'Junk DNA' yields gold in genome map to help fight disease
October 8, 2009
Noor Javed
STAFF REPORTER
To the untrained eye, it looks like a database filled with random numbers, letters and colourful bars – meant to represent the placement of certain genes within DNA.
But to geneticists, physicians and researchers around the world, the new comprehensive genome map developed in part by researchers in Toronto, holds the key to a future of accurate clinical diagnosis, personalized medicine and possibly even cures for hereditary disease.
The map, described extensively in a study released online Wednesday in the journal Nature, is a compilation of years of work in identifying genetic variation within the genome, said Dr. Stephen Scherer, a senior scientist at Sick Kids hospital and a co-author of the study. A rudimentary map of the genome was created in 2006.
"Our goal was to develop the map to study the landscape of the genome to impact everything from clinical to diagnostic to research," said Scherer, director of the Centre for Applied Genomics. "Previous work in this field would be like a paper fold-up map; this advancement is like GPS that takes you where you need to go."
Almost a decade ago, scientists began to map out the human genome as part of the Human Genome Project, in which they identified the sequences of DNA code. Scientists thought at the time they knew all there was to know about mapping our genes. Around that time, Scherer and his team decided to focus on the "junk DNA," the parts of the DNA that had no particular function.
That is when they first discovered hundreds of genetic variations, called copy number variants (CNVs) where a large segment of DNA is missing or copied. In some cases, the CNV can result in physical differences and disease, but in most cases they are simply benign, hinting at other evolutionary tendencies.
For years, scientists believed humans were 99 per cent genetically the same. This new map compares the DNA of 450 individuals with European, Asian and African descent and finds that there are nearly 1,500 unique CNV regions in each person, adding to the growing theory that there is more genetic diversity among people than previously thought.
"Every person on earth has a little bit missing, a lit bit extra in their genes, that is what makes us individuals," said Marsha Speevak, a laboratory geneticist at Credit Valley Hospital who spends her days scanning patients' genetic code using the new map to help build a diagnosis for autism, developmental diseases and congenital disorders.
"They have found that all the human variation we see on the outside, is present on the inside, down to the genetic level," she said.
The researchers also identified 30 new regions in the genome that could be responsible for susceptibility to certain diseases. Over the past two years, researchers have found more than a hundred diseases associated with CNVs, including autism, heart disease, obesity and cancer.
"It's not a guarantee that they will get the disease, but it indicates susceptibility to it," Speevak said.
The new genetic variation map was made public to health professionals a few months ago, and already doctors across Canada and the United States are using the database in their clinical practice thousands of times a day.
"We estimate that last year 40,000 to 50,000 diagnoses were made using this approach," Scherer said.
This map is expected to be the future of personalized medicine, to help people determine diseases they are likely to get, or explain why they have the conditions they do.
This is not the last of the maps to come, Scherer said.
The next step is to take DNA samples of thousands of individuals to add to the growing map, which is expected to take three to four years to complete.
Toronto Star
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