Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil

Detalhes bibliográficos
Autor(a) principal: Naslavsky, Michel S.
Data de Publicação: 2022
Outros Autores: 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
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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spelling 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
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author
author
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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
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