Genomics consortium provides new challenge for OICR's expert team of bioinformaticians

For Dr. Lincoln Stein, searching the human genome for the genetic variations that cause cancer is as much about servers and software as it is about samples and sequencers.

Stein is Director of the Informatics and Biocomputing Platform at the Ontario Institute for Cancer Research (OICR), a team of computational biologists and computer specialists who use cutting-edge computer technologies to solve complex biological problems. When fully scaled up in 2010, 10 principal investigators and dozens of staff will provide data interpretation and management expertise to researchers working on a wide range of studies, from basic science to population health.

“In essence, our team is responsible for making sense of data that comes out of the laboratory. Sometimes we are working to identify biological processes involved in cancer – for example, finding the genes that are associated with cancer. Other times, we are trying to learn more about specific aspects of biological processes – for example, using data to actually diagnose cancer and predict the course of treatment,” he explains.

One of the team’s most active areas is cancer genomics. Along with Stein, principal investigators Dr. Arek Kasprzyk and Francis Ouellette lead teams of biostatisticians and programmers to develop strategies to store, manage and interpret the massive amounts of data that flow rapidly out of next-generation sequencing machines. When OICR’s 10 next-generation sequencers are all fully online, they could produce several terabytes of data every week. (A terabyte is one thousand gigabytes, which is the equivalent of 220 standard DVDs)

Since last year, Stein and his team have also been gearing up for a much larger-challenge: hosting the data centre of the International Cancer Genome Consortium (ICGC), a worldwide effort to sequence 500 samples of each of the 50 most common types of cancer. This means they’ll be working closely not just with OICR’s laboratory researchers, but with labs throughout the world.

“To efficiently carry out the ICGC’s mandate, we will need to develop new strategies and technologies to manage and interpret the data,” Stein explains. “At OICR we will develop data quality standards that will guide research institutes throughout the world. We are also building databases to store the data. And we’ll be developing a data management system which will give all of the project participants a birds-eye view of what is going on with the data – this is important because it helps identify problems early and ensures everyone is kept in the loop.”

OICR was chosen to host the data centre because it has made significant investments in scaling up its bioinformatics infrastructure and recruited international leaders to help meet the data-related challenges posed by new sequencing technologies. Stein, for example, is a pioneer in the field, with previous experience working on the Human Genome Project and the International HapMap.

“There is no one who has made a more significant a contribution to the development of bioinformatics as Dr. Lincoln Stein,” says Dr. Tom Hudson, President and Scientific Director of OICR. “As an early leader in the field, he has seen bioinformatics grow alongside genomics and has risen to the challenge of providing vital research on using computers to make sense of the data produced in the laboratory.”

Like many researchers at OICR, including Hudson and Cancer Genomics Director John McPherson, Stein has relocated to Ontario in order to pursue his research.

"What attracted me to OICR was the opportunity to do truly translational work, in order to see the fruits of basic research turned into techniques and products that will directly benefit cancer patients and their families. Moving to Toronto also gave me the chance to work in a vibrant community of cancer researchers," Stein says.

With OICR’s Informatics and Biocomputing Platform growing every month, these researchers now have unprecedented access to technologies that can make the most of their data. And thanks to the recruitment of leaders like Dr. Stein, they will also have access to world-leading expertise.

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Informatics and Biocomputing Platform principal investigators

Dr. Lincoln Stein's page on the OICR website

Francis Ouellete's page and public lecture slides on the OICR website

Dr. Arek Kasprzyk's page on the OICR website

Dr. Vincent Ferretti's page on the OICR website