Establishment of a next generation sequencing facility as a tool for research in biological systems

• Grant number: 12/25387-2
• Support Opportunities: Regular Research Grants
• Start date: June 01, 2013
• End date: May 31, 2017
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Carlos Frederico Martins Menck
• Grantee: Carlos Frederico Martins Menck
• Host Institution: Instituto de Ciências Biomédicas (ICB). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

In this country, the development of scientific core facilities of any kind is a major challenge for various reasons, including lack of culture, limited support for infrastructure and management, difficulties of reagent importations, etc. For next generation sequencing cores even more challenges are found, due to the rapid technological evolution for new equipments and the high costs of reagents for performing sequencing runs, that in general promote the generation data amount greater than the actually required by users. This huge amount of data also implies the need of Bioinformatics cores, able to analyze the data for the researcher. These issues make the sequencing facilities in Brazil as uncompetitive with similar services abroad, reducing the ability of nucleate competent groups in these technologies in the country. In this project, we propose centralizing the purchase of reagents in the facility GENIAL (Genome Investigation and Analysis Laboratory) inserted in CEFAP (Centro de Facilidades de Apoio à Pesquisa - Center of Facilities to Support Research), through own funding and importation by FAPESP, especially for those who need to sequence small genomes (<50 Mb as exomes and microbial genomes) and transcriptomes. This centralization would make the use of the equipments in the CEFAP-USP much more simple and practical, greatly expanding the capacity to use such devices. The specific sequencing of exomes from mutated mice of the ICB Vivarium is also planned in this project, in the hope to find the mutations responsible for the phenotypes. Furthermore, the request for scholarships for two technicians can troubleshoot Bioinformatics limitations related to data analysis, driving the use of this technology. Support to buy a new sequencer is also included. This sequencer, also of next generation, is more limited in terms of quantity of material to be sequenced, but it produces longer reads and uses a different technology, complementary to the one available today. This will certainly be helpful for various uses including confirmation results of DNA sequence requiring validation and the generation of sequences from unknown genomes. (AU)

Scientific publications

(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)

MAZZONETTO, P. C.; ARIZA, C. B.; OCANHA, S. G.; DE SOUZ, T. A.; KO, G. M.; MENCK, C. F. M.; MASSIRONI, S. M. G.; PORCIONATTO, M. A.. Mutation in NADPH oxidase 3 (NOX3) impairs SHH signaling and increases cerebellar neural stem/progenitor cell proliferation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE, v. 1865, n. 6, p. 1502-1515, JUN 1 2019. (18/05635-8, 14/19204-8, 12/25387-2, 17/18765-4)

YAMAMOTO, PEDRO K.; DE SOUZA, TIAGO A.; ANTIORIO, ANA T. F. B.; ZANATTO, DENNIS A.; GARCIA-GOMES, MARIANA DE SOUZA A.; ALEXANDRE-RIBEIRO, SANDRA R.; OLIVEIRA, NICASSIA DE SOUZA; MENCK, CARLOS F. M.; BERNARDI, MARIA M.; MASSIRONI, SILVIA M. G.; et al. Genetic and behavioral characterization of a Kmt2d mouse mutant, a new model for Kabuki Syndrome. GENES BRAIN AND BEHAVIOR, v. 18, n. 8, NOV 2019. (17/21103-3, 16/23659-6, 12/25387-2)