reino Unido. University College London; Estados Unidos Fil: Mendoza Revilla, Javier. Universidad Peruana Cayetano Heredia; Perú. Institut Pasteur de Paris.; Francia Fil: Fuentes Guajardo, Macarena. Universidad de Tarapacá; Chile Fil: Silva de Cerqueira, Caio Cesar. Scientific Police of São Paulo State; Brasil Fil: Bonfante, Betty. Aix-Marseille Université; Francia. Centre National de la Recherche Scientifique; Francia Fil: Chacón Duque, Juan Camilo. Natural History Museum; Reino Unido Fil: Sohail, Anood. Kinnaird College for Women. Department of Biotechnology; Pakistán Fil: Hurtadeo, Malena. Universidad Peruana Cayetano Heredia; Perú Fil: Villegas, Valeria. Universidad Peruana Cayetano Heredia; Perú Fil: Granja, Vanessa. Universidad Peruana Cayetano Heredia; Perú Fil: Jaramillo, Claudia. Kinnaird College for Women. Department of Biotechnology; Pakistán. Universidad de Antioquia; Colombia Fil: Arias, Williams. Universidad de Antioquia; Colombia Fil: Barquera Lozano, Rodrigo. Instituto Nacional de Antropología e Historia; México. Max Planck Institute for the Science of Human History. Department of Archaeogenetics; Alemania Fil: Everardo Martínez, Paola. Instituto Nacional de Antropología e Historia; México Fil: Gómez Valdés, Jorge. Instituto Nacional de Antropología e Historia; México Fil: Villamil Ramirez, Hugo. Universidad Nacional Autónoma de México; México Fil: Hünemeier, Tábita. Universidade de Sao Paulo; Brasil Fil: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina. Universidade Federal do Rio Grande do Sul; Brasil Fil: Parolin, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentina Fil: Gonzalez, Rolando Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Schüler-Faccini, Lavinia. Universidade Federal do Rio Grande do Sul, Porto Alegre; Brasil Fil: Bortolini, María Cátira. Universidade Federal do Rio Grande do Sul; Brasil Fil: Acuña Alonzo, Victor. Instituto Nacional de Antropología e Historia; México. Universidade Federal do Rio Grande do Sul; Brasil Fil: Canizales Quinteros, Samuel. Universidad Nacional Autónoma de México; México Fil: Gallo, Carla. Universidad Peruana Cayetano Heredia; Perú Fil: Poletti, Giovanni. Universidad Peruana Cayetano Heredia; Perú Fil: Bedoya, Gabriel. Universidad de Antioquia; Colombia Fil: Rothhammer, Francisco. Universidad de Tarapacá; Chile. Universidad de Chile; Chile Fil: Balding, David. University College London; Reino Unido. University of Melbourne; Australia Fil: Faux, Pierre. Aix-Marseille Université; Francia. Centre National de la Recherche Scientifique; Francia Fil: Ruiz Linares, Andrés. Aix-Marseille Université; Francia. Centre National de la Recherche Scientifique; Francia. University College London; Reino Unido. Fudan University; República de China

