Acquisition of a genetic analyzer for automated DNA sequencing

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)