Launch of Latin America's first public human genome database

The platform was developed as part of BIPMed, the Brazilian Initiative on Precision Medicine, an effort promoted by members of five research centers supported by FAPESP.

By Karina Toledo

Agência FAPESP – Latin America’s first public human genome database went online on November 13 and can be accessed free of charge at bipmed.iqm.unicamp.br.

The virtual environment is open both to scientists who wish to query the data, covering genes, transcripts and genomic variants so far, and to anyone who wants to upload data from their own research.

“This is the first product launched by BIPMed, the Brazilian Initiative on Precision Medicine, a venture that aims to create the conditions for implementation of precision medicine in Brazil,” said Iscia Lopes-Cendes, a professor at the University of Campinas’s School of Medical Sciences (FCM-UNICAMP) and one of the project’s creators.

Launched on the same day as the genome database in a ceremony held at FAPESP’s headquarters, BIPMed is staffed by members of five Research, Innovation and Dissemination Centers (RIDCs) supported by FAPESP: the Center for Computational Engineering and Sciences (CCES), the Center for Cell-Based Therapy (CTC), the Obesity and Comorbidities Research Center (OCRC), the Center for Research on Inflammatory Diseases (CRID), and as lead institution the Brazilian Research Institute for Neuroscience and Neurotechnology (BRAINN).

The first contributions to the genome database came from research by the teams from these five RIDCs. “We began with a modest amount of information, obtained from 29 whole-exome sequences,” said Lopes-Cendes, who is also a researcher at BRAINN. Whole exome sequencing (WES) is a technique for sequencing all the protein-coding genes in a genome. “However, the idea is that this should be the embryo of a big repository, which will grow with the help of other groups in Brazil and abroad. Our dream is to be international.”

According to Wilson Araújo da Silva Júnior, a professor at the University of São Paulo’s Ribeirão Preto Medical School (FMRP-USP) and a researcher at CTC, the newly launched platform is only the first stage of a much more ambitious project to create a repository of information on the genetic diversity of the Brazilian population. This would encompass not just patient data but also data on thousands of healthy individuals for use as a reference framework.

A database of this type, he added, would be a key stepping-stone toward both personalized genomic medicine, permitting the comprehensive deployment of individually tailored treatments, and genuinely preventive medicine as a basis for more efficient and effective public policy with lower costs for the Unified Health System (SUS).

“It’s an expensive project but will have a significant impact on health,” Silva Júnior said. “We’ve been discussing it with FAPESP for about two years. Countries like the United States and United Kingdom are already sequencing thousands of individuals. Here in Brazil, we’ve used information from other populations as a reference framework, but Brazilians are very different from a genetic standpoint because of the high degree of miscegenation.”

In pursuit of precision

Precision medicine, which American President Barack Obama has made a priority for his administration in 2015, combines personalized, genomic, translational and preventive medicine, according to Iscia Lopes-Cendes. It requires the networked compilation of massive amounts of medical data at various levels, from clinical, laboratory and epidemiological data to the results of studies with animal models of disease, as well as demographic risk factors and information relating to the “-omics” (e.g., genomics, transcriptomics, proteomics).

 “All these data have to be collected from a significant number of individuals, on the order of thousands at least,” she said. “They must then be stored and interpreted so that we can produce more appropriate knowledge about the mechanisms of diseases as a basis for diagnosing and proposing the optimal treatment for each patient.”

It would not be possible to analyze all these Big Data without the collaboration of specialists in bioinformatics, said Fernando Lopes-Cendes, head of BRAINN, during the BIPMed launch ceremony.

“In this case, the health sciences can’t do everything on their own. The exact sciences are the basis for this process, albeit interfacing with biology and health sciences,” he said.

Sustaining the initiative will require not only the efforts of the RIDCs involved and FAPESP but also of the host institutions for the research centers, he stressed.

“The project only makes sense over the long run because we’ll reap the benefits as the database becomes larger and more robust,” he said.

The institutions that support the initiative were represented by FAPESP President José Goldemberg and VP Eduardo Moacyr Krieger; Carlos Eduardo Negrão, a member of FAPESP’s Life Sciences Area Panel; Marco Antonio Sago, Rector of the University of São Paulo (USP); Glaucia Maria Pastore, UNICAMP’s Pro-Rector for Research; Carlos Gilberto Carlotti Júnior, Head of FMRP-USP; and Roberto Teixeira Mendes, Deputy Head of FCM-UNICAMP.

“Thanks to precision medicine, serious diseases such as cancer are starting to be tackled in a more focused manner,” Goldemberg said.

According to Krieger, initiatives designed to develop precision medicine require considerable investment of public money but will result in significant social and economic benefits, as exemplified by the Human Genome Project.

“Instead of treating patients, we’ll be able to treat their health, delaying the appearance of disorders and ending up with a lower burden of disease,” he said. “Some clinics and health centers belonging to the national health system (SUS) can and should implement this new approach at once. If they do, there will be concrete benefits for the health of Brazilians and the national economy. I’m immensely pleased to see FAPESP’s RIDCs taking the lead in this process.”

Zago recalled that physicians began only after World War II to base diagnoses and treatment on concrete patient data such as analysis of blood samples. “In those days, precision was very low. Knowledge of the molecular structures that cause diseases has enabled us to move forward. For example, we can now individualize treatment for the more than 20 subtypes of leukemia,” he said.

“We need to exorcize the habit of regarding clinical, laboratory and genomic data as personal property. I’m a firm believer in the advantages of sharing data. It’s much more productive and yields more results.”

Pastore stressed that if the huge amounts of data stored are to yield effective benefits for society, good research projects and financial conditions to implement them will be needed.

“This is a huge responsibility,” he said. “The data will be appropriated by whoever is most active and capable of establishing projects quickly to achieve specific goals.”

Responsible sharing

Hosted by UNICAMP’s servers (and soon to be fully backed up by the University of São Paulo at Ribeirão Preto), the data sharing platform was constructed in accordance with parameters established by the Global Alliance for Genomics & Health (GA4GH), an international consortium of over 300 leading institutions in healthcare, research, disease advocacy, life science and information technology that are working together to create a common framework of harmonized approaches to enable the responsible, voluntary and secure sharing of genomic and clinical data.

“Our database is therefore born global and with a genuine concern to mitigate the risks of data leaks that could allow donors of genetic material to be identified,” Iscia Lopes-Cendes said.

Benilton de Sá Carvalho, a professor at UNICAMP and a member of BRAINN, explained that there are different levels of access to the information and any data that might be used to identify people who donate samples is strictly confidential.

“We’re constantly enhancing the search engine and welcome suggestions,” he said. “Collaboration makes all the difference.”

Other specialists in bioinformatics in attendance included Munir Salomão Skaf and Claudia Bauzer Medeiros, Director and Vice Director of CCES, respectively.