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Gong B, Lababidi S, Kusko R, Bouri K, Prezek S, Thovarai V, Prasanna A, Maier EJ, Golkaram M, Sun X, Kyriakidis K, Kitajima JP, Ebrahim Sahraeian SM, Guo Y, Johanson E, Jones W, Tong W, Xu J. Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA. Sci Rep 2024; 14:8165. [PMID: 38589653 PMCID: PMC11001604 DOI: 10.1038/s41598-024-58573-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/01/2024] [Indexed: 04/10/2024] Open
Abstract
Accurately calling indels with next-generation sequencing (NGS) data is critical for clinical application. The precisionFDA team collaborated with the U.S. Food and Drug Administration's (FDA's) National Center for Toxicological Research (NCTR) and successfully completed the NCTR Indel Calling from Oncopanel Sequencing Data Challenge, to evaluate the performance of indel calling pipelines. Top performers were selected based on precision, recall, and F1-score. The performance of many other pipelines was close to the top performers, which produced a top cluster of performers. The performance was significantly higher in high confidence regions and coding regions, and significantly lower in low complexity regions. Oncopanel capture and other issues may have occurred that affected the recall rate. Indels with higher variant allele frequency (VAF) may generally be called with higher confidence. Many of the indel calling pipelines had good performance. Some of them performed generally well across all three oncopanels, while others were better for a specific oncopanel. The performance of indel calling can further be improved by restricting the calls within high confidence intervals (HCIs) and coding regions, and by excluding low complexity regions (LCR) regions. Certain VAF cut-offs could be applied according to the applications.
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Affiliation(s)
- Binsheng Gong
- Division of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Samir Lababidi
- Health Informatics Staff, Office of Data, Analytics, and Research, Office of Digital Transformation, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Rebecca Kusko
- Cellino Biotech, 750 Main Street, Cambridge, MA, 02143, USA
| | - Khaled Bouri
- Office of Regulatory Science and Innovation, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | | | | | | | | | | | | | | | | | | | - Yunfei Guo
- Roche Sequencing Solutions, Santa Clara, CA, 95050, USA
| | - Elaine Johanson
- Health Informatics Staff, Office of Data, Analytics, and Research, Office of Digital Transformation, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Wendell Jones
- Q squared Solutions Genomics, 2400 Elis Road, Durham, NC, 27703, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
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Paiva ARBD, Pessoa ALS, Nóbrega PR, Moreno CAM, Lynch DS, Taniguti LM, Kitajima JP, Freua F, Della-Ripa B, Cunha P, Peixoto de Barcelos I, Macedo-Souza LI, Takeuchi CA, Garcia AMS, Nardes F, Fontão R, Antoniuk SA, Troncoso M, Spécola N, Durand C, Madeiro BDACS, Doriqui MJR, Vergara D, Houlden H, Kok F. Ceroid lipofuscinosis type 5: novel pathogenic variants and unexpected phenotypic findings. J Neurol Neurosurg Psychiatry 2023; 94:405-408. [PMID: 36737246 DOI: 10.1136/jnnp-2022-330135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Affiliation(s)
- Anderson Rodrigues Brandão de Paiva
- Mendelics Genomic Analysis, São Paulo, SP, Brazil
- Neurology Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Neurology Department, Hospital São Rafael - Rede D'or São Luiz, Salvador, BA, Brazil
| | - André Luiz Santos Pessoa
- Hospital Infantil Albert Sabin, Fortaleza, CE, Brazil
- Universidade Estadual do Ceara, Fortaleza, CE, Brazil
| | - Paulo Ribeiro Nóbrega
- Neurology Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Neurology Department, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Cristiane Araujo Martins Moreno
- Mendelics Genomic Analysis, São Paulo, SP, Brazil
- Neurology Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - David S Lynch
- Department of Neurogenetics, National Hospital for Neurology & Neurosurgery, Queen Square, London, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | | | | | - Fernando Freua
- Neurology Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Neurology Department, Beneficência Portuguesa de São Paulo, São Paulo, SP, Brazil
| | - Bruno Della-Ripa
- Mendelics Genomic Analysis, São Paulo, SP, Brazil
- Neurology Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Paulina Cunha
- Neurology Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Institut du Cerveau (ICM), APHP, Pitié Salpêtrière Hospital, Paris, France
| | - Isabella Peixoto de Barcelos
- Neurology Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Flávia Nardes
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Ramiro Fontão
- Neuropediatrics, Penna Hospital, Bahía Blanca, Buenos Aires, Argentina
| | | | - Monica Troncoso
- Pediatric Neurology Department, Hospital Clínico San Borja Arriarán, University of Chile, Santiago, Chile
| | - Norma Spécola
- Hospital de Niños Sor María Ludovica, La Plata, Argentina
| | - Consuelo Durand
- Laboratorio de Neuroquímica Dr. N.A. Chamoles, Buenos Aires, Argentina
| | | | | | - Diane Vergara
- Pediatric Neurology Department, Hospital Clínico San Borja Arriarán, University of Chile, Santiago, Chile
| | - Henry Houlden
- Department of Neurogenetics, National Hospital for Neurology & Neurosurgery, Queen Square, London, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Fernando Kok
- Mendelics Genomic Analysis, São Paulo, SP, Brazil
- Neurology Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
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Pires Ramos LL, Kitajima JP, Sampaio de Athayde Costa L, Monteiro FP, Kok F. Correspondence on "A gene-to-patient approach uplifts novel disease gene discovery and identifies 18 putative novel disease genes" by Seaby et al. Genet Med 2022; 24:2591-2592. [PMID: 36098740 DOI: 10.1016/j.gim.2022.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/20/2022] [Accepted: 08/20/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Luiza Lorena Pires Ramos
- Department of Neurology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil; Molecular Neurogenomics Group, VIB-UAntwerp Center for Molecular Neurology, University of Antwerp, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | | | | | | | - Fernando Kok
- Department of Neurology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil; Medical Department, Mendelics Genomic Analysis, Sao Paulo, Brazil
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4
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Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San EJ, Rodrigues ES, Santos EV, Aburjaile F, Xavier J, Fritsch H, Adelino TER, Pereira F, Leal A, Iani FCDM, de Carvalho Pereira G, Vazquez C, Sanabria GME, Oliveira ECD, Demarchi L, Croda J, Dos Santos Bezerra R, Paola Oliveira de Lima L, Martins AJ, Renata Dos Santos Barros C, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Mariani PDSC, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Nardy VB, Reboredo de Oliveira da Silva L, Gómez MKA, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Barbosa Da Silva L, da Silva Ferreira R, da Penha MPF, Ortega MJ, de la Fuente AG, Villalba S, Torales J, Gamarra ML, Aquino C, Figueredo GPM, Fava WS, Motta-Castro ARC, Venturini J, do Vale Leone de Oliveira SM, Gonçalves CCM, do Carmo Debur Rossa M, Becker GN, Giacomini MP, Marques NQ, Riediger IN, Raboni S, Mattoso G, Cataneo AD, Zanluca C, Duarte Dos Santos CN, Assato PA, Allan da Silva da Costa F, Poleti MD, Lesbon JCC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Grotto RMT, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, Bispo de Filippis AM, Venancio da Cunha R, Freitas C, Peterka CRL, de Fátima Rangel Fernandes C, Navegantes W, do Carmo Said RF, Campelo de A E Melo CF, Almiron M, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, Junior de Alcantara LC, Covas DT. Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil. Nat Microbiol 2022; 7:1490-1500. [PMID: 35982313 PMCID: PMC9417986 DOI: 10.1038/s41564-022-01191-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 06/28/2022] [Indexed: 01/01/2023]
Abstract
The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.
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Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
| | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Butantan Institute, São Paulo, Brazil
| | - Vagner Fonseca
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Pan American Health Organization (PAHO)/World Health Organization (WHO), Brasilia, Distrito Federal, Brazil
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Emmanuel James San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Evandra Strazza Rodrigues
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Elaine Vieira Santos
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Flavia Aburjaile
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Joilson Xavier
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Hegger Fritsch
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Talita Emile Ribeiro Adelino
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Felicidade Pereira
- Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil
| | - Arabela Leal
- Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil
| | - Felipe Campos de Melo Iani
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Glauco de Carvalho Pereira
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | | | - Gladys Mercedes Estigarribia Sanabria
- Laboratório Central de Salud Pública, Asunción, Paraguay
- Instituto Regional de Investigación em Salud, Universidad Nacional del Caaguazú, Caaguazú, Paraguay
- Laboratório de Biología Molecular, Hospital Regional de Coronel Oviedo, Ministerio de Salud Pública y Bienestar Social, Asunción, Paraguay
| | | | - Luiz Demarchi
- Laboratório Central de Saúde Pública do Estado de Mato Grosso do Sul (LACEN-MS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Julio Croda
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Rafael Dos Santos Bezerra
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | - Vlademir Vicente Cantarelli
- Universidade Federal de Ciencias da Saúde de Porto Alegre (UFCSPA), Universidade Feevale, Grupo Exame Laboratórios, Rio Grande do Sul, Brazil
| | - Stephane Tosta
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil
| | - Vanessa Brandão Nardy
- Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil
| | | | | | - Jaqueline Gomes Lima
- Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil
| | - Adriana Aparecida Ribeiro
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Natália Rocha Guimarães
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Luiz Takao Watanabe
- Laboratório Central de Saúde Pública do Estado de Mato Grosso (LACEN-MT), Cuiabá, Mato Grosso, Brazil
| | - Luana Barbosa Da Silva
- Laboratório Central de Saúde Pública do Estado de Mato Grosso (LACEN-MT), Cuiabá, Mato Grosso, Brazil
| | - Raquel da Silva Ferreira
- Laboratório Central de Saúde Pública do Estado de Mato Grosso (LACEN-MT), Cuiabá, Mato Grosso, Brazil
| | | | | | | | | | - Juan Torales
- Laboratório Central de Salud Pública, Asunción, Paraguay
| | | | | | - Gloria Patricia Martínez Figueredo
- Laboratório Central de Salud Pública, Asunción, Paraguay
- Instituto Regional de Investigación em Salud, Universidad Nacional del Caaguazú, Caaguazú, Paraguay
- Laboratório de Biología Molecular, Hospital Regional de Coronel Oviedo, Ministerio de Salud Pública y Bienestar Social, Asunción, Paraguay
| | | | | | - James Venturini
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | | | | | - Guilherme Nardi Becker
- Laboratório Central de Saúde Pública do Estado do Paraná (Lacen-PR), Curitiba, Paraná, Brazil
| | | | - Nelson Quallio Marques
- Laboratório Central de Saúde Pública do Estado do Paraná (Lacen-PR), Curitiba, Paraná, Brazil
| | | | - Sonia Raboni
- Hospital de Clínicas da Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Gabriela Mattoso
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Allan D Cataneo
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Camila Zanluca
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | | | - Patricia Akemi Assato
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Felipe Allan da Silva da Costa
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Cecilia Artico Banho
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil
| | - Lívia Sacchetto
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil
| | - Marília Mazzi Moraes
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil
| | - Rejane Maria Tommasini Grotto
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
- Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, São Paulo, Brazil
| | - Jayme A Souza-Neto
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | | | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Rodrigo Tocantins Calado
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | | | | | - Carla Freitas
- Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, (CGLAB/SVS-MS), Brasília, Distrito Federal, Brazil
| | - Cassio Roberto Leonel Peterka
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil
| | - Cássia de Fátima Rangel Fernandes
- Departamento de Imunização e Doenças Transmissíveisa/Secretaria de Vigilancia em Saude, Ministerio da Saude, Brasılia, Distrito Federal, Brazil
| | - Wildo Navegantes
- Pan American Health Organization (PAHO)/World Health Organization (WHO), Brasilia, Distrito Federal, Brazil
| | | | | | - Maria Almiron
- Pan American Health Organization (PAHO)/World Health Organization (WHO), Brasilia, Distrito Federal, Brazil
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, UK
- Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Lisboa, Portugal
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | | | | | | | - Simone Kashima
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Luiz Carlos Junior de Alcantara
- Laboratório de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Dimas Tadeu Covas
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
- Butantan Institute, São Paulo, Brazil.
