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Genetic sequencing software will help speed up HIV/AIDS treatment

A woman carrying an umbrella is framed by the Lights of Hope display at St. Paul's Hospital in Vancouver, Wednesday December 19, 2012. A software innovation promises to supercharge treatment for HIV/AIDS patients at the hospital’s British Columbia Centre for Excellence in HIV/AIDS.

DARRYL DYCK/The Globe and Mail

The business software currently running oil fields and factories will soon be put to work creating genetic maps of the virus attacking patients at British Columbia's leading HIV facility, a first in Canada.

When patients enter the The British Columbia Centre for Excellence in HIV/AIDS at St. Paul's Hospital, it can take up to 10 days to sequence each blood sample to identify the strain of HIV they have. The sequencing is essential and allows doctors to know which of about two dozen HIV drugs a patient should get.

Under a new system developed in a partnership between Vancouver-based tech start up PHEMI Health Systems and global software giant SAP, results could be delivered up to 100 times faster.

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That means more patients can be helped faster and for less money.

The challenge, according to Adam Lorant, a vice-president of PHEMI, is that the data files containing genetic information are massive. A "typical" gene sequence can be many hundreds of gigabytes in size, a test for most conventional computer systems.

Using PHEMI software, the St. Paul's lab will extract the basic genetic information from the samples and hand it off to SAP's system for sequencing and analysis. "That's where all the speed and raw horsepower comes in," Mr. Lorant said.

German-based SAP became the world's largest business software company creating programs that help companies plan and analyze their operations. According to SAP Canada's John Ramsell, the new program merges "world-leading" HIV research with an exportable platform.

Julio Montaner, head of the BC Centre, Canada's largest HIV-AIDS research and treatment facility, helped design the system that pairs patients with their best treatment plan. The new system will provide not only the data to help his patients, but eventually, patients around the world.

"This will help us save time and money while also significantly decreasing the number of new HIV and AIDS cases. For the first time, we shall have access to vast amounts of information and get answers immediately," Dr. Montaner said in a statement.

In development since December, the project will initially help physicians at the Vancouver-area facility transition from doctor's letters and printed lab results to what is described as "searchable information."

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Once the transition is complete, expected around the summer, the plan is to provide access to the database across British Columbia and then around the world.

With partnerships already planned in China, South Africa and Panama, according to Mr. Lorant, doctors in far-flung hospitals could one day access the database and computing power with iPhones. According to Mr. Ramsell, future access will be provided free.

With a patient's genetic data stored in a database, concerns about privacy and security are paramount. All the information is currently kept in a data centre at the facility and it does not leave the building.

The program was designed under an international standard known as Privacy by Design. Under the system, "privacy" is the software's default setting.

"It's a very challenging and stringent process," Mr. Lorant said.

"We collect the patient information and when we store it, we store it with certain rules on how the data can be used, when it can be used and who can use it."

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In light of several announcements of large losses of personal information by civil servants or broken computer systems, some British Columbians will be skeptical. A 2011 poll from Angus Reid showed that more than 80 per cent of people in the province supported the use of data by health care professionals – after it was depersonalized.

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