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Whole-genome sequencing of 1,171 elderly admixed individuals from the largest Latin American metropolis (São Paulo, Brazil)

View ORCID ProfileMichel S. Naslavsky, View ORCID ProfileMarilia O. Scliar, View ORCID ProfileGuilherme L. Yamamoto, Jaqueline Yu Ting Wang, Stepanka Zverinova, Tatiana Karp, Kelly Nunes, View ORCID ProfileJosé Ricardo Magliocco Ceroni, Diego Lima de Carvalho, Carlos Eduardo da Silva Simões, Daniel Bozoklian, Ricardo Nonaka, Nayane dos Santos Brito Silva, Andreia da Silva Souza, Heloísa de Souza Andrade, Marília Rodrigues Silva Passos, Camila Ferreira Bannwart Castro, View ORCID ProfileCelso T. Mendes-Junior, Rafael L. V. Mercuri, Thiago L. A. Miller, Jose Leonel Buzzo, Fernanda O. Rego, Nathalia M Araújo, Wagner CS Magalhães, View ORCID ProfileRegina Célia Mingroni-Netto, View ORCID ProfileVictor Borda, View ORCID ProfileHeinner Guio, Mauricio L Barreto, View ORCID ProfileMaria Fernanda Lima-Costa, View ORCID ProfileBernardo L Horta, View ORCID ProfileEduardo Tarazona-Santos, View ORCID ProfileDiogo Meyer, View ORCID ProfilePedro A. F. Galante, Victor Guryev, View ORCID ProfileErick C. Castelli, View ORCID ProfileYeda A. O. Duarte, View ORCID ProfileMaria Rita Passos-Bueno, View ORCID ProfileMayana Zatz
doi: https://doi.org/10.1101/2020.09.15.298026
Michel S. Naslavsky
1Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil
2Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
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  • For correspondence: mnaslavsky@usp.br mayazatz@usp.br
Marilia O. Scliar
1Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil
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Guilherme L. Yamamoto
1Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil
3Instituto da Criança, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
4Orthopedic Research Labs, Boston Children’s Hospital and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
5Laboratório DASA, São Paulo, Brazil
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Jaqueline Yu Ting Wang
1Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil
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Stepanka Zverinova
6Laboratory of Genome Structure and Ageing, European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, Netherlands
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Tatiana Karp
6Laboratory of Genome Structure and Ageing, European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, Netherlands
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Kelly Nunes
2Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
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José Ricardo Magliocco Ceroni
1Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil
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Diego Lima de Carvalho
1Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil
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Carlos Eduardo da Silva Simões
1Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil
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Daniel Bozoklian
1Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil
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Ricardo Nonaka
1Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil
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Nayane dos Santos Brito Silva
7São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, State of São Paulo, Brazil
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Andreia da Silva Souza
7São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, State of São Paulo, Brazil
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Heloísa de Souza Andrade
7São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, State of São Paulo, Brazil
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Marília Rodrigues Silva Passos
7São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, State of São Paulo, Brazil
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Camila Ferreira Bannwart Castro
7São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, State of São Paulo, Brazil
8São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, State of São Paulo, Brazil
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Celso T. Mendes-Junior
9Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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Rafael L. V. Mercuri
10Centro de Oncologia Molecular, Hospital Sirio-Libanes, São Paulo, Brazil
11Department of Biochemistry, Institute of Chemistry, University of São Paulo São Paulo, Brazil
12Bioinformatics Graduate program, University of São Paulo, São Paulo, Brazil
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Thiago L. A. Miller
10Centro de Oncologia Molecular, Hospital Sirio-Libanes, São Paulo, Brazil
11Department of Biochemistry, Institute of Chemistry, University of São Paulo São Paulo, Brazil
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Jose Leonel Buzzo
10Centro de Oncologia Molecular, Hospital Sirio-Libanes, São Paulo, Brazil
11Department of Biochemistry, Institute of Chemistry, University of São Paulo São Paulo, Brazil
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Fernanda O. Rego
10Centro de Oncologia Molecular, Hospital Sirio-Libanes, São Paulo, Brazil
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Nathalia M Araújo
13Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Wagner CS Magalhães
13Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
14Núcleo de Ensino e Pesquisa, Instituto Mário Penna, Belo Horizonte, MG, Brazil
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Regina Célia Mingroni-Netto
1Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil
2Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
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Victor Borda
13Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Heinner Guio
15Instituto Nacional de Salud, Lima, Peru
16Universidad de Huánuco, Huánuco, Peru
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Mauricio L Barreto
17Instituto de Saúde Coletiva, Universidade Federal da Bahia, 40110-040, Salvador, BA, Brazil
18Center for Data and Knowledge Integration for Health, Institute Gonçalo Muniz, Fundação Oswaldo Cruz, Salvador, BA, Brazil
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Maria Fernanda Lima-Costa
19Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG, Brazil
20Programa De Pós-Graduação em Saúde Pública, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Bernardo L Horta
21Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
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Eduardo Tarazona-Santos
13Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
22Mosaico Translational Genomics Initiative, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
23Facultad de Salud Pública y Administración. Universidad Peruana Cayetano Heredia, Lima, Peru
24Instituto de Estudos Avançados Transdisciplinares, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
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Diogo Meyer
2Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
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Pedro A. F. Galante
10Centro de Oncologia Molecular, Hospital Sirio-Libanes, São Paulo, Brazil
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Victor Guryev
6Laboratory of Genome Structure and Ageing, European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, Netherlands
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Erick C. Castelli
7São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, State of São Paulo, Brazil
8São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, State of São Paulo, Brazil
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Yeda A. O. Duarte
25Medical-Surgical Nursing Department, School of Nursing, University of São Paulo, São Paulo, SP, Brazil
26Epidemiology Department, Public Health School, University of São Paulo, São Paulo, SP, Brazil
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Maria Rita Passos-Bueno
1Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil
2Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
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Mayana Zatz
1Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil
2Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
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  • For correspondence: mnaslavsky@usp.br mayazatz@usp.br
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Abstract