Published
2021

3. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation

Author

Tábita Hünemeier, Andres Ruiz-Linares, Samuel Canizales-Quinteros, Christel Thauvin-Robinet, Betty Bonfante, Juan Camilo Chacón-Duque, Laurence Duplomb, Charlotte Montillot, Sagnik Palmal, Javier Mendoza-Revilla, Justin Cotney, Laurence Faivre, Seth M. Weinberg, Victor Acuña-Alonzo, Emma Wentworth, Philip H. Jones, Claudia Jaramillo, Caroline Costedoat, Morgane Dubied, David J. Balding, Manfred Kayser, Pierre Faux, Francisco Rothhammer, Mirsha Sánchez-Quinto, Carla Gallo, Paola Everardo-Martínez, Macarena Fuentes-Guajardo, Evie Stergiakouli, Pirro G. Hysi, Ziyi Xiong, Giovanni Poletti, Ceferino Varón-González, Rodrigo Barquera, Maria Cátira Bortolini, Laurence J. Howe, Lauriane Poloni, Rolando González-José, Valeria Villegas, Malena Hurtado, Kaustubh Adhikari, William Arias, Vanessa Granja, Lavinia Schuler-Faccini, Virginia Ramallo, John R. Shaffer, Timothy C. Cox, Tim D. Spector, Gabriel Bedoya, Hugo Villamil-Ramírez, Caio Cesar Silva de Cerqueira, Fan Liu, Binnaz Yalcin, Jorge Gómez-Valdés, Nicolas Navarro, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL), Universidad Peruana Cayetano Heredia (UPCH), Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Connecticut Health Center [Farmington], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University College of London [London] (UCL), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Universidad de Tarapaca, The Natural History Museum [London] (NHM), Universidad de Antioquia = University of Antioquia [Medellín, Colombia], National School of Anthropology and History [Mexico City, Mexico] (NSAH), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Instituto Nacional de Medicina Genomica, Scientific Police of São Paulo State [Ourinhos, Brazil], Universidade de São Paulo = University of São Paulo (USP), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Centro Nacional Patagónico (CENPAT), Beijing Genomics Institute [Shenzhen] (BGI), University of Chinese Academy of Sciences [Beijing] (UCAS), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), University of Bristol [Bristol], King‘s College London, FHU TRANSLAD (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), University of Melbourne, University of Missouri [Kansas City] (UMKC), University of Missouri System, The Open University [Milton Keynes] (OU), Fudan University [Shanghai], Work leading to this publication was funded by grants from the National Natural Science Foundation of China (#31771393), the Scientific and Technology Committee of Shanghai Municipality (18490750300), the Ministry of Science and Technology of China (2020YFE0201600), the Shanghai Municipal Science and Technology Major Project (2017SHZDZX01) and the 111 Project (B13016), the Leverhulme Trust (F/07 134/DF), BBSRC (BB/I021213/1), the Excellence Initiative of Aix-Marseille University–A*MIDEX (a French 'Investissements d’Avenir' program), Universidad de Antioquia (CODI sostenibilidad de grupos 2013-2014 and MASO 2013-2014), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (Apoio a Núcleos de Excelência Program), Fundação de Aperfeiçoamento de Pessoal de Nível Superior, the National Institute of Dental and Craniofacial Research (R01-DE027023, U01-DE020078, R01-DE016148, and X01-HG007821), and a Santander Research and Scholarship Award. B.B. is supported by a doctoral scholarship from Ecole Doctorale 251 Aix-Marseille Université., ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, École pratique des hautes études (EPHE), Laboratorios de Investigación y Desarrollo (LID), Unit of Human Evolutionary Genetics, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Department of Genetics and Genome Sciences, University of Connecticut (UCONN), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, Department of Genetic Identification, Departamento de Tecnología Médica, Division of Vertebrates and Anthropology, Genética Molecular (GENMOL), Molecular Genetics Laboratory, National School of Anthropology and History, Department of Archaeogenetics [Jena] (DAG), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Forensic Science, Universidad Nacional Autónoma de México (UNAM), Unidad de Genomica de Poblaciones Aplicada a la Salud, Universidad Nacional Autónoma de México (UNAM)-Instituto Nacional de Medicina Genomica, Scientific Police of São Paulo State, Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Instituto Patagónico de Ciencias Sociales y Humanas, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Key Laboratory of Genomic and Precision Medicine [Beijing, China], Beijing Genomics Institute [Shenzhen] (BGI)-University of Chinese Academy of Sciences [Beijing] (UCAS), Center for Craniofacial and Dental Genetics, University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Department of Human Genetics, Department of Anthropology, Medical Research Council Integrative Epidemiology Unit, University of the West of England [Bristol] (UWE Bristol), School of Oral and Dental Sciences, Department of Twin Research & Genetic Epidemiology, King's College London, Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne-University of Melbourne, Department of Oral and Craniofacial Sciences, University of Missouri System-University of Missouri System, School of Mathematics and Statistics [Milton Keynes], Faculty of Science, Technology, Engineering and Mathematics [Milton Keynes], The Open University [Milton Keynes] (OU)-The Open University [Milton Keynes] (OU), State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-School of Life Sciences, Work leading to this publication was funded by grantsfrom the National Natural Science Foundation of China (#31771393), the Scientific andTechnology Committee of Shanghai Municipality (18490750300), the Ministry ofScience and Technology of China (2020YFE0201600), the Shanghai Municipal Scienceand Technology Major Project (2017SHZDZX01) and the 111 Project (B13016), theLeverhulme Trust (F/07 134/DF), BBSRC (BB/I021213/1), the Excellence Initiative ofAix-Marseille University–A*MIDEX (a French 'Investissements d’Avenir' program),Universidad de Antioquia (CODI sostenibilidad de grupos 2013-2014 and MASO 2013-2014), Conselho Nacional de Desenvolvimento Científico e Tecnológico,Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (Apoio a Núcleos deExcelência Program), Fundação de Aperfeiçoamento de Pessoal de Nível Superior, theNational Institute of Dental and Craniofacial Research (R01-DE027023, U01-DE020078,R01-DE016148, and X01-HG007821), and a Santander Research and Scholarship Award.B.B. is supported by a doctoral scholarship from Ecole Doctorale 251 Aix-MarseilleUniversité., and Genetic Identification

