Acquisition of a genetic analyzer for automated DNA sequencing

• Grant number: 09/53946-3
• Support Opportunities: Multi-user Equipment Program
• Start date: October 01, 2010
• End date: September 30, 2012
• Field of knowledge: Biological Sciences - Microbiology - Applied Microbiology
• Principal Investigator: João Renato Rebello Pinho
• Grantee: João Renato Rebello Pinho
• Host Institution: Instituto de Medicina Tropical de São Paulo (IMT). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• EMU web page: Página do Equipamento Multiusuário não informada
• Type of equipment: Tipo de Equipamento Multiusuário não informado
• Manufacturer: Fabricante não informado
• Model: Modelo não informado

Abstract

The availability of a next-generation DNA genetic analyzer for DNA sequencing, to be used by several laboratories of the USP School of Tropical Medicine and São Paulo Institute of Tropical Medicine is very important, because there is no such device currently available at either institution. The device requested in this proposal will replace the ABI 377 sequencers currently in use, which produce sequences of good quality. However, those devices require much more care, and technical assistance will soon be discontinued. Another advantage of the new sequencers is the new software used for the interpretation of sequences: whereas the ABI 377 and ABI 3100 DNA sequencers use the ABI basecaller program, model 3500 uses the KB basecaller program. The KB basecaller program allows the identification of mixed bases, which has to be done manually with the ABI basecaller program. In addition, this new software version has its own method of evaluating the quality of sequences, which can dispense with the need for other software, such as Phred and Phrap, with the advantage that the new software already assesses the quality of sequences with mixed bases. Although sequences with mixed bases are found in eukaryotic organisms that are heterozygous, sequences with mixed bases are found much more frequently in the sequencing of viral populations, such as those viruses that replicate through enzyme activity without revising, such as the viruses that replicate RNA-dependent DNA polymerase (reverse transcriptase) or RNA-dependent RNA polymerase. Therefore, the acquisition of this device will meet the needs of laboratories working with viruses and will also be used for the sequencing of nucleic acids and the genomic study of polymorphisms of microsatellites (short tandem repeat polymorphisms), all of which are quite important for the analysis of the human host. The device will be operated by a team with extensive experience in the sequencing of viral nucleic acids and will be of great benefit to the groups involved, who will be able to conduct their studies in a more timely manner. (AU)

Scientific publications

(9)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

EVANGELISTA, ANDREIA SILVA; NAKHLE, MARIA CRISTINA; DE ARAUJO, THIAGO FERREIRA; ABRANTES-LEMOS, CLARICE PIRES; DEGUTI, MARTA MITIKO; CARRILHO, FLAIR JOSE; RACHID CANCADO, EDUARDO LUIZ. HFE Genotyping in Patients with Elevated Serum Iron Indices and Liver Diseases. BIOMED RESEARCH INTERNATIONAL, 2015. (09/53946-3)

GODOY, BIBIANE A.; GOMES-GOUVEA, MICHELE S.; ZAGONEL-OLIVEIRA, MARCELO; ALVARADO-MORA, MONICA V.; SALZANO, FRANCISCO M.; PINHO, JOAO R. R.; FAGUNDES, NELSON J. R.. High prevalence of HBV/A1 subgenotype in native south Americans may be explained by recent economic developments in the Amazon. INFECTION GENETICS AND EVOLUTION, v. 43, p. 354-363, SEP 2016. (09/53946-3)

FLORENCIO CHACHA, SILVANA GAMA; SOARES GOMES-GOUVEA, MICHELE; MALTA, FERNANDA DE MELLO; FERREIRA, SANDRO DA COSTA; VILLANOVA, MRCIA GUIMARAES; SOUZA, FERNANDA FERNANDES; TEIXEIRA, ANDREZA CORREA; DA COSTA PASSOS, AFONSO DINIS; REBELLO PINHO, JOAO RENATO; CANDOLO MARTINELLI, ANA DE LOURDES. Basal core promoter and precore mutations among hepatitis B virus circulating in Brazil and its association with severe forms of hepatic diseases. Memórias do Instituto Oswaldo Cruz, v. 112, n. 9, p. 626-631, SEP 2017. (08/11472-2, 09/53946-3)