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5
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Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San JE, Rodrigues ES, Santos EV, Aburjaile F, Xavier J, Fritsch H, Adelino TER, Pereira F, Leal A, de Melo Iani FC, de Carvalho Pereira G, Vazquez C, Mercedes Estigarribia Sanabria G, de Oliveira EC, Demarchi L, Croda J, dos Santos Bezerra R, de Lima LPO, Martins AJ, dos Santos Barros CR, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Mariani PDSC, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Nardy VB, de Oliveira da Silva LR, Kelly Astete Gómez M, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Da Silva LB, da Silva Ferreira R, da Penha MPF, Ortega MJ, de la Fuente AG, Villalba S, Torales J, Gamarra ML, Aquino C, Martínez Figueredo GP, Fava WS, Motta-Castro ARC, Venturini J, de Oliveira SMDVL, Gonçalves CCM, do Carmo Debur Rossa M, Becker GN, Presibella MM, Marques NQ, Riediger IN, Raboni S, Coelho GM, Cataneo AHD, Zanluca C, dos Santos CND, Assato PA, da Costa FADS, Poleti MD, Lesbon JCC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Grotto RMT, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, de Filippis AMB, da Cunha RV, Freitas C, Peterka CRL, de Fátima Rangel Fernandes C, de Araújo WN, do Carmo Said RF, Almiron M, de Albuquerque e Melo CFC, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, de Alcantara LCJ, Covas DT. Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil. medRxiv 2022:2021.10.07.21264644. [PMID: 35378755 PMCID: PMC8978948 DOI: 10.1101/2021.10.07.21264644] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.
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Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Svetoslav Nanev Slavov
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Butantan Institute, São Paulo, Brazil
| | - Vagner Fonseca
- Laboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde (CGLAB/SVS-MS) Brasília, Distrito Federal, Brazil
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
| | | | | | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
| | - Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Elaine Vieira Santos
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Flavia Aburjaile
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Joilson Xavier
- Laboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Hegger Fritsch
- Laboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Talita Emile Ribeiro Adelino
- Laboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Felicidade Pereira
- Laboratorio Central de Saude Publica da Bahia–LACEN-BA, Salvador, Bahia, Brazil
| | - Arabela Leal
- Laboratorio Central de Saude Publica da Bahia–LACEN-BA, Salvador, Bahia, Brazil
| | - Felipe Campos de Melo Iani
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Glauco de Carvalho Pereira
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | | | - Gladys Mercedes Estigarribia Sanabria
- Universidad Nacional del Caaguazú, Instituto Regional de Investigación en Salud
- Laboratorio de Biología Molecular, Hospital Regional de Coronel Oviedo
- Ministerio de Salud Pública y Bienestar Social
| | | | - Luiz Demarchi
- Laboratório Central de Saúde Pública do Estado de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Rafael dos Santos Bezerra
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | - Vlademir Vicente Cantarelli
- Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Universidade Feevale, Grupo Exame Laboratórios, Rio Grande do Sul, Brazil
| | - Stephane Tosta
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratorio Central de Saude Publica da Bahia–LACEN-BA, Salvador, Bahia, Brazil
| | | | | | | | | | - Adriana Aparecida Ribeiro
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Natália Rocha Guimarães
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Luiz Takao Watanabe
- Laboratório Central de Saúde Pública do Estado de Mato Grosso, Cuiabá, Brazil
| | | | | | | | | | | | | | - Juan Torales
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | | | | | - Gloria Patricia Martínez Figueredo
- Universidad Nacional del Caaguazú, Instituto Regional de Investigación en Salud
- Laboratorio de Biología Molecular, Hospital Regional de Coronel Oviedo
- Ministerio de Salud Pública y Bienestar Social
| | | | | | | | | | | | | | | | | | | | | | - Sonia Raboni
- Hospital de Clínicas da Universidade Federal do Paraná, Curitiba, PR
| | | | | | - Camila Zanluca
- Laboratório de Virologia Molecular - Instituto Carlos Chagas/Fiocruz PR, Curitiba, PR
| | | | - Patricia Akemi Assato
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Felipe Allan da Silva da Costa
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, São Paulo, Brazil
| | - Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, São Paulo, Brazil
| | - Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, São Paulo, Brazil
| | - Cecilia Artico Banho
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto
| | - Lívia Sacchetto
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto
| | - Marília Mazzi Moraes
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto
| | - Rejane Maria Tommasini Grotto
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
- Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, Brazil
| | - Jayme A. Souza-Neto
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Rodrigo Tocantins Calado
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | | | | | - Carla Freitas
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde (CGLAB/SVS-MS) Brasília, Distrito Federal, Brazil
| | - Cassio Roberto Leonel Peterka
- Coordenação Geral das Arboviroses, Secretaria de Vigilaçncia em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil
| | - Cássia de Fátima Rangel Fernandes
- Departamento de Imunização e Doenças Transmissíveisa/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | | | | | - Maria Almiron
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil
| | | | - José Lourenço
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, UK
- Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Lisboa, Portugal
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | | | | | | | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Luiz Carlos Junior de Alcantara
- Laboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Dimas Tadeu Covas
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Butantan Institute, São Paulo, Brazil
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6
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Slavov SN, Bezerra RDS, Rodrigues ES, Santos EV, Borges JS, de la Roque DGL, Patané JSL, Lima ARJ, Ribeiro G, Viala VL, de Lima LPO, Martins AJ, Dos Santos Barros CR, Marqueze EC, Bernardino JDST, Moretti DB, Brassaloti RA, Cassano RDLRC, Mariani PDSC, Kitajima JP, Santos B, Assato PA, da Silva da Costa FA, Poleti MD, Lesbon JCC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Grotto RMT, Souza-Neto JA, Giovanetti M, de Alcantara LCJ, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, Covas DT, Coccuzzo Sampaio S, Elias MC, Kashima S. Genomic monitoring of the SARS-CoV-2 B1.1.7 (WHO VOC Alpha) in the Sao Paulo state, Brazil. Virus Res 2022; 308:198643. [PMID: 34848213 PMCID: PMC8636783 DOI: 10.1016/j.virusres.2021.198643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/22/2022]
Abstract
The SARS-CoV-2 alpha VOC (also known as lineage B.1.1.7) initially described in the autumn, 2020 in UK, rapidly became the dominant lineage across much of Europe. Despite multiple studies reporting molecular evidence suggestive of its circulation in Brazil, much is still unknown about its genomic diversity in the state of São Paulo, the main Brazilian economic and transportation hub. To get more insight regarding its transmission dynamics into the State we performed phylogenetic analysis on all alpha VOC strains obtained between February and August 2021 from the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants. The performed phylogenetic analysis showed that most of the alpha VOC genomes were interspersed with viral strains sampled from different Brazilian states and other countries suggesting that multiple independent Alpha VOC introductions from Brazil and overseas have occurred in the São Paulo State over time. Nevertheless, large monophyletic clusters were also observed especially from the Central-West part of the São Paulo State (the city of Bauru) and the metropolitan region of the São Paulo city. Our results highlight the Alpha VOC molecular epidemiology in the São Paulo state and reinforce the need for continued genomic surveillance strategies for the real-time monitoring of potential emerging SARS-CoV-2 variants during the ever-growing vaccination process.
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Affiliation(s)
- Svetoslav Nanev Slavov
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil; Butantan Institute, São Paulo, Brazil.
| | - Rafael Dos Santos Bezerra
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Elaine Vieira Santos
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Joseane Serrano Borges
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Patricia Akemi Assato
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Felipe Allan da Silva da Costa
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | - Cecilia Artico Banho
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Lívia Sacchetto
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Marília Mazzi Moraes
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Rejane Maria Tommasini Grotto
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil; Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, Brazil
| | - Jayme A Souza-Neto
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Marta Giovanetti
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Luiz Carlos Junior de Alcantara
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Maurício Lacerda Nogueira
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | | | - Rodrigo Tocantins Calado
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil; University of São Paulo, Ribeirão Preto Medical School, Ribeirão Preto, SP, Brazil
| | | | - Dimas Tadeu Covas
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil; Butantan Institute, São Paulo, Brazil; University of São Paulo, Ribeirão Preto Medical School, Ribeirão Preto, SP, Brazil
| | | | | | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
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7
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Costa ZP, Varani AM, Cauz-Santos LA, Sader MA, Giopatto HA, Zirpoli B, Callot C, Cauet S, Marande W, Souza Cardoso JL, Pinheiro DG, Kitajima JP, Dornelas MC, Harand AP, Berges H, Monteiro-Vitorello CB, Carneiro Vieira ML. A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis. Plant Genome 2021; 14:e20117. [PMID: 34296827 DOI: 10.1002/tpg2.20117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/09/2021] [Indexed: 06/13/2023]
Abstract
The genus Passiflora comprises a large group of plants popularly known as passionfruit, much appreciated for their exotic flowers and edible fruits. The species (∼500) are morphologically variable (e.g., growth habit, size, and color of flowers) and are adapted to distinct tropical ecosystems. In this study, we generated the genome of the wild diploid species Passiflora organensis Gardner by adopting a hybrid assembly approach. Passiflora organensis has a small genome of 259 Mbp and a heterozygosity rate of 81%, consistent with its reproductive system. Most of the genome sequences could be integrated into its chromosomes with cytogenomic markers (satellite DNA) as references. The repeated sequences accounted for 58.55% of the total DNA analyzed, and the Tekay lineage was the prevalent retrotransposon. In total, 25,327 coding genes were predicted. Passiflora organensis retains 5,609 singletons and 15,671 gene families. We focused on the genes potentially involved in the locus determining self-incompatibility and the MADS-box gene family, allowing us to infer expansions and contractions within specific subfamilies. Finally, we recovered the organellar DNA. Structural rearrangements and two mitoviruses, besides relics of other mobile elements, were found in the chloroplast and mt-DNA molecules, respectively. This study presents the first draft genome assembly of a wild Passiflora species, providing a valuable sequence resource for genomic and evolutionary studies on the genus, and support for breeding cropped passionfruit species.
