Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1038/s41467-022-28648-3 http://hdl.handle.net/11449/231631 |
Resumo: | 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 enables identification of ~2,000 previously undescribed mobile element insertions without previous description, nearly 5 Mb of genomic segments absent from the human genome reference, and over 140 alleles from HLA genes absent from public resources. We reclassify and curate pathogenicity assertions for nearly four hundred variants in genes associated with dominantly-inherited Mendelian disorders and calculate the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observe 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. |
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Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, BrazilAs 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 enables identification of ~2,000 previously undescribed mobile element insertions without previous description, nearly 5 Mb of genomic segments absent from the human genome reference, and over 140 alleles from HLA genes absent from public resources. We reclassify and curate pathogenicity assertions for nearly four hundred variants in genes associated with dominantly-inherited Mendelian disorders and calculate the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observe 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.National Institute of General Medical SciencesHuman Genome and Stem Cell Research Center University of São Paulo, SPDepartment of Genetics and Evolutionary Biology Biosciences Institute University of São Paulo, SPHospital Israelita Albert Einstein, SPInstituto da Criança Faculdade de Medicina da Universidade de São Paulo, SPOrthopedic Research Labs Boston Children’s Hospital and Department of Genetics Harvard Medical SchoolLaboratório DASALaboratory of Genome Structure and Ageing European Research Institute for the Biology of Ageing University Medical Center GroningenSão Paulo State University (UNESP) Molecular Genetics and Bioinformatics Laboratory School of Medicine, State of São PauloSão Paulo State University (UNESP) Department of Pathology School of Medicine, State of São PauloDepartamento de Química Faculdade de Filosofia Ciências e Letras de Ribeirão Preto Universidade de São Paulo, São PauloCentro de Oncologia Molecular Hospital Sirio-LibanesDepartment of Biochemistry Institute of Chemistry University of São Paulo São PauloBioinformatics Graduate program University of São PauloDepartamento de Genética Ecologia e Evolução Instituto de Ciências Biológicas Universidade Federal de Minas Gerais, MGNúcleo de Ensino e Pesquisa Instituto Mário Penna, MGLaboratorio de Biotecnologia y Biologia Molecular Instituto Nacional de SaludUniversidad de HuánucoDivision of Cancer Epidemiology and Genetics National Cancer InstituteInstituto de Saúde Coletiva Universidade Federal da Bahia, BACenter for Data and Knowledge Integration for Health Institute Gonçalo Muniz Fundação Oswaldo Cruz, BAInstituto de Pesquisas René Rachou Fundação Oswaldo Cruz, MGPrograma De Pós-Graduação em Saúde Pública Universidade Federal de Minas Gerais, MGPrograma de Pós-Graduação em Epidemiologia Universidade Federal de Pelotas, RSMosaico Translational Genomics Initiative Universidade Federal de Minas Gerais, MGFacultad de Salud Pública y Administración Universidad Peruana Cayetano HerediaInstituto de Estudos Avançados Transdisciplinares Universidade Federal de Minas Gerais, MGMedical-Surgical Nursing Department School of Nursing University of São Paulo, SPEpidemiology Department Public Health School University of São Paulo, SPSão Paulo State University (UNESP) Molecular Genetics and Bioinformatics Laboratory School of Medicine, State of São