Genomic ancestry and ethnoracial self-classification based on 5,871 community-dwelling Brazilians (The Epigen Initiative)

Barreto, Mauricio Lima “Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta à informação no documento”. Cibele C. Cesar1, Jackson S. Conceição2, Gustavo N.O. Costa2, Nubia Esteban3, Rosemeire L. Fiaccone2, Camila A. Figueiredo2, Josélia O.A. Firmo4, Andrea R.V.R. Horimoto3, Thiago P. Leal5, Moara Machado5, Wagner C.S. Magalhães5, Isabel Oliveira de Oliveira3, Sérgio V. Peixoto4, Maíra R. Rodrigues, Hadassa C. Santos3 & Thiago M. Silva2 1Universidade Federal de MinasGerais, Instituto de Ciências Exatas, Belo Horizonte, Brazil, 2Universidade Federal da Bahia, Instituto de Saúde Coletiva, Salvador, Brazil, 3Universidade de São Paulo, Instituto do Coração, São Paulo, Brazil, 4Fundação Oswaldo Cruz, Instituto de Pesquisas Rene Rachou, Belo Horizonte, Brazil, 5Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, BrazilSubmitted by Ana Maria Fiscina Sampaio ([email protected]) on 2017-08-01T13:53:30Z No. of bitstreams: 1 Costa MFL Genomic ancestry....pdf: 480721 bytes, checksum: 23b31e00169b8c01cc95b6c11b0343b1 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2017-08-01T14:24:30Z (GMT) No. of bitstreams: 1 Costa MFL Genomic ancestry....pdf: 480721 bytes, checksum: 23b31e00169b8c01cc95b6c11b0343b1 (MD5)Made available in DSpace on 2017-08-01T14:24:30Z (GMT). No. of bitstreams: 1 Costa MFL Genomic ancestry....pdf: 480721 bytes, checksum: 23b31e00169b8c01cc95b6c11b0343b1 (MD5) Previous issue date: 2015Department of Science and Technology (DECIT,Ministry of Health) and National Fund for Scientific and Technological Development (FNDCT, Ministry of Science and Technology), Funding of Studies and Projects (FINEP, Ministry of Science and Technology, Brazil), Coordination of Improvement of Higher Education Personnel (CAPES, Ministry of Education, Brazil). MFLC, MLB, BLH, ACP, CGV, ETS, CBC, JOAF and SVP are supported by the Brazilian National Research Council (CNPq).Fundação Oswaldo Cruz. Instituto de Pesquisas Rene Rachou. Belo Horizonte, MG, BrasilLondon School of Hygiene and Tropical Medicine. Department of Infectious Disease Epidemiology. London, UKUniversidade Federal da Bahia. Instituto de Saúde Coletiva. Salvador, BA, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Belo Horizonte, MG, BrasilUniversidade Federal de Pelotas. Programa de Pós Graduação em Epidemiologia. Pelotas, RS, BrasilFundação Oswaldo Cruz. Instituto de Pesquisas Rene Rachou. Belo Horizonte, MG, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Belo Horizonte, MG, BrasilUniversidade de São Paulo. Instituto doCoração. São Paulo, SP, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Belo Horizonte, MG, BrasilUniversidade Federal de Pelotas. Programa de Pós Graduação em Epidemiologia. Pelotas, RS, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Belo Horizonte, MG, BrasilMúltipla – ver em NotasBrazil never had segregation laws defining membership of an ethnoracial group. Thus, the composition of the Brazilian population is mixed, and its ethnoracial classification is complex. Previous studies showed conflicting results on the correlation between genome ancestry and ethnoracial classification in Brazilians. We used 370,539 Single Nucleotide Polymorphisms to quantify this correlation in 5,851 community-dwelling individuals in the South (Pelotas), Southeast (Bambui) and Northeast (Salvador) Brazil. European ancestry was predominant in Pelotas and Bambui (median = 85.3% and 83.8%, respectively). African ancestry was highest in Salvador (median = 50.5%). The strength of the association between the phenotype and median proportion of African ancestry varied largely across populations, with pseudo R(2) values of 0.50 in Pelotas, 0.22 in Bambui and 0.13 in Salvador. The continuous proportion of African genomic ancestry showed a significant S-shape positive association with self-reported Blacks in the three sites, and the reverse trend was found for self reported Whites, with most consistent classifications in the extremes of the high and low proportion of African ancestry. In self-classified Mixed individuals, the predicted probability of having African ancestry was bell-shaped. Our results support the view that ethnoracial self-classification is affected by both genome ancestry and non-biological factors

