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bioinformatics

Genomic difference

Analyzing alterations in nucleotides is a theme for Scylla's first commercial software

After getting a big boost in its development with the genome projects that have spread over the world and over Brazil, bioinformatics is beginning to stand out as an important area for the generation of technological innovation. One of these fruits originating from genomic research is software produced by Scylla, a company from Campinas, for the Psychiatry Institute of the University of São Paulo (USP). It is a system for identifying genetic differences, called polymorphisms, in the sequences of the chemical bases that form genes, the famous adenine, cytosine, thymine and guanine, also known as nucleotides. A differentiated sequence, or just one letter – which indicates one of these substances in a given gene – may lead to a predisposition towards mental illnesses, for example.

Called a Polymorphisms Identification System (SIP), the software will enablethe USP researchers to identify these differences more easily and to compare them with the physical condition of the person being analyzed, relating polymorphism to the disease.”SIP is a tool for verifying the single-nucleotide polymorphisms, or SNPs, that exist in the DNA. The great majority of people always have one sequence, like, for example, ATTGCATG. If we find in the same gene, but in another person, the sequence ATTGCTTG, with an A being replaced by a T, then, one first sees whether there has been some error in the process of getting the data; if the difference persists, a comparison is made with the person’s medical condition”, explains Professor João Meidanis, from the Theory of Computing Department of the State University of Campinas (Unicamp) and Scylla’s founder. Two former pupils of Meidanis, Alexandre Corrêa Barbosa and Zanoni Dias, are in the company as partners. They started Scylla in 2002, after a long period taking part in the bioinformatics area of the genome projects on the Xyllela fastidiosa and Xanthomonas citri bacteria and on sugarcane, of which Meidanis was one of the coordinators.

World-wide database
In the Human Genome alone, there are over 4 million SNPs. They are identified as such if they are present in 1% of the population. What is known about them is recorded in world-wide databases of polymorphisms, which, with the help of the software, will be accessed to identify and classify the SNPs by the team coordinated by Professor Emmanuel Dias Neto, from the Neurosciences Laboratory of the Psychiatry Institute at USP’s Hospital and Clinics. “This information will be useful, for example, for us to analyze a group of 500 persons, of which 250 with schizophrenia and 250 from a control group without this illness. We can then see the differences in the bases and relate them to an ailment”, Dias Neto explains. “We are also looking for polymorphisms that may mean resistance to medicines. The SNPs may be responsible for the ineffectiveness of certain drugs in some people.”

Synthesizing an altered protein, caused by a given SNP, may influence the chemical connections that make the medicine be an efficient one. “There are individuals who respond to lithium (a substance used against depression), and others who don’t. We want to understand and to characterize the genes connected with these clinical responses”, says Dias Neto. The software developed by Scylla may thus be useful for other research centers and laboratories and for the pharmaceutical industry.

Clients in a network
In a practical way, the software has a server that makes it possible for several clients to participate. They can then run the program on a local network or not, on a Linux or Windows platform. SIP is Scylla’s first commercial product. The company received financial investments from Votorantim Ventures, the venture capital arm of the Votorantim group.

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