PauloSão Paulo State University (UNESP) Department of Pathology School of Medicine, State of São PauloNational Institute of General Medical Sciences: R01 GM075091Universidade de São Paulo (USP)Hospital Israelita Albert EinsteinHarvard Medical SchoolLaboratório DASAUniversity Medical Center GroningenUniversidade Estadual Paulista (UNESP)Hospital Sirio-LibanesUniversidade Federal de Minas Gerais (UFMG)Instituto Mário PennaInstituto Nacional de SaludUniversidad de HuánucoNational Cancer InstituteUniversidade Federal da Bahia (UFBA)Fundação Oswaldo CruzUniversidade Federal de PelotasUniversidad Peruana Cayetano HerediaNaslavsky, Michel S.Scliar, Marilia O.Yamamoto, Guilherme L.Wang, Jaqueline Yu TingZverinova, StepankaKarp, TatianaNunes, KellyCeroni, José Ricardo Maglioccode Carvalho, Diego Limada Silva Simões, Carlos EduardoBozoklian, DanielNonaka, Ricardodos Santos Brito Silva, Nayane [UNESP]da Silva Souza, Andreia [UNESP]de Souza Andrade, Heloísa [UNESP]Passos, Marília Rodrigues Silva [UNESP]Castro, Camila Ferreira Bannwart [UNESP]Mendes-Junior, Celso T.Mercuri, Rafael L. V.Miller, Thiago L. A.Buzzo, Jose LeonelRego, Fernanda O.Araújo, Nathalia M.Magalhães, Wagner C. S.Mingroni-Netto, Regina CéliaBorda, VictorGuio, HeinnerRojas, Carlos P.Sanchez, CesarCaceres, OmarDean, MichaelBarreto, Mauricio L.Lima-Costa, Maria FernandaHorta, Bernardo L.Tarazona-Santos, EduardoMeyer, DiogoGalante, Pedro A. F.Guryev, VictorCastelli, Erick C. [UNESP]Duarte, Yeda A. O.Passos-Bueno, Maria RitaZatz, Mayana2022-04-29T08:46:40Z2022-04-29T08:46:40Z2022-12-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1038/s41467-022-28648-3Nature Communications, v. 13, n. 1, 2022.2041-1723http://hdl.handle.net/11449/23163110.1038/s41467-022-28648-32-s2.0-85125792333Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengNature Communicationsinfo:eu-repo/semantics/openAccess2024-08-15T18:47:31Zoai:repositorio.unesp.br:11449/231631Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-15T18:47:31Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil |
title |
Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil |
spellingShingle |
Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil Naslavsky, Michel S. |
title_short |
Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil |
title_full |
Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil |
title_fullStr |
Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil |
title_full_unstemmed |
Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil |
title_sort |
Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil |
author |
Naslavsky, Michel S. |
author_facet |
Naslavsky, Michel S. Scliar, Marilia O. Yamamoto, Guilherme L. Wang, Jaqueline Yu Ting Zverinova, Stepanka Karp, Tatiana Nunes, Kelly Ceroni, José Ricardo Magliocco de Carvalho, Diego Lima da Silva Simões, Carlos Eduardo Bozoklian, Daniel Nonaka, Ricardo dos Santos Brito Silva, Nayane [UNESP] da Silva Souza, Andreia [UNESP] de Souza Andrade, Heloísa [UNESP] Passos, Marília Rodrigues Silva [UNESP] Castro, Camila Ferreira Bannwart [UNESP] Mendes-Junior, Celso T. Mercuri, Rafael L. V. Miller, Thiago L. A. Buzzo, Jose Leonel Rego, Fernanda O. Araújo, Nathalia M. Magalhães, Wagner C. S. Mingroni-Netto, Regina Célia Borda, Victor Guio, Heinner Rojas, Carlos P. Sanchez, Cesar Caceres, Omar Dean, Michael Barreto, Mauricio L. Lima-Costa, Maria Fernanda Horta, Bernardo L. Tarazona-Santos, Eduardo Meyer, Diogo Galante, Pedro A. F. Guryev, Victor Castelli, Erick C. [UNESP] Duarte, Yeda A. O. Passos-Bueno, Maria Rita Zatz, Mayana |
author_role |
author |
author2 |
