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Thursday, August 1, 2013
New project will perform large-scale exome sequencing in IBD
The Broad Institute and Massachusetts General Hospital (MGH) are launching a new initiative to perform large-scale exome sequencing in inflammatory bowel disease (Crohn's disease and ulcerative colitis). Given the considerable unmet therapeutic need in inflammatory bowel disease (IBD), the recent emergence of rapid and efficient genome sequencing technologies and the compelling evidence for the role of genetics in these disorders have motivated the founding of a collaborative sequencing effort geared toward the discovery of high-impact genetic variants influencing IBD risk that can serve as guides to future therapeutic development and diagnostic tools.
The initiative will be directed by experienced IBD researchers from MGH and the Broad Institute but aims to develop a collaborative exome sequencing network that will partner with researchers worldwide. Two large pilot exome sequencing projects are being launched immediately as part of this initiative based on established genetic study designs that enrich for the discovery of rare, high-impact risk and protective variants.1) Early-onset pediatric IBD: a major focus of the work will surround full-exome sequencing of the earliest-onset childhood IBD cases. It has long been recognized in many diseases that penetrant genetic risk factors are much more likely to be found in cases with unusually early onset. The Broad Institute has completed more than 50,000 exomes in the past two years; and their technical expertise in generating and processing such sequencing data, along with population genetic variation patterns from these experiments, will provide a foundation for obtaining the best outcome in the interpretation of these cases. Samples with IBD onset before 6 years of age – and in some cases going up to age 10 – collected by IBD researchers around the world are welcomed for inclusion in this study.
2) Adult-onset IBD case-control study: Genetic mapping has provided dramatic insights into IBD pathogenesis in recent years, but a substantial amount of heritability – in particular the role of strong-acting rare mutations – is yet to be elucidated. To deliver those insights, IBD cases with an unusually low burden of known genetic risk factors (particularly emphasizing those with positive family history and/or from isolated or enriched populations) will be contrasted with population controls that have an extremely high burden of known IBD risk factors, enhancing discovery of critical protective variants that may provide the best clues for therapeutic development. This project will also be initiated as an international collaboration, particularly among researchers with sample sets with Immunochip genotyping that will enable the immediate genetic identification of these enriched target populations.Pilot work for this project will be supported in the next 12 months by the NHGRI Large-Scale Sequencing Program, with all generated data made publicly available to the research community through standard NIH databases. “Genetics offers a peek into the pathways that protect against or predispose to the development of IBD,” says Ramnik Xavier, chief of Gastroenterology at MGH and a senior associate member at the Broad Institute. “Contributing results to public resources will allow the data to be integrated by researchers from a variety of disciplines. In the current research environment, important advances in biology are often made by finding innovative ways to analyze ‘big data,’ and I believe this open-access exome sequencing project will provide an example of how publicly available data can inspire significant progress in the field of IBD.”“This project will enable IBD genetics to take further leaps forward toward a clear and therapeutically actionable understanding of the molecular causes of disease,” says Mark Daly, chief of Analytic and Translational Genetics at MGH and a senior associate member at the Broad Institute. “It is extremely exciting to be able to launch this transformative initiative as an international collaboration with rapid and open data sharing.” Researchers who are interested in collaborating on this initiative should contact Mark Daly (firstname.lastname@example.org) for more information.
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