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Affiliation(s)
- Zirlane Portugal Costa
- Dep. de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Univ. de São Paulo, Piracicaba, 13418-900, Brazil
| | - Alessandro Mello Varani
- Dep. de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Univ. Estadual Paulista, Jaboticabal, 14884-900, Brazil
| | - Luiz Augusto Cauz-Santos
- Dep. de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Univ. de São Paulo, Piracicaba, 13418-900, Brazil
- Present address: Dep. of Botany and Biodiversity Research, Univ. of Vienna, Vienna, 1030, Austria
| | | | - Helena Augusto Giopatto
- Dep. de Biologia Vegetal, Instituto de Biologia, Univ. Estadual de Campinas, Campinas, 13083-862, Brazil
| | - Bruna Zirpoli
- Dep. de Botânica, Univ. Federal de Pernambuco, Recife, 50670-901, Brazil
| | - Caroline Callot
- Institut National de la Recherche Agronomique, Centre National de Ressources Génomique Végétales, Castanet-Tolosan, 31326, France
| | - Stephane Cauet
- Institut National de la Recherche Agronomique, Centre National de Ressources Génomique Végétales, Castanet-Tolosan, 31326, France
| | - Willian Marande
- Institut National de la Recherche Agronomique, Centre National de Ressources Génomique Végétales, Castanet-Tolosan, 31326, France
| | - Jessica Luana Souza Cardoso
- Dep. de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Univ. de São Paulo, Piracicaba, 13418-900, Brazil
| | - Daniel Guariz Pinheiro
- Dep. de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Univ. Estadual Paulista, Jaboticabal, 14884-900, Brazil
| | | | - Marcelo Carnier Dornelas
- Dep. de Biologia Vegetal, Instituto de Biologia, Univ. Estadual de Campinas, Campinas, 13083-862, Brazil
| | | | - Helene Berges
- Institut National de la Recherche Agronomique, Centre National de Ressources Génomique Végétales, Castanet-Tolosan, 31326, France
| | | | - Maria Lucia Carneiro Vieira
- Dep. de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Univ. de São Paulo, Piracicaba, 13418-900, Brazil
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8
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Leoni TB, González-Salazar C, Rezende TJR, Hernández ALC, Mattos AHB, Coimbra Neto AR, da Graça FF, Gonçalves JPN, Martinez ARM, Taniguti L, Kitajima JP, Kok F, Rogério F, da Silva AMS, de Oliveira ALR, Zanoteli E, Nucci A, França MC. A Novel Multisystem Proteinopathy Caused by a Missense ANXA11 Variant. Ann Neurol 2021; 90:239-252. [PMID: 34048612 DOI: 10.1002/ana.26136] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Protein misfolding plays a central role not only in amyotrophic lateral sclerosis (ALS), but also in other conditions, such as frontotemporal dementia (FTD), inclusion body myopathy (hIBM) or Paget's disease of bone. The concept of multisystem proteinopathies (MSP) was created to account for those rare families that segregate at least 2 out of these 4 conditions in the same pedigree. The calcium-dependent phospholipid-binding protein annexin A11 was recently associated to ALS in European pedigrees. Herein, we describe in detail 3 Brazilian families presenting hIBM (isolated or in combination with ALS/FTD) caused by the novel p.D40Y change in the gene encoding annexin A11 (ANXA11). METHODS We collected clinical, genetic, pathological and skeletal muscle imaging from 11 affected subjects. Neuroimaging was also obtained from 8 patients and 8 matched controls. RESULTS Clinico-radiological phenotype of this novel hIBM reveals a slowly progressive predominant limb-girdle syndrome, but with frequent axial (ptosis/dropped head) and distal (medial gastrocnemius) involvement as well. Muscle pathology identified numerous rimmed vacuoles with positive annexin A11, TDP-43 and p62 inclusions, but no inflammation. Central nervous system was also involved: two patients had FTD, but diffusion tensor imaging uncovered multiple areas of cerebral white matter damage in the whole group (including the corticospinal tracts and frontal subcortical regions). INTERPRETATION These findings expand the phenotypic spectrum related to ANXA11. This gene should be considered the cause of a novel multisystem proteinopathy (MSP type 6), rather than just ALS. ANN NEUROL 2021;90:239-252.
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Affiliation(s)
- Tauana Bernardes Leoni
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Carelis González-Salazar
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Ana Luisa C Hernández
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | | | | | - Felipe Franco da Graça
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Alberto R M Martinez
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | | | | | - Fernando Kok
- Mendelics Genomic Analyses, São Paulo, Brazil.,Department of Neurology, School of Medicine, University of São Paulo (USP), São Paulo, Brazil
| | - Fábio Rogério
- Department of Pathology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | | | | | - Edmar Zanoteli
- Department of Neurology, School of Medicine, University of São Paulo (USP), São Paulo, Brazil
| | - Anamarli Nucci
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Marcondes C França
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
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9
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Inuzuka LM, Macedo-Souza LI, Della-Ripa B, Cabral KSS, Monteiro F, Kitajima JP, de Souza Godoy LF, de Souza Delgado D, Kok F, Garzon E. Corrigendum to "Neurodevelopmental disorder associated with de novo SCN3A pathogenic variants: Two new cases and review of the literature" [Brain Dev. 42(2) (2020) 211-216]. Brain Dev 2021; 43:671. [PMID: 33608194 DOI: 10.1016/j.braindev.2021.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Luciana Midori Inuzuka
- Epilepsy Clinic, Hospital Sírio-Libanês, São Paulo, Brazil; Department of Neurology, University of São Paulo School of Medicine, Brazil.
| | | | - Bruno Della-Ripa
- Department of Neurology, University of São Paulo School of Medicine, Brazil.
| | - Katiane S S Cabral
- Department of Neurology, University of São Paulo School of Medicine, Brazil.
| | | | | | | | | | - Fernando Kok
- Mendelics Genomic Analysis, São Paulo, Brazil; Department of Neurology, University of São Paulo School of Medicine, Brazil.
| | - Eliana Garzon
- Epilepsy Clinic, Hospital Sírio-Libanês, São Paulo, Brazil; Department of Neurology, University of São Paulo School of Medicine, Brazil.
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10
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Crestana GS, Taniguti LM, Dos Santos CP, Benevenuto J, Ceresini PC, Carvalho G, Kitajima JP, Monteiro-Vitorello CB. Complete Chromosome-Scale Genome Sequence Resource for Sporisorium panici-leucophaei, the Causal Agent of Sourgrass Smut Disease. Mol Plant Microbe Interact 2021; 34:448-452. [PMID: 33369501 DOI: 10.1094/mpmi-08-20-0218-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Here, we present the first complete chromosome-level genome assembly of the smut fungus strain Sporisorium panici-leucophaei SPL10A, the causal agent of the sourgrass (Digitaria insularis) smut disease. Combining Illumina paired-end and Nanopore long reads, we generated a final assembly composed of 23 chromosomes (22 nuclear and one mitochondrial) with 18,915,934 bp. Gene prediction accomplished using extrinsic evidence from the sugarcane smut fungus Sporisorium scitamineum originated a total of 6,402 protein-encoding genes. The secretome (388 proteins) and the effectorome repertoires (68 candidates) were also predicted, given their crucial roles in plant-pathogen interactions. The complete telomere-to-telomere chromosome sequences of this poorly studied fungus will provide a valuable resource for future comparative genomic studies among smuts to unravel their underlying pathogenicity mechanisms.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Gustavo Schiavone Crestana
- Genomics Group, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba SP 13418-900, Brazil
| | | | - Clesivan Pereira Dos Santos
- Genomics Group, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba SP 13418-900, Brazil
| | - Juliana Benevenuto
- Genomics Group, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba SP 13418-900, Brazil
| | - Paulo Cezar Ceresini
- Molecular Phytopathology Lab, Plant Health, Rural Engineering and Soils Department, São Paulo State University (UNESP), Ilha Solteira SP 15385-000, Brazil
| | - Giselle Carvalho
- SENAI Innovation Institute in Biomass, Três Lagoas MS 79640-250, Brazil
| | | | - Claudia Barros Monteiro-Vitorello
- Genomics Group, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba SP 13418-900, Brazil
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11
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Pierry PM, de Santana WO, Kitajima JP, Martins-Junior J, Zaini PA, Uceda-Campos G, Feitosa-Junior OR, Pessoa PIS, Coletta-Filho HD, de Souza AA, Machado MA, Gesteira ADS, Martins LF, Amaral MS, Beckedorff FC, de Almeida LGP, de Vasconcelos ATR, Verjovski-Almeida S, Setubal JC, da Silva AM. High-Quality Draft Genome Sequence Resources of Eight Xylella fastidiosa Strains Isolated from Citrus, Coffee, Plum, and Hibiscus in South America. Phytopathology 2020; 110:1751-1755. [PMID: 32520631 DOI: 10.1094/phyto-05-20-0162-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Xylella fastidiosa subsp. pauca, once confined to South America and infecting mainly citrus and coffee plants, has been found to be associated with other hosts and in other geographic regions. We present high-quality draft genome sequences of X. fastidiosa subsp. pauca strains J1a12, B111, U24D, and XRB isolated from citrus plants in Brazil, strain Fb7 isolated from a citrus plant in Argentina and strains 3124, Pr8x, and Hib4 isolated, respectively, from coffee, plum, and hibiscus plants in Brazil. Sequencing was performed using Roche 454-GS FLX, MiSeq-Illumina or Pacific Biosciences platforms. These high-quality genome assemblies will be useful for further studies about the genomic diversity, evolution, and biology of X. fastidiosa.