Scliar, Marilia O. Yamamoto, Guilherme L. Wang, Jaqueline Yu Ting Zverinova, Stepanka Karp, Tatiana Nunes, Kelly Ceroni, José Ricardo Magliocco de Carvalho, Diego Lima da Silva Simões, Carlos Eduardo Bozoklian, Daniel Nonaka, Ricardo dos Santos Brito Silva, Nayane [UNESP] da Silva Souza, Andreia [UNESP] de Souza Andrade, Heloísa [UNESP] Passos, Marília Rodrigues Silva [UNESP] Castro, Camila Ferreira Bannwart [UNESP] Mendes-Junior, Celso T. Mercuri, Rafael L. V. Miller, Thiago L. A. Buzzo, Jose Leonel Rego, Fernanda O. Araújo, Nathalia M. Magalhães, Wagner C. S. Mingroni-Netto, Regina Célia Borda, Victor Guio, Heinner Rojas, Carlos P. Sanchez, Cesar Caceres, Omar Dean, Michael Barreto, Mauricio L. Lima-Costa, Maria Fernanda Horta, Bernardo L. Tarazona-Santos, Eduardo Meyer, Diogo Galante, Pedro A. F. Guryev, Victor Castelli, Erick C. [UNESP] Duarte, Yeda A. O. Passos-Bueno, Maria Rita Zatz, Mayana |
author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade de São Paulo (USP) Hospital Israelita Albert Einstein Harvard Medical School Laboratório DASA University Medical Center Groningen Universidade Estadual Paulista (UNESP) Hospital Sirio-Libanes Universidade Federal de Minas Gerais (UFMG) Instituto Mário Penna Instituto Nacional de Salud Universidad de Huánuco National Cancer Institute Universidade Federal da Bahia (UFBA) Fundação Oswaldo Cruz Universidade Federal de Pelotas Universidad Peruana Cayetano Heredia |
dc.contributor.author.fl_str_mv |
Naslavsky, Michel S. Scliar, Marilia O. Yamamoto, Guilherme L. Wang, Jaqueline Yu Ting Zverinova, Stepanka Karp, Tatiana Nunes, Kelly Ceroni, José Ricardo Magliocco de Carvalho, Diego Lima da Silva Simões, Carlos Eduardo Bozoklian, Daniel Nonaka, Ricardo dos Santos Brito Silva, Nayane [UNESP] da Silva Souza, Andreia [UNESP] de Souza Andrade, Heloísa [UNESP] Passos, Marília Rodrigues Silva [UNESP] Castro, Camila Ferreira Bannwart [UNESP] Mendes-Junior, Celso T. Mercuri, Rafael L. V. Miller, Thiago L. A. Buzzo, Jose Leonel Rego, Fernanda O. Araújo, Nathalia M. Magalhães, Wagner C. S. Mingroni-Netto, Regina Célia Borda, Victor Guio, Heinner Rojas, Carlos P. Sanchez, Cesar Caceres, Omar Dean, Michael Barreto, Mauricio L. Lima-Costa, Maria Fernanda Horta, Bernardo L. Tarazona-Santos, Eduardo Meyer, Diogo Galante, Pedro A. F. Guryev, Victor Castelli, Erick C. [UNESP] Duarte, Yeda A. O. Passos-Bueno, Maria Rita Zatz, Mayana |
description |
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 enables identification of ~2,000 previously undescribed mobile element insertions without previous description, nearly 5 Mb of genomic segments absent from the human genome reference, and over 140 alleles from HLA genes absent from public resources. We reclassify and curate pathogenicity assertions for nearly four hundred variants in genes associated with dominantly-inherited Mendelian disorders and calculate the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observe 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. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-04-29T08:46:40Z 2022-04-29T08:46:40Z 2022-12-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1038/s41467-022-28648-3 Nature Communications, v. 13, n. 1, 2022. 2041-1723 http://hdl.handle.net/11449/231631 10.1038/s41467-022-28648-3 2-s2.0-85125792333 |
url |
http://dx.doi.org/10.1038/s41467-022-28648-3 http://hdl.handle.net/11449/231631 |
identifier_str_mv |
Nature Communications, v. 13, n. 1, 2022. 2041-1723 10.1038/s41467-022-28648-3 2-s2.0-85125792333 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Nature Communications |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
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UNESP |
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Repositório Institucional da UNESP |
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Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1808128197120753664 |