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May 9, 2011

Researchers advance microarray technology to improve discovery of copy number variation

TORONTO - Exploring the vast landscape of the human genome has been crucial in the understanding of human diseases. An international research team led by scientists at The Hospital for Sick Children (SickKids) in Toronto and Uppsala University in Sweden has described new approaches to discovering copy number variation (CNV) of genes implicated in diseases.  The study is published in the May 8 advance online edition of Nature Biotechnology.

The researchers led by Dr. Stephen Scherer, Senior Scientist and Director of The Centre for Applied Genomics at SickKids and the McLaughlin Centre at the University of Toronto and Lars Feuk, PhD, of the Rudbeck Laboratory, Uppsala University, tested every available microarray platform for the ability to detect CNVs. They found current methods of analysis only detect a portion of the CNVs in the genome in any given experiment.

In 2004, Scherer and Feuk along with Charles Lee, PhD at Brigham and Women's Hospital in Boston discovered that CNVs are an abundant form of genetic variation in the genome. In research and diagnostic settings, detection of these CNVs and other genetic variants through the use of microarrays represents  an approximate $1.0 USD billion dollar market.

The current study shows that for most microarray platforms, reproducibility of replicate samples is below 70 per cent. Results from different analysis tools applied to the same data typically show less than 50 per cent reproducibility.

“CNVs have now been found to be involved in all classes of disease including autism spectrum disorder, heart disease, and developmental disorders, but they typically only account for a small proportion of the subjects examined indicating many of the genetic or heritable forms are still to be found”, says Scherer. “Our study finds that using multiple microarray platforms will lead to a much better discovery yield of CNVs, which may account for some of this so-called “missing-heritability” in disease studies.”

“The striking heterogeneity of CNV found when using different microarray platforms warrants careful assessment of applicability of CNV data in disease association studies, and highlight the risks of incorporating less strict filtering in diagnostics,” says Feuk.

Other co-authors of the study are from the Department of Pathology at Brigham and Women’s Hospital and the Wellcome Trust Sanger Institute.

Funding was provided by the Genome Canada/Ontario Genomics Institute, the Canadian Institutes of Health Research (CIHR), the McLaughlin Centre, the Canadian Institute of Advanced Research, and SickKids Foundation.

Scherer holds the GlaxoSmithKline-CIHR Pathfinder Chair in Genetics and Genomics at the University of Toronto and The Hospital for Sick Children.

Dr. Dalila Pinto, the first author of the study, was supported by fellowships from the Canadian Institutes of Health Research and the Netherlands Organization for Scientific Research.

About The Hospital for Sick Children
The Hospital for Sick Children (SickKids) is recognized as one of the world’s foremost paediatric health-care institutions and is Canada’s leading centre dedicated to advancing children’s health through the integration of patient care, research and education. Founded in 1875 and affiliated with the University of Toronto, SickKids is one of Canada’s most research-intensive hospitals and has generated discoveries that have helped children globally.  Its mission is to provide the best in complex and specialized family-centred care; pioneer scientific and clinical advancements; share expertise; foster an academic environment that nurtures health-care professionals; and champion an accessible, comprehensive and sustainable child health system.  SickKids is proud of its vision of Healthier Children. A Better World.™ For more information, please visit www.sickkids.ca. 

About Peter Gilgan Centre for Research and Learning 
The Peter Gilgan Centre for Research and Learning will bring together researchers from different scientific disciplines and a variety of clinical perspectives, to accelerate discoveries, new knowledge and their application to child health — a different concept from traditional research building designs. The facility will physically connect SickKids science, discovery and learning activities to its clinical operations. Designed by award-winning architects Diamond Schmitt Architects Inc. and HDR Inc. with a goal to achieve LEED® Gold Certification for sustainable design, the Gilgan Centre will create an architectural landmark as the eastern gateway to Toronto’s Discovery District. The Peter Gilgan Centre for Research and Learning is funded by a grant from the Canada Foundation for Innovation, the Government of Ontario, philanthropist Peter Gilgan and community support for the ongoing fundraising campaign. For more information, please visit www.sickkidsfoundation.com/bepartofit.

For more information, please contact:

Matet Nebres
The Hospital for Sick Children
Phone: 416-813-6380
email: matet.nebres@sickkids.ca

Suzanne Gold
The Hospital for Sick Children
Phone: 416-813-7654 ext. 2059
email: suzanne.gold@sickkids.ca