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Affiliation(s)
- Paulo Marques Pierry
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - Joaquim Martins-Junior
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Paulo Adriano Zaini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Department of Plant Sciences, University of California, Davis, CA, U.S.A
| | - Guillermo Uceda-Campos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Oseias R Feitosa-Junior
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | | | - Marcos Antonio Machado
- Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, SP, Brazil
| | | | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Murilo Sena Amaral
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Felipe Cesar Beckedorff
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - Sergio Verjovski-Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
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Inuzuka LM, Macedo-Souza LI, Della-Ripa B, Monteiro FP, Ramos L, Kitajima JP, Garzon E, Kok F. Additional observation of a de novo pathogenic variant in KCNT2 leading to epileptic encephalopathy with clinical features of frontal lobe epilepsy. Brain Dev 2020; 42:691-695. [PMID: 32773162 DOI: 10.1016/j.braindev.2020.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/16/2022]
Abstract
INTRODUCTION KCNT2 was recently recognized as a gene associated with neurodevelopmental disorder and epilepsy. CASE REPORT We present an additional observation of a 16-year-old male patient with a novel de novo KCNT2 likely pathogenic variant and review the five previously reported cases of de novo variants in this gene. DISCUSSION Whole exome sequencing identified the missense variant c.725C > A p.(Thr242Asn), which was confirmed by Sanger sequencing. Our patient has a refractory stereotyped and monomorphic type of hyperkinetic focal motor seizure, similar to what is seen in frontal lobe epilepsy, occurring only during sleep. This type of seizure is not usually seen in epileptic encephalopathies.
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Affiliation(s)
- Luciana Midori Inuzuka
- Epilepsy Clinic, Hospital Sírio-Libanês, São Paulo, Brazil; Department of Neurology, University of São Paulo School of Medicine, Brazil.
| | | | - Bruno Della-Ripa
- Department of Neurology, University of São Paulo School of Medicine, Brazil
| | | | - Luiza Ramos
- Mendelics Genomic Analysis, São Paulo, Brazil
| | | | - Eliana Garzon
- Epilepsy Clinic, Hospital Sírio-Libanês, São Paulo, Brazil; Department of Neurology, University of São Paulo School of Medicine, Brazil
| | - Fernando Kok
- Mendelics Genomic Analysis, São Paulo, Brazil; Department of Neurology, University of São Paulo School of Medicine, Brazil
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13
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Mendonça RDH, Matsui C, Polido GJ, Silva AMS, Kulikowski L, Torchio Dias A, Zanardo EA, Solla DJF, Gurgel-Giannetti J, de Moura ACML, Sampaio GPC, Oliveira ASB, de Souza PVS, Pinto WBVDR, Gonçalves EA, Farias IB, Nardes F, Araújo APDQC, Marques W, Tomaselli PJ, Ribeiro MDO, Kitajima JP, Paoli Monteiro F, Saute JAM, Becker MM, Saraiva-Pereira ML, Brusius-Facchin AC, van der Linden V, Florêncio RN, Barbosa AVS, Machado-Costa MC, Pessoa ALS, Souza LS, Franca MC, Kok F, Reed UC, Zanoteli E. Intragenic variants in the SMN1 gene determine the clinical phenotype in 5q spinal muscular atrophy. Neurol Genet 2020; 6:e505. [PMID: 33062891 PMCID: PMC7524579 DOI: 10.1212/nxg.0000000000000505] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 07/09/2020] [Indexed: 02/01/2023]
Abstract
Objective The aim of the study was to report the proportion of homozygous and compound heterozygous variants in the survival motor neuron 1 (SMN1) gene in a large population of patients with spinal muscular atrophy (SMA) and to correlate the severity of the disease with the presence of specific intragenic variants in SMN1 and with the SMN2 copy number. Methods Four hundred fifty Brazilian patients with SMA were included in a retrospective study, and clinical data were analyzed compared with genetic data; the SMN2 copy number was obtained by multiplex ligation-dependent probe amplification and pathogenic variants in SMN1 by next-generation sequencing. Results Four hundred two patients (89.3%) presented homozygous exon 7-SMN1 deletion, and 48 (10.7%) were compound heterozygous for the common deletion in one allele and a point mutation in the other allele. Recurrent variants in exons 3 and 6 (c.460C>T, c.770_780dup and c.734_735insC) accounted for almost 80% of compound heterozygous patients. Another recurrent pathogenic variant was c.5C>G at exon 1. Patients with c.770_780dup and c.734_735insC had a clinical phenotype correlated with SMN2 copy number, whereas the variants c.460C>T and c.5C>G determined a milder phenotype independently of the SMN2 copies. Conclusions Patients with specific pathogenic variants (c.460C>T and c.5C>G) presented a milder phenotype, and the SMN2 copy number did not correlate with disease severity in this group.
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Affiliation(s)
- Rodrigo de Holanda Mendonça
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Ciro Matsui
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Graziela Jorge Polido
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - André Macedo Serafim Silva
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Leslie Kulikowski
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Alexandre Torchio Dias
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Evelin Aline Zanardo
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Davi Jorge Fontoura Solla
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Juliana Gurgel-Giannetti
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Ana Carolina Monteiro Lessa de Moura
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Gabriela Palhares Campolina Sampaio
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Acary Souza Bulle Oliveira
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Paulo Victor Sgobbi de Souza
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Wladimir Bocca Vieira de Rezende Pinto
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Eduardo Augusto Gonçalves
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Igor Braga Farias
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Flávia Nardes
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Alexandra Prufer de Queiroz Campos Araújo
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Wilson Marques
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Pedro José Tomaselli
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Mara Dell Ospedale Ribeiro
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - João Paulo Kitajima
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Fabíola Paoli Monteiro
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Jonas Alex Morales Saute
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Michele Michelin Becker
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Maria Luiza Saraiva-Pereira
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Ana Carolina Brusius-Facchin
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Vanessa van der Linden
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Rodrigo Neves Florêncio
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - André Vinícius Soares Barbosa
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Marcela Camara Machado-Costa
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - André Luiz Santos Pessoa
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Leticia Silva Souza
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Marcondes Cavalcante Franca
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Fernando Kok
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Umbertina Conti Reed
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
| | - Edmar Zanoteli
- Department of Neurology (R.H.M., C.M., G.J.P., A.M.S.S., D.J.F.S., F.K., U.C.R., E.Z.); Department of Pathology (L.K., A.T.D., E.A.Z.), Faculdade de Medicina da Universidade de São Paulo (FMUSP); Departamento de Pediatria e Neuropediatria (J.G.-G., A.C.M.L.M., G.P.C.S.), Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte; Departamento de Neurologia - UNIFESP (A.S.B.O., P.V.S.S., W.B.V.R.P., E.A.G., I.B.F.), São Paulo; Departamento de Pediatria, Seção de Neurologia Infantil - UFRJ (F.N., A.P.Q.C.A.), Rio de Janeiro; Departamento de Neurologia (W.M., P.J.T.), FMUSP-RP, Ribeirao Preto; Mendelics Análise Genômica (M.D.O.R., J.P.K., F.P.M., F.K.), São Paulo; Serviço de Neurologia (J.A.M.S.), Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre; Unidade de Neurologia Infantil (M.M.B.), Hospital de Clinicas de Porto Alegre; Serviço de Genética Médica (J.A.M.S., M.L.S.-P., A.C.B.-F.), Hospital de Clinicas de Porto Alegre; UFRGS, Porto Alegre; Departamento de Bioquímica - UFRGS (M.L.S.-P.), Porto Alegre; Hospital Maria Lucinda (V.L., R.N.F.), Recife; Hospital Infantil Joao Paulo II (A.V.S.B.), Fundação Hospitalar de Minas Gerais, Belo Horizonte; Escola Bahiana de Medicina e Saúde Pública (M.C.M.-C.), Salvador; Hospital Infantil Albert Sabin (A.L.S.P.), Universidade Estadual do Ceará, Fortaleza; and Departamento de Neurologia (L.S.S., M.C.F.), Unicamp, Campinas, Brazil
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14
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Inuzuka LM, Macedo-Souza LI, Della-Ripa B, Cabral KSS, Monteiro F, Kitajima JP, de Souza Godoy LF, de Souza Delgado D, Kok F, Garzon E. Neurodevelopmental disorder associated with de novo SCN3A pathogenic variants: two new cases and review of the literature. Brain Dev 2020; 42:211-216. [PMID: 31677917 DOI: 10.1016/j.braindev.2019.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/28/2019] [Accepted: 09/10/2019] [Indexed: 10/25/2022]
Abstract
SCN3A was recently recognized as a gene associated with neurodevelopmental disorder and epilepsy. We present two additional patients with a novel de novo SCN3A pathogenic variant, and a review of all published cases of de novo variants. In one of our patients brain magnetic resonance imaging (MRI) disclosed a severe polymicrogyria and in the other it was normal. The clinical phenotype was characterized by a severe developmental delay and refractory epilepsy in the patient with polymicrogyria and intellectual disability with autistic features and pharmacoresponsive epilepsy in the subject with normal MRI. Polymicrogyria, a disorder of progenitor cells proliferation and migration, is an unanticipated finding for an ion channel dysfunction.
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Affiliation(s)
- Luciana Midori Inuzuka
- Epilepsy Clinic, Hospital Sírio-Libanês, São Paulo, Brazil; Department of Neurology, University of São Paulo School of Medicine, Brazil.
| | | | - Bruno Della-Ripa
- Department of Neurology, University of São Paulo School of Medicine, Brazil.
| | - Katiane S S Cabral
- Department of Neurology, University of São Paulo School of Medicine, Brazil.
| | | | | | | | | | - Fernando Kok
- Mendelics Genomic Analysis, São Paulo, Brazil; Department of Neurology, University of São Paulo School of Medicine, Brazil.
| | - Eliana Garzon
- Epilepsy Clinic, Hospital Sírio-Libanês, São Paulo, Brazil; Department of Neurology, University of São Paulo School of Medicine, Brazil.
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15
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Guindalini RSC, Viana D, Kitajima JP, Valim A, Schlesinger D, Kok F, Koike Folgueira MAA. Detection of inherited mutations in Brazilian breast cancer patients using multi-gene panel testing. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.e13610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | - Andre Valim
- Mendelics Análise Genômica, São Paulo, Brazil
| | | | | | - Maria A. A. Koike Folgueira
- Centro de Investigação Translacional em Oncologia, Instituto do Câncer do Estado de São Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, Sao Paulo, Brazil
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16
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Vilela MDM, Del Bem LE, Van Sluys MA, de Setta N, Kitajima JP, Cruz GMQ, Sforça DA, de Souza AP, Ferreira PCG, Grativol C, Cardoso-Silva CB, Vicentini R, Vincentz M. Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum. Genome Biol Evol 2017; 9:266-278. [PMID: 28082603 PMCID: PMC5381655 DOI: 10.1093/gbe/evw293] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2016] [Indexed: 12/23/2022] Open
Abstract
Whole genome duplication has played an important role in plant evolution and diversification. Sugarcane is an important crop with a complex hybrid polyploid genome, for which the process of adaptation to polyploidy is still poorly understood. In order to improve our knowledge about sugarcane genome evolution and the homo/homeologous gene expression balance, we sequenced and analyzed 27 BACs (Bacterial Artificial Chromosome) of sugarcane R570 cultivar, containing the putative single-copy genes LFY (seven haplotypes), PHYC (four haplotypes), and TOR (seven haplotypes). Comparative genomic approaches showed that these sugarcane loci presented a high degree of conservation of gene content and collinearity (synteny) with sorghum and rice orthologous regions, but were invaded by transposable elements (TE). All the homo/homeologous haplotypes of LFY, PHYC, and TOR are likely to be functional, because they are all under purifying selection (dN/dS ≪ 1). However, they were found to participate in a nonequivalently manner to the overall expression of the corresponding gene. SNPs, indels, and amino acid substitutions allowed inferring the S. officinarum or S. spontaneum origin of the TOR haplotypes, which further led to the estimation that these two sugarcane ancestral species diverged between 2.5 and 3.5 Ma. In addition, analysis of shared TE insertions in TOR haplotypes suggested that two autopolyploidization may have occurred in the lineage that gave rise to S. officinarum, after its divergence from S. spontaneum.