Subjects
haplotype, Latin Americans, [SDV]Life Sciences [q-bio], [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Vesicular Transport Proteins, Genome-wide association study, Genome-wide association studies, Regulatory sequences, purl.org/becyt/ford/1 [https], Mice, 0302 clinical medicine, Native Americans, single nucleotide polymorphism, GWAS, 10. No inequality, Two-dimensional profiles, Research Articles, Mammals, 0303 health sciences, Multidisciplinary, biology, adult, article, SciAdv r-articles, Genomic regions, Hispanic or Latino, craniofacial development, VPS13B, GENÉTICA, Phenotype, American Indian, regulatory sequence, HUMAN POPULATION, Research Article, Morphology, Latin americans, Genotype, animal experiment, introgression, Introgression, Polymorphism, Single Nucleotide, Homo denisovan, 03 medical and health sciences, male, Animals, Humans, controlled study, human, Craniofacial, Facial feature, purl.org/becyt/ford/1.6 [https], Denisovan, Gene, mouse, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, nonhuman, genome-wide association study, Haplotype, face, Human Genetics, Single nucleotide polymorphisms, biology.organism_classification, photography, thickness, purl.org/pe-repo/ocde/ford#3.01.02 [https], facies, DENOSIVAN HAPLOTYPE, Evolutionary biology, Anthropology, Face, 030217 neurology & neurosurgery, purl.org/pe-repo/ocde/ford#1.06.07 [https], Genome-Wide Association Study
Abstract

We carried out a genome-wide association study in Latin Americans and identified novel face morphology loci.., 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.

Published
2021

4. Diversity in immunogenomics: the value and the challenge

Author

Lluis Quintana-Murci, Clive M. Gray, Wei Zhang, Houda Alachkar, Serghei Mangul, Ricardo Fujita, Yana Safonova, Cathrine Scheepers, Purvesh Khatri, Carlos Bustamante, Alice B. Popejoy, K.O. Adekoya, Van Mai Cao-Lormeau, Kerui Peng, Malak Abedalthagafi, Petter Brodin, Oscar L. Rodriguez, Vanessa D. Jonsson, Macarena Fuentes-Guajardo, Felix Breden, Martin Corcoran, Rahaman A. Ahmed, Amanda M. Burkhardt, Yusuke Nakamura, Gur Yaari, Gunilla B. Karlsson Hedestam, Jianming Xie, Maura Rossetti, Victor Greiff, Darragh Duffy, Wei Chiao Chang, Corey T. Watson, Xiao Liu, Mikhail Shugay, William D. Lees, University of Southern California (USC), University of California [San Diego] (UC San Diego), University of California, University of Louisville, Russian Academy of Sciences [Moscow] (RAS), Pirogov Russian National Research Medical University [Moscow, Russia], Stanford University, Simon Fraser University (SFU.ca), Karolinska Institutet [Stockholm], Karolinska University Hospital [Stockholm], Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD), Immunologie Translationnelle - Translational Immunology lab, Institut Pasteur [Paris], Universidad de Tarapaca, Universidad de San Martín de Porres, University of Oslo (UiO), Beckman Research Institute [Duarte, CA], Tsinghua Shenzhen International Graduate School [Shenzhen], Tsinghua University [Beijing] (THU), Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Chaire Génomique humaine et évolution, Collège de France (CdF (institution)), University of California [Los Angeles] (UCLA), Bar-Ilan University [Israël], City University of Hong Kong [Hong Kong] (CUHK), King Abdulaziz City for Science and Technology [Riyadh], University of Lagos, Taipei Medical University, TMU-ShuangHo Hospital [New Taipei City], University of Cape Town, Groote Schuur Hospital, University of Cape Town, South Africa., Japanese Foundation for Cancer Research [Tokyo, Japan], Birkbeck College [University of London], National Institute for Communicable Diseases [Johannesburg] (NICD), University of the Witwatersrand [Johannesburg] (WITS), Y.S. was supported by the National Science Foundation EAGER award (no. 2032783). M.S. is supported by Ministry of Science and Higher Education of the Russian Federation grant no. 075-15-2020-807. A.B.P. and C.D.B. are supported by an award from the National Human Genome Research Institute of the National Institutes of Health (U41HG009649). C.T.W. and O.L.R. are supported in part by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award numbers R24AI138963 and R21AI142590. V.G. is supported by a UiO World-Leading Research Community grant, the UiO:LifeScience Convergence Environment Immunolingo, EU Horizon 2020 iReceptorplus (no. 825821) and a Research Council of Norway FRIPRO project (#300740). V.D.J. was supported by an award from the National Cancer Institute of the National Institutes of Health (K12CA001727). The laboratory of L.Q.-M. is supported by the Institut Pasteur, the Collège de France, the CNRS, the Fondation Allianz-Institut de France and the French Government’s Investissement d’Avenir program, Laboratoires d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID) and ‘Milieu Intérieur’ (ANR-10-LABX-69-01). R.A.A. is supported by the Fogarty International Center of the National Institute of Health under award number D43TW010934. P.K. is supported by the Bill and Melinda Gates Foundation (OPP1113682), National Institute of Allergy and Infectious Diseases (NIAID) (1U19AI109662, U19AI057229, 5R01AI125197), Department of Defense (W81XWH1910235) and Catalyst and Transformational Awards from the Dr. Ralph & Marian Falk Medical Research Trust. C.S. is supported by NIAID of the National Institutes of Health under award number U01AI136677. G.K.H is supported by a grant from the Swedish Research Council (award number 532 2017-00968). S.M. is partially supported by National Science Foundation grants 2041984., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), University of California (UC), Pirogov Russian National Research Medical University, Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Collège de France - Chaire Génomique humaine et évolution, and King Abdulaziz City for Science and Technology [Riyadh] (KACST)