SOUZA DE SOUZA, ALEX JUNIOR; GOMES-GOUVEA, MICHELE SOARES; PEREIRA SOARES, MANOEL DO CARMO; REBELLO PINHO, JOAO RENATO; MALHEIROS, ANDREZA PINHEIRO; CARNEIRO, LILIANE ALMEIDA; LOPES DOS SANTOS, DEBORA REGINA; ASSUNCAO PEREIRA, WASHINGTON LUIZ. HEV infection in swine from Eastern Brazilian Amazon: Evidence of co-infection by different subtypes. COMPARATIVE IMMUNOLOGY MICROBIOLOGY AND INFECTIOUS DISEASES, v. 35, n. 5, p. 477-485, SEP 2012. (09/53946-3, 10/50081-9)

CRUZ SANTOS, MAX DIEGO; GOMES-GOUVEA, MICHELE SOARES; COSTA NUNES, JOMAR DIOGO; FONSECA BARROS, LENA MARIA; CARRILHO, FLAIR JOSE; PAIVA FERREIRA, ADALGISA DE SOUSA; REBELLO PINHO, JOAO RENATO. The hepatitis delta genotype 8 in Northeast Brazil: The North Atlantic slave trade as the potential route for infection. VIRUS RESEARCH, v. 224, p. 6-11, SEP 15 2016. (09/53946-3)

FLORENCIO CHACHA, SILVANA GAMA; SOARES GOMES-GOUVEA, MICHELE; MALTA, FERNANDA DE MELLO; FERREIRA, SANDRO DA COSTA; VILLANOVA, MRCIA GUIMARAES; SOUZA, FERNANDA FERNANDES; TEIXEIRA, ANDREZA CORREA; DA COSTA PASSOS, AFONSO DINIS; REBELLO PINHO, JOAO RENATO; CANDOLO MARTINELLI, ANA DE LOURDES. Basal core promoter and precore mutations among hepatitis B virus circulating in Brazil and its association with severe forms of hepatic diseases. Memórias do Instituto Oswaldo Cruz, v. 112, n. 9, p. 6-pg., 2017-09-01. (09/53946-3, 08/11472-2)

EVANGELISTA, ANDREIA SILVA; NAKHLE, MARIA CRISTINA; DE ARAUJO, THIAGO FERREIRA; ABRANTES-LEMOS, CLARICE PIRES; DEGUTI, MARTA MITIKO; CARRILHO, FLAIR JOSE; RACHID CANCADO, EDUARDO LUIZ. HFE Genotyping in Patients with Elevated Serum Iron Indices and Liver Diseases. BIOMED RESEARCH INTERNATIONAL, v. 2015, p. 8-pg., 2015-01-01. (09/53946-3)

ALBUQUERQUE, INGRID DE CAMPOS; SOUSA, MARINILDE TELES; CRUZ SANTOS, MAX DIEGO; COSTA NUNES, JOMAR DIOGO; DINIZ MORAES, MARIA JOSELIA; GOMES-GOUVEA, MICHELE SOARES; REBELO PINHO, JOAO RENATO; CARRILHO, FLAIR JOSE; BARROS FONSECA, LENA MARIA; PAIVA FERREIRA, ADALGISA DE SOUSA. Mutation in the S Gene a Determinant of the Hepatitis B Virus Associated With Concomitant HBsAg and Anti-HBs in a Population in Northeastern Brazil. Journal of Medical Virology, v. 89, n. 3, p. 458-462, MAR 2017. (09/53946-3)

CRUZ-SANTOS, MAX D.; GOMES-GOUVEA, MICHELE S.; COSTA-NUNES, JOMAR D.; MALTA-ROMANO, CAMILA; TELES-SOUSA, MARINILDE; FONSECA-BARROS, LENA M.; CARRILHO, FLAIR J.; PAIVA-FERREIRA, ADALGISA DE S.; REBELLO-PINHO, JOAO R.. High Prevalence of Hepatitis B Subgenotype D4 in Northeast Brazil: an Ancient Relic from African Continent?. ANNALS OF HEPATOLOGY, v. 17, n. 1, p. 54-63, JAN-FEB 2018. (09/53946-3)