SELAdb: A database of exonic variants in a Brazilian population referred to a quaternary medical center in São Paulo

Authors

  • Antonio Marcondes Lerario Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Clinica Medica, LIM/42
  • Dipika R. Mohan University of Michigan, Medical Scientist Training Program https://orcid.org/0000-0002-6334-9416
  • Luciana Ribeiro Montenegro Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Clinica Medica, LIM/42 https://orcid.org/0000-0002-8401-7613
  • Mariana Ferreira de Assis Funari Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Clinica Medica, LIM/42
  • Mirian Yumie Nishi Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Clinica Medica, LIM/42
  • Amanda de Moraes Narcizo Universidade de Sao Paulo, Faculdade de Medicina, Laboratorio de Sequenciamento em Larga Escala
  • Anna Flavia Figueredo Benedetti Universidade de Sao Paulo, Faculdade de Medicina, Laboratorio de Sequenciamento em Larga Escala
  • Sueli Mieko Oba-Shinjo Universidade de Sao Paulo, Faculdade de Medicina, Departamento de Neurologia, Laboratorio de Biologia Molecular e Celular, LIM/15
  • Aurélio José Vitorino Universidade de Sao Paulo, Faculdade de Medicina, Laboratorio de Informatica Medica – LIM/01
  • Rogério Alexandre Scripnic Xavier dos Santos Universidade de Sao Paulo, Sao Paulo, Faculdade de Medicina, Laboratorio de Informatica Medica – LIM/01
  • Alexander Augusto de Lima Jorge Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Clinica Medica, LIM/42
  • Luiz Fernando Onuchic Universidade de Sao Paulo, Faculdade de Medicina, Departamento de Clinica Medica https://orcid.org/0000-0002-4053-5419
  • Suely Kazue Nagahashi Marie Universidade de Sao Paulo, Faculdade de Medicina, Departamento de Neurologia, Laboratorio de Biologia Molecular e Celular, LIM/15
  • Berenice Bilharinho Mendonça Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Clinica Medica, LIM/42 https://orcid.org/0000-0003-1762-1084

DOI:

https://doi.org/10.6061/clinics/2020/e1913

Keywords:

Next Generation Sequencing, Database, Mendelian Disorders, Brazil, Population Genetics

Abstract

OBJECTIVES: High-throughput sequencing of genomes, exomes, and disease-focused gene panels is becoming increasingly common for molecular diagnostics. However, identifying a single clinically relevant pathogenic variant among thousands of genetic polymorphisms is a challenging task. Publicly available genomic databases are useful resources to filter out common genetic variants present in the population and enable the identification of each disease-causing variant. Based on our experience applying these technologies at Hospital das Clı´nicas da Faculdade de Medicina da Universidade de Sa˜o Paulo (HCFMUSP), Sa˜o Paulo, Brazil, we recognized that the Brazilian population is not adequately represented in widely available genomic databases. METHODS: Here, we took advantage of our 5-year experience as a high-throughput sequencing core facility focused on individuals with putative genetic disorders to build a genomic database that may serve as a more accurate reference for our patient population: SELAdb. RESULTS/CONCLUSIONS: Currently, our database comprises a final cohort of 523 unrelated individuals, including patients or family members managed by different clinics of HCFMUSP. We compared SELAdb with other publicly available genomic databases and demonstrated that this population is very heterogeneous, largely resembling Latin American individuals of mixed origin, rather than individuals of pure European ancestry. Interestingly, exclusively through SELAdb, we identified a spectrum of known and potentially novel pathogenic variants in genes associated with highly penetrant Mendelian disorders, illustrating that pathogenic variants circulating in the Brazilian population that is treated in our clinics are underrepresented in other population databases. SELAdb is freely available for public consultation at: http://intranet.fm.usp.br/sela

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Published

2020-08-17

How to Cite

Lerario, A. M., Mohan, D. R., Montenegro, L. R., Funari, M. F. de A., Nishi, M. Y., Narcizo, A. de M., Benedetti, A. F. F., Oba-Shinjo, S. M., Vitorino, A. J., Santos, R. A. S. X. dos, Jorge, A. A. de L., Onuchic, L. F., Marie, S. K. N., & Mendonça, B. B. (2020). SELAdb: A database of exonic variants in a Brazilian population referred to a quaternary medical center in São Paulo. Clinics, 75, e1913. https://doi.org/10.6061/clinics/2020/e1913

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Original Articles