A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set

Barreto, Mauricio Lima “Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta à informação no documento”.Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2017-08-07T12:22:48Z No. of bitstreams: 1 Santos HC A minimum set....pdf: 1062773 bytes, checksum: 9434fea963814081a138b951934c70aa (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2017-08-07T13:32:45Z (GMT) No. of bitstreams: 1 Santos HC A minimum set....pdf: 1062773 bytes, checksum: 9434fea963814081a138b951934c70aa (MD5)Made available in DSpace on 2017-08-07T13:32:45Z (GMT). No. of bitstreams: 1 Santos HC A minimum set....pdf: 1062773 bytes, checksum: 9434fea963814081a138b951934c70aa (MD5) Previous issue date: 2016Department of Science and Technology (DECIT/ SCTIE) and National Fund for Scientific and Technological Development (FNDCT), Ministry of Health, Brazil; Funding of Studies and Projects (FINEP), Ministry of Science and Technology, Brazil; Coordination of Improvement of Higher Education Personnel (CAPES), Ministry of Education, Brazil. HCS is supported by a grant from the São Paulo Research Foundation (FAPESP).Medical School of University of São Paulo. Heart Institute. Laboratory of Genetics and Molecular Cardiology. São Paulo, SP, BrazilMedical School of University of São Paulo. Heart Institute. Laboratory of Genetics and Molecular Cardiology. São Paulo, SP, BrazilFederal University of Minas Gerais. General Biology Department. Belo Horizonte, MG, BrazilFederal University of Minas Gerais. General Biology Department. Belo Horizonte, MG, BrazilFederal University of Bahia. Institute of Public Health. Salvador, BA, BrazilFederal University of Pelotas. Porto Alegre, RGS, BrazilOswaldo Cruz Foundation. Rene Rachou Research Institute. Belo Horizonte, MG, BrazilFederal University of Minas Gerais. General Biology Department. Belo Horizonte, MG, BrazilFederal University of Minas Gerais. General Biology Department. Belo Horizonte, MG, BrazilFederal University of Bahia. Institute of Public Health. Salvador, BA, BrazilMedical School of University of São Paulo. Heart Institute. Laboratory of Genetics and Molecular Cardiology. São Paulo, SP, BrazilMedical School of University of São Paulo. Heart Institute. Laboratory of Genetics and Molecular Cardiology. São Paulo, SP, BrazilFederal University of Minas Gerais. General Biology Department. Belo Horizonte, MG, BrazilFederal University of Minas Gerais. General Biology Department. Belo Horizonte, MG, BrazilFederal University of Minas Gerais. General Biology Department. Belo Horizonte, MG, BrazilMedical School of University of São Paulo. Heart Institute. Laboratory of Genetics and Molecular Cardiology. São Paulo, SP, BrazilThe Brazilian EPIGEN Project ConsortiumThe Brazilian population is considered to be highly admixed. The main contributing ancestral populations were European and African, with Amerindians contributing to a lesser extent. The aims of this study were to provide a resource for determining and quantifying individual continental ancestry using the smallest number of SNPs possible, thus allowing for a cost- and time-efficient strategy for genomic ancestry determination. We identified and validated a minimum set of 192 ancestry informative markers (AIMs) for the genetic ancestry determination of Brazilian populations. These markers were selected on the basis of their distribution throughout the human genome, and their capacity of being genotyped on widely available commercial platforms. We analyzed genotyping data from 6487 individuals belonging to three Brazilian cohorts. Estimates of individual admixture using this 192 AIM panels were highly correlated with estimates using ~370 000 genome-wide SNPs: 91%, 92%, and 74% of, respectively, African, European, and Native American ancestry components. Besides that, 192 AIMs are well distributed among populations from these ancestral continents, allowing greater freedom in future studies with this panel regarding the choice of reference populations. We also observed that genetic ancestry inferred by AIMs provides similar association results to the one obtained using ancestry inferred by genomic data (370 K SNPs) in a simple regression model with rs1426654, related to skin pigmentation, genotypes as dependent variable. In conclusion, these markers can be used to identify and accurately quantify ancestry of Latin Americans or US Hispanics/Latino individuals, in particular in the context of fine-mapping strategies that require the quantification of continental ancestry in thousands of individuals

Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations

Submitted by Nuzia Santos ([email protected]) on 2016-02-19T13:11:37Z No. of bitstreams: 1 Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations..pdf: 501572 bytes, checksum: 45f5ed2fc0a7c2cb73e047a75457edae (MD5)Approved for entry into archive by Nuzia Santos ([email protected]) on 2016-02-19T13:37:09Z (GMT) No. of bitstreams: 1 Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations..pdf: 501572 bytes, checksum: 45f5ed2fc0a7c2cb73e047a75457edae (MD5)Made available in DSpace on 2016-02-19T13:37:09Z (GMT). No. of bitstreams: 1 Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations..pdf: 501572 bytes, checksum: 45f5ed2fc0a7c2cb73e047a75457edae (MD5) Previous issue date: 2015Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade de São Paulo. Instituto do Coração. São Paulo, SP, BrasilUniversidade Federal de Pelotas. Programa de Pós-Graduação em Epidemiologia. Pelotas, RS, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade de São Paulo. Instituto do Coração. São Paulo, SP, BrasilUniversidade de São Paulo. Instituto do Coração. São Paulo, SP, BrasilUniversidade Federal da Bahia. Instituto de Matemática. Departamento de Estatística. Salvador, Bahia, BrasilUniversidade Federal da Bahia. Instituto de Ciências da Saúde. Departamento de Ciências da Biointeração. Salvador, Bahia, BrasilUniversidade Federal da Bahia. Instituto de Saúde Coletiva. Salvador, BA, BrasilUniversidade Federal da Bahia. Instituto de Saúde Coletiva. Salvador, BA, BrasilUniversity of Leicester. Department of Genetics. Leicester, United KingdomWashington University School of Medicine. Department of Molecular Microbiology. St. Louis, MO/University of California. Department of Medicine. San Diego, CAAsociación Benéfica Proyectos en Informática, Salud, Medicina y Agricultura. Biomedical Research Unit. Lima, PeruUniversidade Federal de Santa Catarina. Embriologia e Genética. Departamento de Biologia Celular. Florianópolis, SC, BrasilUniversidade Federal de Minas Gerais. Departamento de Estatística. Belo Horizonte, MG, BrasilUniversità di Ferrara. Dipartimento di Scienze della Vita e Biotecnologie. Ferrara, ItalyJohns Hopkins University. International Health. Bloomberg School of Public Health. Baltimore, MD, USA/Universidade Peruana Cayetano Heredia. Laboratorio de Investigación de Enfermedades Infecciosas. Lima, PeruUniversity of Toronto. Center for Addiction and Mental Health. Department of Psychiatry and Neuroscience Section. Toronto, ON, CanadaUniversidade Federal de Santa Catarina. Embriologia e Genética. Departamento de Biologia Celular. Florianópolis, SC, BrasilUniversidade Federal de Santa Catarina. Embriologia e Genética. Departamento de Biologia Celular. Florianópolis, SC, BrasilInnsbruck Medical University. Molecular and Clinical Pharmacology. Department of Medical Genetics. Division of Genetic Epidemiology. Innsbruck, AustriaFrederick National Laboratory for Cancer Research. Leidos Biomedical Research. Cancer Genomics Research Laboratory. Frederick, MDLondon School of Hygiene and Tropical Medicine. Faculty of Epidemiology. Department of Infectious Disease Epidemiology. London, United KingdomUniversidade Federal da Bahia. Instituto de Saúde Coletiva. Salvador, BA, BrasilFundação Oswaldo Cruz. Instituto de Pesquisa Rene Rachou. Belo Horizonte, MG, BrasilUniversidade de São Paulo. Instituto do Coração. São Paulo, SP, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, BrasilUniversidade Federal da Bahia. Instituto de Ciências da Saúde. Departamento de Ciências da Biointeração. Salvador, BA, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, Brasil.Universidade Federal de Minas Gerais. Laboratório de Computação Científica. Belo Horizonte, MG, Brasil.Universidade Federal da Bahia. Instituto de Saúde Coletiva. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto de Pesquisa Rene Rachou. Belo Horizonte, MG, Brasil.Universidade Federal de Pelotas. Programa de Pós-Graduação em Epidemiologia. Pelotas, RS, Brasil.Universidade Federal de Rio Grande do Sul. Centro Nacional de Supercomputação. Porto Alegre, RS, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, Brasil.Fundação Oswaldo Cruz. Instituto de Pesquisa Rene Rachou. Grupo de Genômica e Biologia Computacional. Belo Horizonte, MG, Brasil.Universidade Federal de Pelotas. Programa de Pós-Graduação em Epidemiologia. Pelotas, RS, Brasil.Fundação Oswaldo Cruz. Instituto de Pesquisa Rene Rachou. Belo Horizonte, MG, Brasil.Fundação Oswaldo Cruz. Instituto de Pesquisa Rene Rachou. Belo Horizonte, MG, Brasil.Universidade Federal de Minas Gerais. Laboratório de Computação Científica. Belo Horizonte, MG, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, Brasil.Universidade Federal da Bahia. Instituto de Saúde Coletiva. Salvador, BA, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Biologia Geral. Belo Horizonte, MG, Brasil.While South Americans are underrepresented in human genomic diversity studies, Brazil has been a classical model for population genetics studies on admixture.We present the results of the EPIGEN Brazil Initiative, the most comprehensive up-to-date genomic analysis of any Latin-American population. A population-based genomewide analysis of 6,487 individuals was performed in the context of worldwide genomic diversity to elucidate how ancestry, kinship, and inbreeding interact in three populations with different histories from the Northeast (African ancestry: 50%), Southeast, and South (both with European ancestry >70%) of Brazil. We showed that ancestry-positive assortative mating permeated Brazilian history. We traced European ancestry in the Southeast/South to a wider European/Middle Eastern region with respect to the Northeast, where ancestry seems restricted to Iberia. By developing an approximate Bayesian computation framework, we infer more recent European immigration to the Southeast/South than to the Northeast. Also, the observed low Native-American ancestry (6–8%) was mostly introduced in different regions of Brazil soon after the European Conquest. We broadened our understanding of the African diaspora, the major destination of which was Brazil, by revealing that Brazilians display two within-Africa ancestry components: one associated with non-Bantu/western Africans (more evident in the Northeast and African Americans) and one associated with Bantu/eastern Africans (more present in the Southeast/South). Furthermore, the whole-genome analysis of 30 individuals (42-fold deep coverage) shows that continental admixture rather than local post-Columbian history is the main and complex determinant of the individual amount of deleterious genotypes