Subjects
Value (ethics), T-Lymphocytes, media_common.quotation_subject, Receptors, Antigen, T-Cell, Receptors, Antigen, B-Cell, Biology, Biochemistry, Article, 03 medical and health sciences, Databases, Genetic, Immunogenetics, Humans, Quantitative Biology - Genomics, Molecular Biology, 030304 developmental biology, media_common, Genomics (q-bio.GN), B-Lymphocytes, 0303 health sciences, Whole Genome Sequencing, Genomics, Cell Biology, 3. Good health, Germ Cells, Evolutionary biology, FOS: Biological sciences, [SDV.IMM]Life Sciences [q-bio]/Immunology, Biotechnology, Diversity (politics)
Abstract

With the advent of high-throughput sequencing technologies, the fields of immunogenomics and adaptive immune receptor repertoire research are facing both opportunities and challenges. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become an increasingly important tool to characterize T and B cell responses in settings of interest. However, the majority of AIRR-seq studies conducted so far were performed in individuals of European ancestry, restricting the ability to identify variation in human adaptive immune responses across populations and limiting their applications. As AIRR-seq studies depend on the ability to assign VDJ sequence reads to the correct germline gene segments, efforts to characterize the genomic loci that encode adaptive immune receptor genes in different populations are urgently needed. The availability of comprehensive germline gene databases and further applications of AIRR-seq studies to individuals of non-European ancestry will substantially enhance our understanding of human adaptive immune responses, promote the development of effective diagnostics and treatments, and eventually advance precision medicine., 22 pages,1 table

Published
2021
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5. ABCB1/4 gallbladder cancer risk variants identified in India also show strong effects in Chileans

