USP will create a database and stem cell bank from patients with rare genetic diseases

A system being installed at the Human Genome Studies Center will store genomic information and molecular test results from patients served by the center

By Elton Alisson

Agência FAPESP – Since it was founded in 2000 as a FAPESP Research, Innovation and Dissemination Center (CEPID), the Human Genome Studies Center (CEGH) has served approximately 80,000 people belonging to families affected by genetic diseases.

CEGH is currently installing software that will allow the storage of clinical data, genomic information and molecular test results from several patients served by the center, which is linked to Universidade de São Paulo’s (USP) Biosciences Institute.

In this manner, the program will allow CEGH to create one of the largest databases of rare genetic diseases in the Brazilian population, particularly neuromuscular diseases, congenital malformations, cognitive deficits, genetic obesity and autism.

It will also help with the emergence of Brazilian stem cell banks for patients with rare genetic diseases and will contain more than 300 samples at the outset.

An article published in BMC Genomics describes the challenges for the development and implementation of the computational system, which was developed over five years by researchers of the Database Modeling, Transactions and Data Analysis (DATA Group) of the Mathematical and Statistics Institute (IME) and USP’s Bioinformatics Center.

“The software will facilitate monitoring and selection of patients for research we conduct on genetic diseases,” explained Maria Rita dos Santos e Passos-Bueno, a researcher at CEGH and one of the authors of the article, in an interview with Agência FAPESP.

According to dos Santos e Passos-Bueno, one of the main objectives of the program, which is based on a free software platform, is to control the flow of clinical and molecular tests given to patients at CEGH.

These diverse, parameterized tests are conducted at various disease stages and require specific inputs. The tests are conducted according to a cycle, which begins with the collection of blood samples from patients and their families; DNA is extracted from the samples and analysed to produce reports on the genetic disease. In addition, each test is conducted in sets of 10 to 30 patients at a timebecause the cost of doing a single test is often very high.

To control the flow of these tests, the new system restricts access to information according to profession

On the patient page, for example, the doctor or geneticist can request tests on a blood sample. After the material has been collected, the group of technicians responsible for performing the tests is informed, and the technicians should register with the system when they begin the tests and should finalize the process on their respective page.

By registering the information, the doctor or geneticist can track the progress of tests and see when the technicians will prepare the final report on the patient being monitored.
 
“The software covers a cycle that begins with collecting the patient’s material before releasing the patient’s report and has the objective of supporting the decision of CEGH researchers in relation to choosing patients, for example, for closer monitoring,” says João Eduardo Ferreira, IME professor and coordinator of the DATA Group.

Bioinformatics and computing

Ferreira explains that some of the greatest technical challenges to developing the program were creating the control system for the flow of the tests, integrating the clinical and molecular data from patients and their relatives, and providing efficient analysis to CEGH researchers to facilitate decision making.
 
For each of these technical challenges, the researchers of the DATA Group developed a computational solution.  

“In order to control the flow of tests, we used a control and execution tool for activities that was developed by our group. To avoid dispersed clinical and molecular data, we employed database resources that integrate all information that will be registered in the system,” explains Ferreira.

“To analyze the information, we utilized indexation resources to recover the data quicker,” he adds.

According to Ferreira, in addition to technical challenges, another barrier that had to be overcome for the development of the project was communication between researchers in the computing areas and in bioinformatics.

“We managed to overcome at least one of the most fundamental barriers between the two areas — operation — and thereby to generate software dedicated specifically for the researchers. Facilitating this interaction between researchers from different areas, to develop the system, was a learning process both for us and for the CEGH group,” he says.

In the past few months, CEGH researchers began to conduct pilot studies on controlling the flow of some tests in the new system. Through the second half of 2012, they intend to expand the system’s use to most of the tests that they conduct.

The article A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems (doi:10.1186/1471-2164-12-S4-S13) by Ferreira et al can be accessed at BMC Genomics at www.biomedcentral.com/1471-2164/12/S4/S13.