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Affiliation(s)
- Mariane de Mendonça Vilela
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Luiz Eduardo Del Bem
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Nathalia de Setta
- Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | | | | | - Danilo Augusto Sforça
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Anete Pereira de Souza
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | | - Clícia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Parque Califórnia, Campos dos Goytacazes, RJ, Brazil
| | - Claudio Benicio Cardoso-Silva
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Renato Vicentini
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Michel Vincentz
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
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17
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Reis VNDS, Kitajima JP, Tahira AC, Feio-dos-Santos AC, Fock RA, Lisboa BCG, Simões SN, Krepischi ACV, Rosenberg C, Lourenço NC, Passos-Bueno MR, Brentani H. Integrative Variation Analysis Reveals that a Complex Genotype May Specify Phenotype in Siblings with Syndromic Autism Spectrum Disorder. PLoS One 2017; 12:e0170386. [PMID: 28118382 PMCID: PMC5261619 DOI: 10.1371/journal.pone.0170386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/31/2016] [Indexed: 12/30/2022] Open
Abstract
It has been proposed that copy number variations (CNVs) are associated with increased risk of autism spectrum disorder (ASD) and, in conjunction with other genetic changes, contribute to the heterogeneity of ASD phenotypes. Array comparative genomic hybridization (aCGH) and exome sequencing, together with systems genetics and network analyses, are being used as tools for the study of complex disorders of unknown etiology, especially those characterized by significant genetic and phenotypic heterogeneity. Therefore, to characterize the complex genotype-phenotype relationship, we performed aCGH and sequenced the exomes of two affected siblings with ASD symptoms, dysmorphic features, and intellectual disability, searching for de novo CNVs, as well as for de novo and rare inherited point variations—single nucleotide variants (SNVs) or small insertions and deletions (indels)—with probable functional impacts. With aCGH, we identified, in both siblings, a duplication in the 4p16.3 region and a deletion at 8p23.3, inherited by a paternal balanced translocation, t(4, 8) (p16; p23). Exome variant analysis found a total of 316 variants, of which 102 were shared by both siblings, 128 were in the male sibling exome data, and 86 were in the female exome data. Our integrative network analysis showed that the siblings’ shared translocation could explain their similar syndromic phenotype, including overgrowth, macrocephaly, and intellectual disability. However, exome data aggregate genes to those already connected from their translocation, which are important to the robustness of the network and contribute to the understanding of the broader spectrum of psychiatric symptoms. This study shows the importance of using an integrative approach to explore genotype-phenotype variability.
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MESH Headings
- Autism Spectrum Disorder/genetics
- Child
- Chromosomes, Human, Pair 4/genetics
- Chromosomes, Human, Pair 4/ultrastructure
- Chromosomes, Human, Pair 8/genetics
- Chromosomes, Human, Pair 8/ultrastructure
- Comparative Genomic Hybridization
- DNA Copy Number Variations
- Exome/genetics
- Female
- Gene Duplication
- Gene Regulatory Networks
- Genetic Association Studies
- Humans
- In Situ Hybridization, Fluorescence
- Intellectual Disability/genetics
- Learning Disabilities/genetics
- Male
- Megalencephaly/genetics
- Nerve Tissue Proteins/genetics
- Nucleic Acid Amplification Techniques
- Sequence Deletion
- Siblings
- Syndrome
- Translocation, Genetic
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Affiliation(s)
| | | | - Ana Carolina Tahira
- LIM23-Institute of Psychiatry, University of São Paulo School of Medicine, São Paulo, Brazil
| | | | - Rodrigo Ambrósio Fock
- Department of Morphology and Genetics, Federal University of São Paulo, São Paulo, Brazil
| | | | - Sérgio Nery Simões
- Department of Informatics, Federal Institute of Espírito Santo, Serra, Brazil
| | - Ana C. V. Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, São Paulo, Brazil
| | - Naila Cristina Lourenço
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, São Paulo, Brazil
| | - Helena Brentani
- LIM23-Institute of Psychiatry, University of São Paulo School of Medicine, São Paulo, Brazil
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18
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Almeida DD, Kitajima JP, Nishiyama MY, Condomitti GW, de Oliveira UC, Setúbal JC, Junqueira-de-Azevedo ILM. The complete mitochondrial genome of Bothrops jararaca (Reptilia, Serpentes, Viperidae). Mitochondrial DNA B Resour 2016; 1:907-908. [PMID: 33490425 PMCID: PMC7800333 DOI: 10.1080/23802359.2016.1149783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The complete mitochondrial genome, containing 17,526 bp, was determined from the pitviper Bothrops jararaca. It is the first mitogenome for the most medically important genus of snake in Latin America. This mitogenome has common snake mitochondrial features such as a duplicated control region that has nearly identical sequences at two different locations of the mitogenome and a translocation of tRNA-Leu (UUR). Besides, we found a translocation of the tRNA-Pro compared to Colubridae snakes. Finally, an unusual possible duplication containing a tRNA-Phe was observed for the first time and may represent a marker of the genus.
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Figueiredo T, Melo US, Pessoa ALS, Nobrega PR, Kitajima JP, Rusch H, Vaz F, Lucato LT, Zatz M, Kok F, Santos S. A homozygous loss-of-function mutation in inositol monophosphatase 1 (IMPA1) causes severe intellectual disability. Mol Psychiatry 2016; 21:1125-9. [PMID: 26416544 DOI: 10.1038/mp.2015.150] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/17/2015] [Accepted: 08/19/2015] [Indexed: 11/09/2022]
Abstract
The genetic basis of intellectual disability (ID) is extremely heterogeneous and relatively little is known about the role of autosomal recessive traits. In a field study performed in a highly inbred area of Northeastern Brazil, we identified and investigated a large consanguineous family with nine adult members affected by severe ID associated with disruptive behavior. The Genome-Wide Human SNP Array 6.0 microarray was used to determine regions of homozygosity by descent from three affected and one normal family member. Whole-exome sequencing (WES) was performed in one affected patient using the Nextera Rapid-Capture Exome kit and Illumina HiSeq2500 system to identify the causative mutation. Potentially deleterious variants detected in regions of homozygosity by descent and not present in either 59 723 unrelated individuals from the Exome Aggregation Consortium (Browser) or 1484 Brazilians were subject to further scrutiny and segregation analysis by Sanger sequencing. Homozygosity-by-descent analysis disclosed a 20.7-Mb candidate region at 8q12.3-q21.2 (lod score: 3.11). WES identified a homozygous deleterious variant in inositol monophosphatase 1 (IMPA1) (NM_005536), consisting of a 5-bp duplication (c.489_493dupGGGCT; chr8: 82,583,247; GRCh37/hg19) leading to a frameshift and a premature stop codon (p.Ser165Trpfs*10) that cosegregated with the disease in 26 genotyped family members. The IMPA1 gene product is responsible for the final step of biotransformation of inositol triphosphate and diacylglycerol, two second messengers. Despite its many physiological functions, no clinical phenotype has been assigned to this gene dysfunction to date. Additionally, IMPA1 is the main target of lithium, a drug that is at the forefront of treatment for bipolar disorder.
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Affiliation(s)
- T Figueiredo
- Northeast Biotechnology Network (RENORBIO), Federal University of Paraiba (UFPB), Joao Pessoa, Brazil.,Department of Biology, Paraiba State University (UEPB), Campina Grande, Brazil.,Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Biosciences Institute, University of Sao Paulo (USP), Sao Paulo, Brazil
| | - U S Melo
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Biosciences Institute, University of Sao Paulo (USP), Sao Paulo, Brazil
| | - A L S Pessoa
- Department of Neurology, School of Medicine, University of Sao Paulo (USP), Sao Paulo, Brazil.,School of Medicine, Fortaleza University (UNIFOR), Fortaleza, Brazil
| | - P R Nobrega
- Department of Neurology, School of Medicine, University of Sao Paulo (USP), Sao Paulo, Brazil
| | | | - H Rusch
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry, University of Amsterdam, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - F Vaz
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry, University of Amsterdam, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - L T Lucato
- Institute of Radiology, School of Medicine, University of Sao Paulo (USP), Sao Paulo, Brazil
| | - M Zatz
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Biosciences Institute, University of Sao Paulo (USP), Sao Paulo, Brazil
| | - F Kok
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Biosciences Institute, University of Sao Paulo (USP), Sao Paulo, Brazil.,Department of Neurology, School of Medicine, University of Sao Paulo (USP), Sao Paulo, Brazil.,Mendelics Genomic Analysis, Sao Paulo, Brazil
| | - S Santos
- Northeast Biotechnology Network (RENORBIO), Federal University of Paraiba (UFPB), Joao Pessoa, Brazil.,Department of Biology, Paraiba State University (UEPB), Campina Grande, Brazil
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Figueiredo T, Melo US, Pessoa ALS, Nobrega PR, Kitajima JP, Correa I, Zatz M, Kok F, Santos S. Homozygous missense mutation in MED25 segregates with syndromic intellectual disability in a large consanguineous family. J Med Genet 2014; 52:123-7. [PMID: 25527630 DOI: 10.1136/jmedgenet-2014-102793] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Intellectual disability (ID) is a highly heterogeneous condition affecting 2% of the population worldwide. In a field study conducted in a highly inbred area of Northeastern Brazil, we investigated a consanguineous family in which seven adults presented syndromic ID. METHODS Genome-Wide Human SNP Array 6.0 (Affymetrix) microarray was used to determine regions of homozygosity-by-descent and whole exome sequencing (WES) was performed in one affected individual using Extended Nextera Rapid-Capture Exome and Illumina HiSeq2500. RESULTS We found two regions with an logarithm of the odds (LOD) score of 3.234: a region spanning 4.0 Mb in 19q13.32-q13.33 and a pericentromeric 20 Mb area in chromosome 2 (2p12-q11.2). WES disclosed in the critical region of chromosome 19 a homozygous variant (c.418C>T, p.Arg140Trp) in Mediator complex subunit 25 (MED25), predicted as deleterious by PolyPhen-2, Provean, Mutation Taster and Sorting Intolerant From Tolerant (SIFT). MED25 is a component of the Mediator complex, involved in regulation of transcription of nearly all RNA polymerase II-dependent genes. Deleterious mutations in MED12, MED17 and MED23 have already been associated with ID. CONCLUSIONS These findings demonstrate that the combination of field investigation of families in highly inbred regions with modern technologies is an effective way for identifying new genes associated with ID.