Author

Olga Barajas, Domingo Montalvo, Andrés Ruiz Linares, Monica Ahumada, Sergio Portiño, Carla Gallo, Macarena Fuentes Guajardo, Verónica Sanhueza, Francisco Rothhammer, Melanie Waldenberger, Lorena Gutiérrez, Gonzalo de Toro, Justo Lorenzo Bermejo, Maria Enriqueta Bertrán, María Teresa Rivera, Krista Fischer, Christine Fischer, Maria C. Bortolini, Rosa González Silos, Alejandro Ortega, Denisse Loader, Niina Eklund, Jordi Olloquequi, Elisabete Weiderpass, Katherine Marcelain, Mazda Jenab, Bettina Müller, Erik Morales, Pablo Baez Benavides, Krasimira Aleksandrova, G. Bedoya, Javier Retamales, Fernando Gabler, Armando Rojas, Dominique Scherer, Willem J R Bossers, Carol Barahona Ponce, Tahereh Moradi, Felix Boekstegers, Loreto Spencer, Uwe Völker, Kristian Hveem, Samuel Canizales, Verena Katzke, Giuliano Bernal, Rolando González-José, Hermann Brenner, State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-School of Life Sciences, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), and Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, Cancer Research, Epidemiology, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Ethnic group, purl.org/pe-repo/ocde/ford#3.03.09 [https], 0302 clinical medicine, purl.org/pe-repo/ocde/ford#3.02.21 [https], Epidemiology of cancer, Genotype, Medicine, Prospective Studies, 030212 general & internal medicine, Chile, ComputingMilieux_MISCELLANEOUS, Aged, 80 and over, education.field_of_study, Incidence (epidemiology), purl.org/becyt/ford/3.1 [https], Middle Aged, 3. Good health, Europe, Gallbladder Cancer, Population-specific Risk Marker, Cancer Epidemiology, Native American Ancestry, Oncology, 030220 oncology & carcinogenesis, Cohort, purl.org/becyt/ford/3 [https], Female, Gallbladder Neoplasms, Adult, ATP Binding Cassette Transporter, Subfamily B, Population, Population-specific risk marker, Polymorphism, Single Nucleotide, White People, Native American ancestry, 03 medical and health sciences, Cancer epidemiology, Humans, Genetic Predisposition to Disease, Gallbladder cancer, education, Genetic Association Studies, Aged, Retrospective Studies, business.industry, Indians, South American, Odds ratio, medicine.disease, Case-Control Studies, business, Demography
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. Fil: Boekstegers, Felix. Ruprecht Karls Universitat Heidelberg; Alemania Fil: Marcelain, Katherine. Universidad de Chile; Chile Fil: Barahona Ponce, Carol. Ruprecht Karls Universitat Heidelberg; Alemania. Universidad de Chile; Chile Fil: Baez Benavides, Pablo F.. Universidad de Chile; Chile Fil: Müller, Bettina. Instituto Nacional del Cáncer, Chile; Chile Fil: de Toro, Gonzalo. Hospital Puerto Montt; Chile Fil: Retamales, Javier. Instituto Nacional del Cáncer, Chile; Chile Fil: Barajas, Olga. Hospital Clinico de la Universidad de Chile; Chile. Universidad de Chile; Chile Fil: Ahumada, Monica. Hospital Clínico de la Universidad de Chile; Chile. Universidad de Chile; Chile Fil: Morales, Erik. Regional Hospital; Chile Fil: Rojas, Armando. Universidad Catolica de Maule; Chile Fil: Sanhueza, Verónica. Hospital Padre Hurtado; Chile Fil: Loader, Denisse. Hospital Padre Hurtado; Chile Fil: Rivera, María Teresa. Hospital del Salvador; Chile Fil: Gutiérrez, Lorena. Hospital San Juan de Dios, Santiago de Chile; Chile Fil: Bernal, Giuliano. Universidad Católica del Norte; Chile Fil: Ortega, Alejandro. Hospital Regional, Arica; Chile Fil: Montalvo, Domingo. Hospital Regional de Arica Doctor Juan Noé Crevani; Chile Fil: Portiño, Sergio. Hospital Clinico de la Universidad de Chile; Chile Fil: Bertrán, Maria Enriqueta. Ministerio de Salud, Valdivia; Chile Fil: Gabler, Fernando. Universidad de Santiago de Chile. Hospital Clinico San Borja Arriaran; Chile Fil: Spencer, Loreto. Hospital Regional de Concepción - Dr. Guillermo Grant Benavente; Chile Fil: Olloquequi, Jordi. Universidad Autónoma de Chile; Chile Fil: González Silos, Rosa. Ruprecht Karls Universitat Heidelberg; Alemania Fil: Fischer, Christine. Ruprecht Karls Universitat Heidelberg; Alemania Fil: Scherer, Dominique. Ruprecht Karls Universitat Heidelberg; Alemania Fil: Jenab, Mazda. International Agency for Research on Cancer; Francia Fil: Aleksandrova, Krasimira. Universitat Potsdam; Alemania Fil: Katzke, Verena. German Cancer Research Center; Alemania Fil: Gonzalez-jose, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Weiderpass, Elisabete. International Agency for Research on Cancer; Francia Fil: Moradi, Tahereh. Karolinska Huddinge Hospital. Karolinska Institutet; Suecia Fil: Fischer, Krista. University of Tartu; Estonia Fil: Bossers, Willem. Lifelines Cohort Study; Países Bajos Fil: Brenner, Hermann. German Cancer Research Center; Alemania Fil: Hveem, Kristian. Norges Teknisk naturvitenskapelige Universitet; Noruega Fil: Eklund, Niina. National Institute For Health And Welfare; Finlandia Fil: Völker, Uwe. Universitätsmedizin Greifswald; Alemania Fil: Waldenberger, Melanie. Helmholtz Center Munich German Research Center For Environmental Health; Alemania Fil: Fuentes Guajardo, Macarena. Universidad de Tarapaca.; Chile Fil: Bedoya, Gabriel. Universidad de Antioquia; Colombia Fil: Bortolini, Maria C.. Universidade Federal do Rio Grande do Sul; Brasil Fil: Canizales, Samuel. Universidad Nacional Autónoma de México; México Fil: Gallo, Carla. Universidad Peruana Cayetano Heredia; Perú Fil: Ruiz Linares, Andres. Fudan University; China Fil: Rothhammer, Francisco. Universidad de Tarapaca.; Chile Fil: Lorenzo Bermejo, Justo. Ruprecht Karls Universitat Heidelberg; Alemania

