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Double-teaming a whole-genome hunt
Date:7/12/2010

embers (five affected with metachondromatosis and six unaffected) with the whole-genome sequencing of one affected member. The linkage study identified likely regions of the genome where the suspect mutation could be found, considerably reducing the fraction of the genome that could contain the disease. Focusing on these regions, the team identified a mutation in PTPN11 that was sure to cause loss of function of the gene product.

"This whole-genome study, which took only two months, got us to a place where otherwise we wouldn't have arrived very quickly, if ever," says David Valle, M.D., Henry J. Knott Professor and director of the Institute of Genetic Medicine, Johns Hopkins University School of Medicine. "It's a great example of the power of a broad, agnostic approach."

By comparing the one whole genome of the affected individual with eight non-affected control genomes as well as to a database of single-letter variations known to occur in more than one percent of the population, and to other sequencing data, the researchers came up with a list of 100 possible candidate genes. These were analyzed in light of the linkage evidence which, although modest, allowed the team to narrow its search for variants to just a fraction of the genome and narrowed the list to half a dozen genes. Then they combed the literature to understand what was known of the biological function of these candidates, looking for any that might be involved in bone development.

Nara Sobreira, a graduate student in human genetics at Johns Hopkins and a lead author of the study, found that lots had been published about one of the six genes, PTPN11. Mutations in this gene made it hyperactive, causing Noonan syndrome, a genetic disorder that prevents normal development in various parts of the body, including the skeleton.

This newly discovered mutation or altered version involved a so-called "deletion" in which a piece of the genetic code is missing and like
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Contact: Maryalice Yakutchik
myakutc1@jhmi.edu
443-287-2251
Johns Hopkins Medical Institutions
Source:Eurekalert

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