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Affiliation(s)
- Thalita Figueiredo
- Northeast Biotechnology Network (RENORBIO), Federal University of Paraiba (UFPB), Joao Pessoa, PB, Brazil Department of Biology, Paraiba State University (UEPB), Campina Grande, PB, Brazil
| | - Uirá Souto Melo
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - André Luiz Santos Pessoa
- Department of Neurology, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil Fortaleza University (UNIFOR), Fortaleza, CE, Brazil
| | - Paulo Ribeiro Nobrega
- Department of Neurology, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | | | - Igor Correa
- Mendelics Genomic Analysis, Sao Paulo, SP, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - Fernando Kok
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of Sao Paulo (USP), Sao Paulo, SP, Brazil Department of Neurology, School of Medicine, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - Silvana Santos
- Northeast Biotechnology Network (RENORBIO), Federal University of Paraiba (UFPB), Joao Pessoa, PB, Brazil Department of Biology, Paraiba State University (UEPB), Campina Grande, PB, Brazil
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21
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Sperb-Ludwig F, Alegra T, Velho RV, Ludwig N, Kim CA, Kok F, Kitajima JP, van Meel E, Kornfeld S, Burin MG, Schwartz IVD. Exome sequencing for mucolipidosis III: Detection of a novel GNPTAB gene mutation in a patient with a very mild phenotype. Mol Genet Metab Rep 2014. [PMID: 28649523 PMCID: PMC5471150 DOI: 10.1016/j.ymgmr.2014.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mucolipidosis II and III alpha/beta (ML II/III alpha/beta) are rare autosomal recessive lysosomal storage diseases that are caused by a deficiency of UDP-GlcNAc:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase, the enzyme responsible for the synthesis of the mannose 6-phosphate targeting signal on lysosomal hydrolases. A Brazilian patient suspected of having a very mild ML III was investigated using whole next-generation sequencing (NGS). Two mutations in the GNPTAB gene were detected and confirmed to be in trans status by parental analysis: c.1208T>C (p.Ile403Thr), previously reported as being pathogenic, and the novel mutation c.1723G>A (p.Gly575Arg). This study demonstrates the effectiveness of using whole NGS for the molecular diagnosis of very mild ML III alpha/beta patients.
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Affiliation(s)
- F Sperb-Ludwig
- BRAIN (Basic Research and Advanced Investigations in Neurosciences) Laboratory, Hospital de Clínicas de Porto Alegre (HCPA), Brazil.,Postgraduate Program in Medical Sciences: Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil
| | - T Alegra
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Brazil
| | - R V Velho
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Brazil
| | - N Ludwig
- BRAIN (Basic Research and Advanced Investigations in Neurosciences) Laboratory, Hospital de Clínicas de Porto Alegre (HCPA), Brazil
| | - C A Kim
- Genetics Unit, Instituto da Criança da Faculdade de Medicina, Universidade de São Paulo, Brazil
| | - F Kok
- Mendelics Genomic Analysis, São Paulo, Brazil
| | | | - E van Meel
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, USA
| | - S Kornfeld
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, USA
| | - M G Burin
- Medical Genetics Service, HCPA, Brazil
| | - I V D Schwartz
- BRAIN (Basic Research and Advanced Investigations in Neurosciences) Laboratory, Hospital de Clínicas de Porto Alegre (HCPA), Brazil.,Postgraduate Program in Medical Sciences: Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil.,Postgraduate Program in Genetics and Molecular Biology, UFRGS, Brazil.,Medical Genetics Service, HCPA, Brazil.,Genetics Department, UFRGS, Brazil
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22
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de Setta N, Monteiro-Vitorello CB, Metcalfe CJ, Cruz GMQ, Del Bem LE, Vicentini R, Nogueira FTS, Campos RA, Nunes SL, Turrini PCG, Vieira AP, Ochoa Cruz EA, Corrêa TCS, Hotta CT, de Mello Varani A, Vautrin S, da Trindade AS, de Mendonça Vilela M, Lembke CG, Sato PM, de Andrade RF, Nishiyama MY, Cardoso-Silva CB, Scortecci KC, Garcia AAF, Carneiro MS, Kim C, Paterson AH, Bergès H, D'Hont A, de Souza AP, Souza GM, Vincentz M, Kitajima JP, Van Sluys MA. Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics 2014; 15:540. [PMID: 24984568 PMCID: PMC4122759 DOI: 10.1186/1471-2164-15-540] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 06/19/2014] [Indexed: 01/24/2023] Open
Abstract
Background Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome. Results Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences. Conclusion This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-540) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marie-Anne Van Sluys
- Departamento de Botânica - Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo 05508-090, SP, Brazil.
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23
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Vieira NM, Naslavsky MS, Licinio L, Kok F, Schlesinger D, Vainzof M, Sanchez N, Kitajima JP, Gal L, Cavaçana N, Serafini PR, Chuartzman S, Vasquez C, Mimbacas A, Nigro V, Pavanello RC, Schuldiner M, Kunkel LM, Zatz M. A defect in the RNA-processing protein HNRPDL causes limb-girdle muscular dystrophy 1G (LGMD1G). Hum Mol Genet 2014; 23:4103-10. [PMID: 24647604 DOI: 10.1093/hmg/ddu127] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Limb-girdle muscular dystrophies (LGMD) are a heterogeneous group of genetically determined muscle disorders with a primary or predominant involvement of the pelvic or shoulder girdle musculature. More than 20 genes with autosomal recessive (LGMD2A to LGMD2Q) and autosomal dominant inheritance (LGMD1A to LGMD1H) have been mapped/identified to date. Mutations are known for six among the eight mapped autosomal dominant forms: LGMD1A (myotilin), LGMD1B (lamin A/C), LGMD1C (caveolin-3), LGMD1D (desmin), LGMD1E (DNAJB6), and more recently for LGMD1F (transportin-3). Our group previously mapped the LGMD1G gene at 4q21 in a Caucasian-Brazilian family. We now mapped a Uruguayan family with patients displaying a similar LGMD1G phenotype at the same locus. Whole genome sequencing identified, in both families, mutations in the HNRPDL gene. HNRPDL is a heterogeneous ribonucleoprotein family member, which participates in mRNA biogenesis and metabolism. Functional studies performed in S. cerevisiae showed that the loss of HRP1 (yeast orthologue) had pronounced effects on both protein levels and cell localizations, and yeast proteome revealed dramatic reorganization of proteins involved in RNA-processing pathways. In vivo analysis showed that hnrpdl is important for muscle development in zebrafish, causing a myopathic phenotype when knocked down. The present study presents a novel association between a muscular disorder and a RNA-related gene and reinforces the importance of RNA binding/processing proteins in muscle development and muscle disease. Understanding the role of these proteins in muscle might open new therapeutic approaches for muscular dystrophies.
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Affiliation(s)
- Natássia M Vieira
- Human Genome and Stem Cell Center, Biosciences Institute, University of São Paulo, São Paulo, Brazil Program in Genomics, Department of Pediatrics and The Manton Center for Orphan Disease Research, Children's Hospital Boston, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Michel S Naslavsky
- Human Genome and Stem Cell Center, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Luciana Licinio
- Human Genome and Stem Cell Center, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Fernando Kok
- Human Genome and Stem Cell Center, Biosciences Institute, University of São Paulo, São Paulo, Brazil Department of Neurology, University of São Paulo Medical School, São Paulo, Brazil Mendelics Análise Genômica, São Paulo, Brazil
| | - David Schlesinger
- Human Genome and Stem Cell Center, Biosciences Institute, University of São Paulo, São Paulo, Brazil Mendelics Análise Genômica, São Paulo, Brazil Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Mariz Vainzof
- Human Genome and Stem Cell Center, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Nury Sanchez
- Hospital de Clínicas, Montevideu, Montevideo, Uruguay
| | - João Paulo Kitajima
- Human Genome and Stem Cell Center, Biosciences Institute, University of São Paulo, São Paulo, Brazil Mendelics Análise Genômica, São Paulo, Brazil
| | - Lihi Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Natale Cavaçana
- Human Genome and Stem Cell Center, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Peter R Serafini
- Program in Genomics, Department of Pediatrics and The Manton Center for Orphan Disease Research, Children's Hospital Boston, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Silvia Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Adriana Mimbacas
- Department of Genetics, Clemente Estabele Institute, Montevideo, Uruguay
| | - Vincenzo Nigro
- TIGEM (Telethon Institute of Genetics and Medicine), Napoli, Italy
| | - Rita C Pavanello
- Human Genome and Stem Cell Center, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Louis M Kunkel
- Program in Genomics, Department of Pediatrics and The Manton Center for Orphan Disease Research, Children's Hospital Boston, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mayana Zatz
- Human Genome and Stem Cell Center, Biosciences Institute, University of São Paulo, São Paulo, Brazil
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Almeida GT, Amaral MS, Beckedorff FCF, Kitajima JP, DeMarco R, Verjovski-Almeida S. Exploring the Schistosoma mansoni adult male transcriptome using RNA-seq. Exp Parasitol 2011; 132:22-31. [PMID: 21745473 DOI: 10.1016/j.exppara.2011.06.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 06/25/2011] [Accepted: 06/25/2011] [Indexed: 10/18/2022]
Abstract
Schistosoma mansoni is one of the agents of schistosomiasis, a chronic and debilitating disease. Here we present a transcriptome-wide characterization of adult S. mansoni males by high-throughput RNA-sequencing. We obtained 1,620,432 high-quality ESTs from a directional strand-specific cDNA library, resulting in a 26% higher coverage of genome bases than that of the public ESTs available at NCBI. With a 15×-deep coverage of transcribed genomic regions, our data were able to (i) confirm for the first time 990 predictions without previous evidence of transcription; (ii) correct gene predictions; (iii) discover 989 and 1196 RNA-seq contigs that map to intergenic and intronic genomic regions, respectively, where no gene had been predicted before. These contigs could represent new protein-coding genes or non-coding RNAs (ncRNAs). Interestingly, we identified 11 novel Micro-exon genes (MEGs). These data reveal new features of the S. mansoni transcriptional landscape and significantly advance our understanding of the parasite transcriptome.