Published
2020

6. Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance

Author

Juan C. Chacon-Duque, Hugo Villamil-Ramírez, Giovanni Poletti, Samuel Canizales-Quinteros, Mirsha Quinto-Sánchez, Maria Cátira Bortolini, Maria-Laura Parolin, Macarena Fuentes-Guajardo, Francisco Rothhammer, Rolando González-José, Valeria Villegas, Francisco Mauro Salzano, Javier Mendoza-Revilla, Verónica Gomes, Caio Cesar Silva de Cerqueira, Cheryl A. Winkler, José R. Sandoval, Carla Gallo, Elena Llop, Rosenda I. Peñaloza-Espinosa, Vanessa Granja, Daniel Corach, Lavinia Schuler-Faccini, Yali Xue, Garrett Hellenthal, Mercedes Villena, Virginia Ramallo, Victor Acuña-Alonzo, Gabriel Bedoya, Paola Everardo Martínez, Karla Sandoval, Andres Ruiz-Linares, David J. Balding, Claudio M. Bravi, Pedro Moral, Jean-Michel Dugoujon, Tábita Hünemeier, António Amorim, Malena Hurtado, Kaustubh Adhikari, René Vasquez, Julio Molina, Leonor Gusmão, Ramiro Barrantes, Carlos Resende, Jorge Gómez-Valdés, Alberto Salazar-Granara, Héctor Rangel-Villalobos, William Klitz, Rodrigo Barquera, Molecular Genetics Laboratory, Escuela Nacional de Antropologia y Historia, Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Instituto Boliviano de Biologıa de la Altura, Universidad Autonoma Tomas Frias, Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, School of Human Evolution and Social Change, Arizona State University [Tempe] (ASU), Instituto Multidisciplinario de Biología Celular [La Plata] (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional de la Plata [Argentine] (UNLP)-Comisión de Investigaciones Científicas [Buenos Aires] (CIC), Centro de Investigaciones Biomédicas de Guatemala, Servicio de Huellas Digitales Genéticas [Buenos Aires], Facultad de Farmacia y Bioquímica [Buenos Aires] (FFYB), Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA), Escuela de Biologia, Universidad Nacional de Costa Rica, Population Genetics, Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Universidade de Lisboa (ULISBOA), Human Evolution, The Wellcome Trust Sanger Institute [Cambridge], Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Barcelona, Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], University College of London [London] (UCL), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Instituto de Investigação e Inovação em Saúde, Universidade de Lisboa = University of Lisbon (ULISBOA), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
haplotype, Latin Americans, Biología, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, purl.org/pe-repo/ocde/ford#1.03.00 [https], Human physical appearance, Colonialism, migration, CONVERSO JEWS, purl.org/becyt/ford/1 [https], Genética y Herencia, 0302 clinical medicine, genetics, Nose / anatomy & histology, East mediterranean, lcsh:Science, 0303 health sciences, Genealogy, Geography, Indians, South American / genetics, American Indian, Genetic structure, CIENCIAS NATURALES Y EXACTAS, Latin americans, Science, purl.org/pe-repo/ocde/ford#1.06.03 [https], Human Migration, Nose, Article, Ciencias Biológicas, 03 medical and health sciences, Indians, North American / genetics, parasitic diseases, Humans, human, purl.org/becyt/ford/1.6 [https], Mexico, Historical record, 030304 developmental biology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Indians, South American, ANCESTRY INFORMATIVE, Environmental adaptation, South America, Converso jews, LATIN AMERICANS, Haplotypes, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Ancestry informative, purl.org/pe-repo/ocde/ford#1.04.00 [https], Indians, North American, lcsh:Q, 030217 neurology & neurosurgery, anatomy and histology
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., Latin Americans trace their ancestry to the admixture of Native Americans, Europeans and Sub-Saharan Africans. Here, the authors develop a novel haplotype-based approach and analyse over 6,500 Latin Americans to infer the geographically-detailed genetic structure of this population.

