Targeted next-generation sequencing of glandular odontogenic cyst: a preliminary study

Glandular odontogenic cyst (GOC) is an uncommon developmental cyst. Its molecular pathogenesis is unclear, and deep sequencing may help identify causative low-frequency variants in tumors. We investigated in GOC mutations in 50 genes commonly altered in human cancers. Study Design Targeted next-generation sequencing was used to interrogate a panel of approximately 2800 mutations in GOC. Results Six missense single nucleotide variations (SNVs) were reported. Three SNVs (TP53 rs1042522, KDR rs1870377, and KIT rs3822214) are listed as “common single-nucleotide polymorphisms” at the UCSC Genome Browser. The other SNVs (PIK3CA p.Glu689Lys, PIK3CA p.Ala708Thr, and TP53 p.Leu289Phe) are predicted to have deleterious or damaging effects on proteins, but they showed very low frequency in our samples and could not be further validated by orthogonal methods. Conclusions No pathogenic SNV was detected in this cohort of GOCs. Further studies with larger gene panels or whole exome sequencing are needed to find the genetic basis of GOC1245490494CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE MINAS GERAIS - FAPEMIGSem informaçãoSem informaçã

Monitoring the Establishment of VOC Gamma in Minas Gerais, Brazil: A Retrospective Epidemiological and Genomic Surveillance Study

Since its first identification in Brazil, the variant of concern (VOC) Gamma has been associated with increased infection and transmission rates, hospitalizations, and deaths. Minas Gerais (MG), the second-largest populated Brazilian state with more than 20 million inhabitants, observed a peak of cases and deaths in March–April 2021. We conducted a surveillance study in 1240 COVID-19-positive samples from 305 municipalities distributed across MG’s 28 Regional Health Units (RHU) between 1 March to 27 April 2021. The most common variant was the VOC Gamma (71.2%), followed by the variant of interest (VOI) zeta (12.4%) and VOC alpha (9.6%). Although the predominance of Gamma was found in most of the RHUs, clusters of Zeta and Alpha variants were observed. One Alpha-clustered RHU has a history of high human mobility from countries with Alpha predominance. Other less frequent lineages, such as P.4, P.5, and P.7, were also identified. With our genomic characterization approach, we estimated the introduction of Gamma on 7 January 2021, at RHU Belo Horizonte. Differences in mortality between the Zeta, Gamma and Alpha variants were not observed. We reinforce the importance of vaccination programs to prevent severe cases and deaths during transmission peaks

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