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25
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Pascon RC, Kitajima JP, Breton MC, Assumpção L, Greggio C, Zanca AS, Okura VK, Alegria MC, Camargo ME, Silva GGC, Cardozo JC, Vallim MA, Franco SF, Silva VH, Jordão H, Oliveira F, Giachetto PF, Ferrari F, Aguilar-Vildoso CI, Franchiscini FJB, Silva JMF, Arruda P, Ferro JA, Reinach F, da Silva ACR. The Complete Nucleotide Sequence and Genomic Organization of Citrus Leprosis Associated Virus, Cytoplasmatic type (CiLV-C). Virus Genes 2006; 32:289-98. [PMID: 16732481 DOI: 10.1007/s11262-005-6913-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2005] [Revised: 08/25/2005] [Accepted: 08/29/2005] [Indexed: 10/24/2022]
Abstract
The Citrus leprosis disease (CiL) is associated to a virus (CiLV) transmitted by Brevipalpus spp. mites (Acari: Tenuipalpidae). CiL is endemic in Brazil and its recently spreading to Central America represents a threat to citrus industry in the USA. Electron microscopy images show two forms of CiLV: a rare nuclear form, characterized by rod-shaped naked particle (CiLV-N) and a common cytoplasmic form (CiLV-C) associated with bacilliform-enveloped particle and cytoplasmic viroplasm. Due to this morphological feature, CiLV-C has been treated as Rhabdovirus-like. In this paper we present the complete nucleotide sequence and genomic organization of CiLV-C. It is a bipartite virus with sequence similarity to ssRNA positive plant virus. RNA1 encodes a putative replicase polyprotein and an ORF with no known function. RNA2 encodes 4 ORFs. pl5, p24 and p61 have no significant similarity to any known proteins and p32 encodes a protein with similarity to a viral movement protein. The CiLV-C sequences are associated with typical symptoms of CiL by RT-PCR. Phylogenetic analysis suggests that CiLV-C is probably a member of a new family of plant virus evolutionarily related to Tobamovirus.
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Affiliation(s)
- Renata C Pascon
- Alellyx Applied Genomics, Techno Park (Rod. Anhanguera Km 104), Rua James Clerk Maxwell 320, 13069-380, Campinas, SP, Brazil
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Vieira LGE, Andrade AC, Colombo CA, Moraes AHDA, Metha Â, Oliveira ACD, Labate CA, Marino CL, Monteiro-Vitorello CDB, Monte DDC, Giglioti É, Kimura ET, Romano E, Kuramae EE, Lemos EGM, Almeida ERPD, Jorge ÉC, Albuquerque ÉVS, Silva FRD, Vinecky F, Sawazaki HE, Dorry HFA, Carrer H, Abreu IN, Batista JAN, Teixeira JB, Kitajima JP, Xavier KG, Lima LMD, Camargo LEAD, Pereira LFP, Coutinho LL, Lemos MVF, Romano MR, Machado MA, Costa MMDC, Sá MFGD, Goldman MHS, Ferro MIT, Tinoco MLP, Oliveira MC, Van Sluys MA, Shimizu MM, Maluf MP, Eira MTSD, Guerreiro Filho O, Arruda P, Mazzafera P, Mariani PDSC, Oliveira RLD, Harakava R, Balbao SF, Tsai SM, Mauro SMZD, Santos SN, Siqueira WJ, Costa GGL, Formighieri EF, Carazzolle MF, Pereira GAG. Brazilian coffee genome project: an EST-based genomic resource. ACTA ACUST UNITED AC 2006. [DOI: 10.1590/s1677-04202006000100008] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Coffee is one of the most valuable agricultural commodities and ranks second on international trade exchanges. The genus Coffea belongs to the Rubiaceae family which includes other important plants. The genus contains about 100 species but commercial production is based only on two species, Coffea arabica and Coffea canephora that represent about 70 % and 30 % of the total coffee market, respectively. The Brazilian Coffee Genome Project was designed with the objective of making modern genomics resources available to the coffee scientific community, working on different aspects of the coffee production chain. We have single-pass sequenced a total of 214,964 randomly picked clones from 37 cDNA libraries of C. arabica, C. canephora and C. racemosa, representing specific stages of cells and plant development that after trimming resulted in 130,792, 12,381 and 10,566 sequences for each species, respectively. The ESTs clustered into 17,982 clusters and 32,155 singletons. Blast analysis of these sequences revealed that 22 % had no significant matches to sequences in the National Center for Biotechnology Information database (of known or unknown function). The generated coffee EST database resulted in the identification of close to 33,000 different unigenes. Annotated sequencing results have been stored in an online database at <A HREF="http://www.lge.ibi.unicamp.br/cafe">http://www.lge.ibi.unicamp.br/cafe</A>. Resources developed in this project provide genetic and genomic tools that may hold the key to the sustainability, competitiveness and future viability of the coffee industry in local and international markets.
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Affiliation(s)
| | | | | | | | - Ângela Metha
- Embrapa Recursos Genéticos e Biotecnologia, Brazil
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27
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Maccheroni W, Alegria MC, Greggio CC, Piazza JP, Kamla RF, Zacharias PRA, Bar-Joseph M, Kitajima EW, Assumpção LC, Camarotte G, Cardozo J, Casagrande EC, Ferrari F, Franco SF, Giachetto PF, Girasol A, Jordão H, Silva VHA, Souza LCA, Aguilar-Vildoso CI, Zanca AS, Arruda P, Kitajima JP, Reinach FC, Ferro JA, da Silva ACR. Identification and genomic characterization of a new virus (Tymoviridae family) associated with citrus sudden death disease. J Virol 2005; 79:3028-37. [PMID: 15709023 PMCID: PMC548464 DOI: 10.1128/jvi.79.5.3028-3037.2005] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2004] [Accepted: 10/21/2004] [Indexed: 11/20/2022] Open
Abstract
Citrus sudden death (CSD) is a new disease that has killed approximately 1 million orange trees in Brazil. Here we report the identification of a new virus associated with the disease. RNAs isolated from CSD-affected and nonaffected trees were used to construct cDNA libraries. A set of viral sequences present exclusively in libraries of CSD-affected trees was used to obtain the complete genome sequence of the new virus. Phylogenetic analysis revealed that this virus is a new member of the genus Marafivirus. Antibodies raised against the putative viral coat proteins allowed detection of viral antigens of expected sizes in affected plants. Electron microscopy of purified virus confirmed the presence of typical isometric Marafivirus particles. The screening of 773 affected and nonaffected citrus trees for the presence of the virus showed a 99.7% correlation between disease symptoms and the presence of the virus. We also detected the virus in aphids feeding on affected trees. These results suggest that this virus is likely to be the causative agent of CSD. The virus was named Citrus sudden death-associated virus.
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Affiliation(s)
- Walter Maccheroni
- Alellyx Applied Genomics, Techno Park (Rod. Anhanguera Km 104), Rua James Clerk Maxwell 320, 13069-380 Campinas, SP, Brazil
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28
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Calsa Júnior T, Carraro DM, Benatti MR, Barbosa AC, Kitajima JP, Carrer H. Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome. Curr Genet 2004; 46:366-73. [PMID: 15526204 DOI: 10.1007/s00294-004-0542-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2004] [Revised: 09/30/2004] [Accepted: 10/03/2004] [Indexed: 11/29/2022]
Abstract
The complete nucleotide sequence of the chloroplast genome of sugarcane (Saccharum officinarum) was determined. It consists of 141,182 base-pairs (bp), containing a pair of inverted repeat regions (IR(A), IR(B)) of 22,794 bp each. The IR(A) and IR(B) sequences separate a small single copy region (12,546 bp) and a large single copy (83,048 bp) region. The gene content and relative arrangement of the 116 identified genes (82 peptide-encoding genes, four ribosomal RNA genes, 30 tRNA genes), with the 16 ycf genes, are highly similar to maize. Editing events, defined as C-to-U transitions in the mRNA sequences, were comparable with those observed in maize, rice and wheat. The conservation of gene organization and mRNA editing suggests a common ancestor for the sugarcane and maize plastomes. These data provide the basis for functional analysis of plastid genes and plastid metabolism within the Poaceae. The sugarcane chloroplast DNA sequence is available at GenBank under accession NC005878.
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Affiliation(s)
- Tercilio Calsa Júnior
- ESALQ/Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba, 13418-900 São Paulo, Brazil
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29
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Nascimento ALTO, Ko AI, Martins EAL, Monteiro-Vitorello CB, Ho PL, Haake DA, Verjovski-Almeida S, Hartskeerl RA, Marques MV, Oliveira MC, Menck CFM, Leite LCC, Carrer H, Coutinho LL, Degrave WM, Dellagostin OA, El-Dorry H, Ferro ES, Ferro MIT, Furlan LR, Gamberini M, Giglioti EA, Góes-Neto A, Goldman GH, Goldman MHS, Harakava R, Jerônimo SMB, Junqueira-de-Azevedo ILM, Kimura ET, Kuramae EE, Lemos EGM, Lemos MVF, Marino CL, Nunes LR, de Oliveira RC, Pereira GG, Reis MS, Schriefer A, Siqueira WJ, Sommer P, Tsai SM, Simpson AJG, Ferro JA, Camargo LEA, Kitajima JP, Setubal JC, Van Sluys MA. Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis. J Bacteriol 2004; 186:2164-72. [PMID: 15028702 PMCID: PMC374407 DOI: 10.1128/jb.186.7.2164-2172.2004] [Citation(s) in RCA: 312] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leptospira species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in accidental hosts, including humans. Complete genome sequencing of Leptospira interrogans serovar Copenhageni and comparative analysis with the available Leptospira interrogans serovar Lai genome reveal that despite overall genetic similarity there are significant structural differences, including a large chromosomal inversion and extensive variation in the number and distribution of insertion sequence elements. Genome sequence analysis elucidates many of the novel aspects of leptospiral physiology relating to energy metabolism, oxygen tolerance, two-component signal transduction systems, and mechanisms of pathogenesis. A broad array of transcriptional regulation proteins and two new families of afimbrial adhesins which contribute to host tissue colonization in the early steps of infection were identified. Differences in genes involved in the biosynthesis of lipopolysaccharide O side chains between the Copenhageni and Lai serovars were identified, offering an important starting point for the elucidation of the organism's complex polysaccharide surface antigens. Differences in adhesins and in lipopolysaccharide might be associated with the adaptation of serovars Copenhageni and Lai to different animal hosts. Hundreds of genes encoding surface-exposed lipoproteins and transmembrane outer membrane proteins were identified as candidates for development of vaccines for the prevention of leptospirosis.
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Affiliation(s)
- A L T O Nascimento
- Centro de Biotecnologia, Instituto Butantan, Universidade de São Paulo, São Paulo, Brazil.