Taller de Proyecto II - SI646 - 202102

Descripción: El curso de especialidad de Taller de Proyecto II, de las carreras de Ciencias de la Computación (CC), Ingeniería de Software (ISW) e Ingeniería de Sistemas de Información (ISI), es de carácter teórico-práctico y está dirigido a los estudiantes del décimo ciclo. El curso busca desarrollar las competencias generales de comunicación oral y escrita, manejo de la información, ciudadanía y pensamiento innovador. Para CC, las competencias específicas que se desarrollan en el curso son: trabajo en equipos multidisciplinarios, responsabilidad ética y profesional, comunicación efectiva, análisis del impacto de la solución de ingeniería, necesidad de aprendizaje de por vida, aplicación de fundamentos matemáticos, diseño y construcción de sistemas complejos. Propósito: Este curso es importante dentro de la formación de los estudiantes pues permite la aplicación directa de todos los conocimientos adquiridos en ciclos anteriores; es el segundo taller a través de los cuales los estudiantes conjuntamente con los profesores involucrados en los cursos realizan el desarrollo de un Proyecto Profesional final. El taller se desarrolla bajo la aplicación de trabajos por roles. Los estudiantes desempeñan una serie de roles para el análisis, diseño, implementación y producción de un sistema de información que permite ejemplificar muy cercano a la realidad, el trabajo profesional que desarrollarán los futuros egresados. Contribuye con el desarrollo de las competencias generales de comunicación oral, pensamiento crítico, razonamiento cuantitativo, pensamiento innovador a nivel de logro 3 y ciudadanía a nivel de logro 2. Así como las competencias específicas (3) Comunicacicón Efectiva; (4) Responsabilidad ética y profesional; (5) Trabajo en equipos multidisciplinarios; (6) Aprendizaje contínuo y autónomo para la carrera de Ciencias de la Computación. Así como las competencias específicas (3) Comunicacicón Efectiva; (4) Responsabilidad ética y profesional; (5) Trabajo en equipos multidisciplinarios; (6) Análisis y emisión de conclusiones; (7) Aprendizaje contínuo y autónomo para las carreras de Ingeniería de Sistemas de Información e Ingeniería de Software