As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly admixed elderly Brazilians from a census-based cohort, providing over 76 million variants, of which ~2 million are absent from large public databases. WGS enabled identifying ~2,000 novel mobile element insertions, nearly 5Mb of genomic segments absent from human genome reference, and over 140 novel alleles from HLA genes. We reclassified and curated nearly four hundred variant's pathogenicity assertions in genes associated with dominantly inherited Mendelian disorders and calculated the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observed that whole-genome and HLA imputation could be significantly improved compared to available datasets since rare variation represents the largest proportion of input from WGS. These results demonstrate that even smaller sample sizes of underrepresented populations bring relevant data for genomic studies, especially when exploring analyses allowed only by WGS.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • http://abraom.ib.usp.br/

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Whole-genome sequencing of 1,171 elderly admixed individuals from the largest Latin American metropolis (São Paulo, Brazil)
Michel S. Naslavsky, Marilia O. Scliar, Guilherme L. Yamamoto, Jaqueline Yu Ting Wang, Stepanka Zverinova, Tatiana Karp, Kelly Nunes, José Ricardo Magliocco Ceroni, Diego Lima de Carvalho, Carlos Eduardo da Silva Simões, Daniel Bozoklian, Ricardo Nonaka, Nayane dos Santos Brito Silva, Andreia da Silva Souza, Heloísa de Souza Andrade, Marília Rodrigues Silva Passos, Camila Ferreira Bannwart Castro, Celso T. Mendes-Junior, Rafael L. V. Mercuri, Thiago L. A. Miller, Jose Leonel Buzzo, Fernanda O. Rego, Nathalia M Araújo, Wagner CS Magalhães, Regina Célia Mingroni-Netto, Victor Borda, Heinner Guio, Mauricio L Barreto, Maria Fernanda Lima-Costa, Bernardo L Horta, Eduardo Tarazona-Santos, Diogo Meyer, Pedro A. F. Galante, Victor Guryev, Erick C. Castelli, Yeda A. O. Duarte, Maria Rita Passos-Bueno, Mayana Zatz
bioRxiv 2020.09.15.298026; doi: https://doi.org/10.1101/2020.09.15.298026
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Whole-genome sequencing of 1,171 elderly admixed individuals from the largest Latin American metropolis (São Paulo, Brazil)
Michel S. Naslavsky, Marilia O. Scliar, Guilherme L. Yamamoto, Jaqueline Yu Ting Wang, Stepanka Zverinova, Tatiana Karp, Kelly Nunes, José Ricardo Magliocco Ceroni, Diego Lima de Carvalho, Carlos Eduardo da Silva Simões, Daniel Bozoklian, Ricardo Nonaka, Nayane dos Santos Brito Silva, Andreia da Silva Souza, Heloísa de Souza Andrade, Marília Rodrigues Silva Passos, Camila Ferreira Bannwart Castro, Celso T. Mendes-Junior, Rafael L. V. Mercuri, Thiago L. A. Miller, Jose Leonel Buzzo, Fernanda O. Rego, Nathalia M Araújo, Wagner CS Magalhães, Regina Célia Mingroni-Netto, Victor Borda, Heinner Guio, Mauricio L Barreto, Maria Fernanda Lima-Costa, Bernardo L Horta, Eduardo Tarazona-Santos, Diogo Meyer, Pedro A. F. Galante, Victor Guryev, Erick C. Castelli, Yeda A. O. Duarte, Maria Rita Passos-Bueno, Mayana Zatz
bioRxiv 2020.09.15.298026; doi: https://doi.org/10.1101/2020.09.15.298026

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