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30
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Sakabe NJ, de Souza JES, Galante PAF, de Oliveira PSL, Passetti F, Brentani H, Osório EC, Zaiats AC, Leerkes MR, Kitajima JP, Brentani RR, Strausberg RL, Simpson AJG, de Souza SJ. ORESTES are enriched in rare exon usage variants affecting the encoded proteins. C R Biol 2003; 326:979-85. [PMID: 14744104 DOI: 10.1016/j.crvi.2003.09.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A significant fraction of the variability found in the human transcriptome is due to alternative splicing, including alternative exon usage (AEU), intron retention and use of cryptic splice sites. We present a comparison of a large-scale analysis of AEU in the human transcriptome through genome mapping of Open Reading Frame ESTs (ORESTES) and conventional ESTs. It is shown here that ORESTES probe low abundant messages more efficiently. In addition, most of the variants detected by ORESTES affect the structure of the corresponding proteins.
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Affiliation(s)
- Noboru Jo Sakabe
- Ludwig Institute for Cancer Research, Sao Paulo Branch, Rua Prof Antonio Prudente 109, 4(o) andar, 01509-010, Sao Paulo, Brazil
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31
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Van Sluys MA, de Oliveira MC, Monteiro-Vitorello CB, Miyaki CY, Furlan LR, Camargo LEA, da Silva ACR, Moon DH, Takita MA, Lemos EGM, Machado MA, Ferro MIT, da Silva FR, Goldman MHS, Goldman GH, Lemos MVF, El-Dorry H, Tsai SM, Carrer H, Carraro DM, de Oliveira RC, Nunes LR, Siqueira WJ, Coutinho LL, Kimura ET, Ferro ES, Harakava R, Kuramae EE, Marino CL, Giglioti E, Abreu IL, Alves LMC, do Amaral AM, Baia GS, Blanco SR, Brito MS, Cannavan FS, Celestino AV, da Cunha AF, Fenille RC, Ferro JA, Formighieri EF, Kishi LT, Leoni SG, Oliveira AR, Rosa VE, Sassaki FT, Sena JAD, de Souza AA, Truffi D, Tsukumo F, Yanai GM, Zaros LG, Civerolo EL, Simpson AJG, Almeida NF, Setubal JC, Kitajima JP. Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J Bacteriol 2003; 185:1018-26. [PMID: 12533478 PMCID: PMC142809 DOI: 10.1128/jb.185.3.1018-1026.2003] [Citation(s) in RCA: 270] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2002] [Accepted: 10/16/2002] [Indexed: 11/20/2022] Open
Abstract
Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the American continent, and induces diverse disease phenotypes. Previous molecular analyses indicated three distinct groups of X. fastidiosa isolates that were expected to be genetically divergent. Here we report the genome sequence of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with Pierce's disease (PD) in a wine-grape-growing region of California. Comparative analyses with a previously sequenced X. fastidiosa strain responsible for citrus variegated chlorosis (CVC) revealed that 98% of the PD X. fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain 9a5c genes. Furthermore, the average amino acid identity of the open reading frames in the strains is 95.7%. Genomic differences are limited to phage-associated chromosomal rearrangements and deletions that also account for the strain-specific genes present in each genome. Genomic islands, one in each genome, were identified, and their presence in other X. fastidiosa strains was analyzed. We conclude that these two organisms have identical metabolic functions and are likely to use a common set of genes in plant colonization and pathogenesis, permitting convergence of functional genomic strategies.
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Affiliation(s)
- M A Van Sluys
- Instituto de Biociência, Universidade de São Paulo, R. do Matão 227, 05508-900 São Paulo, Brazil.
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32
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da Silva ACR, Ferro JA, Reinach FC, Farah CS, Furlan LR, Quaggio RB, Monteiro-Vitorello CB, Van Sluys MA, Almeida NF, Alves LMC, do Amaral AM, Bertolini MC, Camargo LEA, Camarotte G, Cannavan F, Cardozo J, Chambergo F, Ciapina LP, Cicarelli RMB, Coutinho LL, Cursino-Santos JR, El-Dorry H, Faria JB, Ferreira AJS, Ferreira RCC, Ferro MIT, Formighieri EF, Franco MC, Greggio CC, Gruber A, Katsuyama AM, Kishi LT, Leite RP, Lemos EGM, Lemos MVF, Locali EC, Machado MA, Madeira AMBN, Martinez-Rossi NM, Martins EC, Meidanis J, Menck CFM, Miyaki CY, Moon DH, Moreira LM, Novo MTM, Okura VK, Oliveira MC, Oliveira VR, Pereira HA, Rossi A, Sena JAD, Silva C, de Souza RF, Spinola LAF, Takita MA, Tamura RE, Teixeira EC, Tezza RID, Trindade dos Santos M, Truffi D, Tsai SM, White FF, Setubal JC, Kitajima JP. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 2002; 417:459-63. [PMID: 12024217 DOI: 10.1038/417459a] [Citation(s) in RCA: 782] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genus Xanthomonas is a diverse and economically important group of bacterial phytopathogens, belonging to the gamma-subdivision of the Proteobacteria. Xanthomonas axonopodis pv. citri (Xac) causes citrus canker, which affects most commercial citrus cultivars, resulting in significant losses worldwide. Symptoms include canker lesions, leading to abscission of fruit and leaves and general tree decline. Xanthomonas campestris pv. campestris (Xcc) causes black rot, which affects crucifers such as Brassica and Arabidopsis. Symptoms include marginal leaf chlorosis and darkening of vascular tissue, accompanied by extensive wilting and necrosis. Xanthomonas campestris pv. campestris is grown commercially to produce the exopolysaccharide xanthan gum, which is used as a viscosifying and stabilizing agent in many industries. Here we report and compare the complete genome sequences of Xac and Xcc. Their distinct disease phenotypes and host ranges belie a high degree of similarity at the genomic level. More than 80% of genes are shared, and gene order is conserved along most of their respective chromosomes. We identified several groups of strain-specific genes, and on the basis of these groups we propose mechanisms that may explain the differing host specificities and pathogenic processes.
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Affiliation(s)
- A C R da Silva
- Departamento de Bioquímica, Instituto de Química, Av. Prof. Lineu Prestes 748, São Paulo, SP, Brazil
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33
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Van Sluys MA, Monteiro-Vitorello CB, Camargo LEA, Menck CFM, Da Silva ACR, Ferro JA, Oliveira MC, Setubal JC, Kitajima JP, Simpson AJ. Comparative genomic analysis of plant-associated bacteria. Annu Rev Phytopathol 2002; 40:169-189. [PMID: 12147758 DOI: 10.1146/annurev.phyto.40.030402.090559] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This review deals with a comparative analysis of seven genome sequences from plant-associated bacteria. These are the genomes of Agrobacterium tumefaciens, Mesorhizobium loti, Sinorhizobium meliloti, Xanthomonas campestris pv campestris, Xanthomonas axonopodis pv citri, Xylella fastidiosa, and Ralstonia solanacearum. Genome structure and the metabolism pathways available highlight the compromise between the genome size and lifestyle. Despite the recognized importance of the type III secretion system in controlling host compatibility, its presence is not universal in all necrogenic pathogens. Hemolysins, hemagglutinins, and some adhesins, previously reported only for mammalian pathogens, are present in most organisms discussed. Different numbers and combinations of cell wall degrading enzymes and genes to overcome the oxidative burst generally induced by the plant host are characterized in these genomes. A total of 19 genes not involved in housekeeping functions were found common to all these bacteria.
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Affiliation(s)
- M A Van Sluys
- Depto de Botânica, Instituto de Biociências, Universidade de São Paulo, Brazil.
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34
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Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida NF, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee D, Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li MJ, McClelland E, Palmieri A, Raymond C, Rouse G, Saenphimmachak C, Wu Z, Romero P, Gordon D, Zhang S, Yoo H, Tao Y, Biddle P, Jung M, Krespan W, Perry M, Gordon-Kamm B, Liao L, Kim S, Hendrick C, Zhao ZY, Dolan M, Chumley F, Tingey SV, Tomb JF, Gordon MP, Olson MV, Nester EW. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 2001; 294:2317-23. [PMID: 11743193 DOI: 10.1126/science.1066804] [Citation(s) in RCA: 569] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont Sinorhizobium meliloti suggest a recent evolutionary divergence. Their similarities include metabolic, transport, and regulatory systems that promote survival in the highly competitive rhizosphere; differences are apparent in their genome structure and virulence gene complement. Availability of the A. tumefaciens sequence will facilitate investigations into the molecular basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles.
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Affiliation(s)
- D W Wood
- Department of Microbiology, University of Washington, 1959 NE Pacific Street, Box 357242, Seattle, WA 98195, USA
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35
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Simpson AJ, Reinach FC, Arruda P, Abreu FA, Acencio M, Alvarenga R, Alves LM, Araya JE, Baia GS, Baptista CS, Barros MH, Bonaccorsi ED, Bordin S, Bové JM, Briones MR, Bueno MR, Camargo AA, Camargo LE, Carraro DM, Carrer H, Colauto NB, Colombo C, Costa FF, Costa MC, Costa-Neto CM, Coutinho LL, Cristofani M, Dias-Neto E, Docena C, El-Dorry H, Facincani AP, Ferreira AJ, Ferreira VC, Ferro JA, Fraga JS, França SC, Franco MC, Frohme M, Furlan LR, Garnier M, Goldman GH, Goldman MH, Gomes SL, Gruber A, Ho PL, Hoheisel JD, Junqueira ML, Kemper EL, Kitajima JP, Krieger JE, Kuramae EE, Laigret F, Lambais MR, Leite LC, Lemos EG, Lemos MV, Lopes SA, Lopes CR, Machado JA, Machado MA, Madeira AM, Madeira HM, Marino CL, Marques MV, Martins EA, Martins EM, Matsukuma AY, Menck CF, Miracca EC, Miyaki CY, Monteriro-Vitorello CB, Moon DH, Nagai MA, Nascimento AL, Netto LE, Nhani A, Nobrega FG, Nunes LR, Oliveira MA, de Oliveira MC, de Oliveira RC, Palmieri DA, Paris A, Peixoto BR, Pereira GA, Pereira HA, Pesquero JB, Quaggio RB, Roberto PG, Rodrigues V, de M Rosa AJ, de Rosa VE, de Sá RG, Santelli RV, Sawasaki HE, da Silva AC, da Silva AM, da Silva FR, da Silva WA, da Silveira JF, Silvestri ML, Siqueira WJ, de Souza AA, de Souza AP, Terenzi MF, Truffi D, Tsai SM, Tsuhako MH, Vallada H, Van Sluys MA, Verjovski-Almeida S, Vettore AL, Zago MA, Zatz M, Meidanis J, Setubal JC. The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. Nature 2000; 406:151-9. [PMID: 10910347 DOI: 10.1038/35018003] [Citation(s) in RCA: 538] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis--a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived and include virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer.
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Affiliation(s)
- A J Simpson
- Instituto Ludwig de Pesquisa sobre o Câncer, São Paulo, SP, Brazil
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