Published
2018

7. Developmental pathways inferred from modularity, morphological integration and fuctuating asymmetry patterns in the human face

Author

Virginia Ramallo, Andres Ruiz-Linares, Williams Arias, Francisco Rothhammer, Rolando González-José, Javier Rosique, Carolina Paschetta, Paola Everardo, Victor Acuña-Alonzo, Soledad de Azevedo, Jorge Gómez-Valdés, Samuel Canizales-Quinteros, Mirsha Quinto-Sánchez, Francesc Muñoz-Muñoz, Francisco de Avila, G. Poletti, Pablo E. Navarro, Claudia Jaramillo, Caio Cesar Silva de Cerqueira, Celia Cintas, Kaustubh Adhikari, Macarena Fuentes-Guajardo, Gabriel Bedoya, Maria Cátira Bortolini, Carla Gallo, Tábita Hünemeier, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-School of Life Sciences, Molecular Genetics Laboratory, Escuela Nacional de Antropologia y Historia, Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, and Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)

Subjects
Male, 0301 basic medicine, Developmental noise, [SDV]Life Sciences [q-bio], Biological anthropology, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, lcsh:Medicine, Genome-wide association study, Evolutionary biology, Fluctuating asymmetry, HUMAN FACE, purl.org/becyt/ford/1 [https], 0302 clinical medicine, FLUCTUATING ASYMMETRY, lcsh:Science, Maxillofacial Development, purl.org/pe-repo/ocde/ford#1.06.15 [https], ComputingMilieux_MISCELLANEOUS, Multidisciplinary, Middle Aged, Phenotype, Female, CIENCIAS NATURALES Y EXACTAS, GEOMETRIC MORPHOMETRIC, Adult, Rostro humano, Adolescent, Otras Ciencias Biológicas, Biology, GENOMAS, Article, Ciencias Biológicas, Young Adult, 03 medical and health sciences, Humans, Set (psychology), purl.org/becyt/ford/1.6 [https], Modularity (networks), Modularidad, lcsh:R, Quantitative genetics, Antropología biológica, Genetic architecture, LATIN AMERICANS, Latin America, 030104 developmental biology, Face, Evolutionary developmental biology, lcsh:Q, 030217 neurology & neurosurgery, Genome-Wide Association Study
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. Fil: Quinto Sanchez, Mirsha Emmanuel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Muñoz-Muñoz, Francesc. Universidad Nacional Autónoma de México; México Fil: Gomez-Valdes, Jorge. Universitat Autònoma de Barcelona; España Fil: Cintas, Celia. Instituto Nacional de Antropologia E Historia, Mexico; México Fil: Navarro, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Cerqueira, Caio Cesar Silva De. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Paschetta, Carolina Andrea. Equipe de Perícias Criminalísticas de Ourinhos; Fil: de Azevedo, Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Acuña-Alonzo, Victor. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Adhikari, Kaustubh. Colegio Universitario de Londres; Reino Unido Fil: Fuentes-Guajardo, MacArena. Instituto Nacional de Antropologia E Historia, Mexico; México Fil: Hünemeier, Tábita. Colegio Universitario de Londres; Reino Unido Fil: Everardo, Paola. Universidad de Tarapaca de Arica; Chile Fil: De Avila, Francisco. Colegio Universitario de Londres; Reino Unido Fil: Jaramillo, Claudia. Universidade de Sao Paulo; Brasil Fil: Arias, Williams. Instituto Nacional de Antropologia E Historia, Mexico; México Fil: Gallo, Carla. Universidad Nacional Autónoma de México; México Fil: Poletti, Giovani. Instituto Nacional de Antropologia E Historia, Mexico; México Fil: Bedoya Berrío, Gabriel. Universidad de Antioquia; Colombia Fil: Bortolini, Maria Catira. Universidad de Antioquia; Colombia Fil: Canizales-Quinteros, Samuel. Universidad Peruana Cayetano Heredia; Perú Fil: Rothhammer, Francisco. Universidad Peruana Cayetano Heredia; Perú Fil: Rosique, Javier. Universidad de Antioquia; Colombia Fil: Ruiz-Linares, Andres. Universidade Federal do Rio Grande do Sul; Brasil Fil: González José, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina

Published
2018

8. The Genetic Diversity of the Americas

Author

Andres Ruiz-Linares, Macarena Fuentes-Guajardo, Javier Mendoza-Revilla, Juan Camilo Chacón-Duque, Kaustubh Adhikari, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), and Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Male, Range (biology), Demographic history, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Black People, White People, 03 medical and health sciences, European colonialism, Native Americans, Genetic variation, Genetics, Humans, European Continental Ancestry Group/genetics, Molecular Biology, Genetics (clinical), American Indian or Alaska Native, ComputingMilieux_MISCELLANEOUS, Demography, Western hemisphere, Genetic diversity, American Native Continental Ancestry Group/genetics, History of the Americas, Genetic data, African Continental Ancestry Group/genetics, Genetic Variation, demographic history, purl.org/pe-repo/ocde/ford#3.01.02 [https], 030104 developmental biology, Geography, Genetics, Population, Ethnology, admixture, Female, African slavery, Americas
Abstract

The history of the Americas involved the encounter of millions of Native Americans, Europeans, and Africans. A variable admixture of these three continental groups has taken place throughout the continent, influenced by demography and a range of social factors. This variable admixture has had a major influence on the genetic makeup of populations across the continent. Here, we summarize the demographic history of the region, highlight some social factors that affected historical admixture, and review major patterns of ancestry across the Western Hemisphere based on genetic data.

