Researchers develop 'hi-def' copy number variation decoder

November 1, 2010 By Paul Cantin, University of Toronto

University of Toronto researchers have developed a new "high definition" computer program to analyze human DNA and more accurately detect genetic variants that affect individual traits like disease susceptibility and varying drug responses.

A multidisciplinary team combining computer science and biomedical data developed new theory and code to enable the precise determination of the number of copies of in the human . In the past few years, such copy number variation (or CNV) of genes has been shown to be a universal form of and also found to cause diseases like autism and cancer, but until now it has remained very difficult to identify. This new computer algorithm, which promises to simplify CNV discovery, is unveiled in the cover story of this month's Genome Research.

“Most, but not all, genes occur in two copies in our genome, one inherited from each parent. When examining genome sequences we need to distinguish genes that may be present in zero or one copy or present in three or more copies and the complexity of DNA itself can make that very difficult,” said Professor Michael Brudno of computer science and the Donnelly Centre for Cellular and Biomolecular Research, senior author.

Brudno, Canada Research Chair in Computational Biology, likens his new invention, called CNVer, to a game of “spot the difference,” in this case searching for glitches in sub-microscopic pieces of DNA.

"Imagine two near-identical images - one photograph contains two cars, the other only one. If you cut those images into snippets and shuffled them (precisely what happens when you sequence DNA), it would be difficult to detect which image fragment belonged with the original picture. We have developed sophisticated methods to scrutinize connecting fragments around, or between, the vehicles, allowing both the number of cars (or copies of a gene) within the photograph and their location to be accurately reconstructed. Together this information allows us to see a high-definition view of the genome, while only looking at the individual small pieces,” said Brudno.

Professor Stephen Scherer, director of the McLaughlin Centre U of T and the Centre for Applied Genomics at The Hospital for Sick Children who co-discovered genome-wide CNVs in 2004, commented: "This new tool will have tremendous impact in our ability to understand the medical relevance of CNVs in the massive amounts of data coming from personal genome sequencing projects."

Co-authors on this research are Paul Medvedev, Marc Fiume, Misko Dzamba and Tim Smith of the Department of Computer Science. Support for this research came from the Canadian Institutes of Health Research.

Related Stories

Recommended for you

Peers' genes may help friends stay in school, new study finds

January 18, 2018
While there's scientific evidence to suggest that your genes have something to do with how far you'll go in school, new research by a team from Stanford and elsewhere says the DNA of your classmates also plays a role.

Two new breast cancer genes emerge from Lynch syndrome gene study

January 18, 2018
Researchers at Columbia University Irving Medical Center and NewYork-Presbyterian have identified two new breast cancer genes. Having one of the genes—MSH6 and PMS2—approximately doubles a woman's risk of developing breast ...

A centuries-old math equation used to solve a modern-day genetics challenge

January 18, 2018
Researchers developed a new mathematical tool to validate and improve methods used by medical professionals to interpret results from clinical genetic tests. The work was published this month in Genetics in Medicine.

Can mice really mirror humans when it comes to cancer?

January 18, 2018
A new Michigan State University study is helping to answer a pressing question among scientists of just how close mice are to people when it comes to researching cancer.

Epigenetics study helps focus search for autism risk factors

January 16, 2018
Scientists have long tried to pin down the causes of autism spectrum disorder. Recent studies have expanded the search for genetic links from identifying genes toward epigenetics, the study of factors that control gene expression ...

Group recreates DNA of man who died in 1827 despite having no body to work with

January 16, 2018
An international team of researchers led by a group with deCODE Genetics, a biopharmaceutical company in Iceland, has partly recreated the DNA of a man who died in 1827, despite having no body to take tissue samples from. ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.