Research profile – Bedside genomics

New software will enable clinicians to compare, analyze genomes from hundreds of people.

[ Back to main article ]

Software that can compare the entire genomes of over a hundred people is bringing health care closer to the era of personalized medicine. Developed by researchers at the University of Toronto, the software, tentatively called MedSavant, could help diagnose genetic disorders, identify who should be screened for specific diseases, and improve our understanding of the disorders themselves.

Your genome is the entirety of your hereditary information, encoded in your DNA. Mutations in specific genes can increase your risk of developing certain diseases, such as breast cancer, diabetes, certain heart conditions and Alzheimer’s disease. Comparing your genome to other people’s genomes can help detect disease-causing mutations.

But most genetic variation between individuals is harmless. It can be tricky figuring out which variations are healthy (such as genes that code for different hair colours) and which cause disease. For clinicians to accurately detect harmful mutations in a patient, they must be able to quickly compare the genomes of hundreds, if not thousands, of people.

That is what MedSavant aims to do. Although the project is still in its infancy, the software should eventually be able to compare thousands of genomes in a short period of time, according to Dr. Michael Brudno, an associate professor at the University of Toronto and director of the Centre for Computational Medicine at the Hospital for Sick Children.

“What we’re doing is a bioinformatics software to enable the interpretation. Because if you compare any two humans, there will be several million differences between their genomes. Most of these differences either are non-functional, or are for normal, healthy things...you need to look at many genomes in order to be able to interpret just one,” Dr. Brudno says.

Current commercially available bioinformatics software does genome comparisons, but they are pricey, are not commonly accessible, and don’t have as extensive a database as MedSavant will, according to Dr. Brudno. At this point, MedSavant contains data for about 100 genomes, but will eventually contain data for thousands.

Also, while basic commercial genome analysis can cost up to $5,000 for a single patient, MedSavant will be freely available. “We’re building an open-source, free version of such bioinformatics tools to enable hospitals to use the software much more cheaply than it would be possible if they had to pay a company to do it,” says Dr. Brudno.

For some, the reduced cost and increased ease of genetic analysis may bring to mind the dystopian world depicted in the 1997 movie Gattaca. But for researchers like Dr. Brudno, this technology represents opportunity to develop more effective, personalized treatment for patients.

“A classic example is breast cancer. There are certain mutations which make individuals very likely to get breast cancer. If you can sequence their genome and find that someone has a very high likelihood of developing breast cancer, increased screenings can be done to catch problems early,” he says.

As well as helping with diagnosing disease, the software can be used to help researchers learn more about the genetic causes of diseases. While people may carry genes for a particular disease, those genes aren’t always turned on. Comparing genomes between groups of people with those genes will help elucidate the reasons why some individuals develop a disease and some don’t.

“We’re building an open-source, free version of such bioinformatics tools to enable hospitals to use the software much more cheaply than it would be possible if they had to pay a company to do it.”
– Dr. Michael Brudno, University of Toronto