Published
2017

9. Admixture in Latin America

Author

Andres Ruiz-Linares, Juan Camilo Chacón-Duque, Kaustubh Adhikari, Macarena Fuentes-Guajardo, and Javier Mendoza-Revilla

Subjects
0301 basic medicine, Natural experiment, Latin Americans, Demographic history, media_common.quotation_subject, Human Migration, Population, Black People, Biology, White People, 03 medical and health sciences, Genetics, Humans, education, media_common, Genetic association, History, 15th Century, education.field_of_study, Human migration, business.industry, Genome, Human, Genealogy, Genetic architecture, 030104 developmental biology, Genetics, Population, Latin America, History, 16th Century, business, Developmental Biology, Diversity (politics)
Abstract

Latin Americans arguably represent the largest recently admixed populations in the world. This reflects a history of massive settlement by immigrants (mostly Europeans and Africans) and their variable admixture with Natives, starting in 1492. This process resulted in the population of Latin America showing an extensive genetic and phenotypic diversity. Here we review how genetic analyses are being applied to examine the demographic history of this population, including patterns of mating, population structure and ancestry. The admixture history of Latin America, and the resulting extensive diversity of the region, represents a natural experiment offering an advantageous setting for genetic association studies. We review how recent analyses in Latin Americans are contributing to elucidating the genetic architecture of human complex traits.

Published
2016

10. Inbreeding, Native American ancestry and child mortality: linking human selection and paediatric medicine

Author

Felix Boekstegers, Maria Cátira Bortolini, Carla Gallo, Andrés Ruiz Linares, James F. Wilson, Victor Acuña-Alonzo, Rolando González-José, Francisco Rothhammer, Justo Lorenzo Bermejo, Macarena Fuentes-Guajardo, Gabriel Bedoya, and Fabienne Koenigstein

Subjects
Runs of Homozygosity, child mortality, purl.org/becyt/ford/1 [https], 0302 clinical medicine, newborn, congenital abnormality, Genotype, Inbreeding, Child, Genetics (clinical), 2. Zero hunger, 0303 health sciences, child, LATINOAMERICA, chile, General Medicine, 3. Good health, fetus, 030220 oncology & carcinogenesis, Child Mortality, Gestation, pregnancy, medicine.symptom, hemorrhage, genotype|homozygote, anencephaly, pediatrics, native americans, inbreeding, Hemorrhage, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, low birth weight infant, Anencephaly, Genetics, medicine, Humans, POBLACIONES MESTIZAS, purl.org/becyt/ford/1.6 [https], Molecular Biology, genome, American Indian or Alaska Native, 030304 developmental biology, death of child, trisomy, Infant, Newborn, GENOMICA, medicine.disease, mortality, Child mortality, Low birth weight, parent, heterogeneity, Trisomy, Demography
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 newborn (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. Fil: Koenigstein, Fabienne. Ruprecht Karls Universitat Heidelberg; Alemania Fil: Boekstegers, Felix. Ruprecht Karls Universitat Heidelberg; Alemania Fil: Wilson, James F.. University of Edinburgh; Reino Unido Fil: Fuentes Guajardo, Macarena. Universidad de Tarapacá; Chile Fil: Gonzalez-Jose, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Bedoya Berrío, Gabriel. Universidad de Antioquia; Colombia Fil: Bortolini, Maria Cátira. Universidade Federal do Rio Grande do Sul; Brasil Fil: Acuña Alonzo, Victor. Instituto Nacional de Antropología e Historia. Escuela Nacional de Antropología e Historia; México Fil: Gallo, Carla. Universidad Peruana Cayetano Heredia; Perú Fil: Ruiz-Linares, Andres. Fudan University; China. Aix-Marseille Université; Francia. Centre National de la Recherche Scientifique; Francia. University College London; Reino Unido Fil: Rothhammer, Francisco. Universidad de Tarapaca. Instituto de Alta Investigación; Chile Fil: Lorenzo Bermejo, Justo. Ruprecht Karls Universitat Heidelberg; Alemania

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