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Genotyping: Beyond Basic

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If everything goes according to plan, Norman Gerry will be a very busy man. Gerry is director of the genotyping and array resource at the Coriell Institute for Medical Research, which recently launched a project to genotype 100,000 people in a large-scale personalized medicine initiative based in New Jersey.

Gerry says the idea behind what's known as the Delaware Valley Personalized Medicine Project came from an institute-wide goal to make basic research more relevant to medical practice. "We know we can do the genotyping and we can do the basic research and basic analysis," Gerry says. "How do we bring it back to the clinic?"

In this case, the answer is: by enrolling a massive number of patients into a personalized medicine project that aims not only to perform some level of research — including plans for association studies — but also to help establish guidelines for the ethical and practical issues associated with releasing genomic information to people.

The Coriell Institute, working in conjunction with local hospitals such as the Fox Chase Cancer Center in Philadelphia and Cooper University Hospital in Camden, NJ, has dedicated funding to perform genotyping on the first 10,000 patients. (Getting to that point is expected to take about three years; the institute was on target to enroll its first 1,000 patients by this month.) Gerry says genotyping will be performed using the Affymetrix 6.0 array, and that next-gen sequencing technology, which may be used for targeted deep resequencing later in the project, remains "prohibitively expensive for the number of patients we plan on enrolling."

On the research side, that information will be paired with patients' answers to a basic medical questionnaire, as well as any available phenotypic information for patients who come to the project through a partner hospital. The work with Fox Chase patients, for instance, will involve a project focusing on breast and prostate cancer. Any other associations found with the general enrollees will "to some degree … be determined by what the data and the medical questionnaires actually look like in the end," Gerry says.

As for the clinical side, patients involved in the project will have a personal website where they can view their own genotype data — but not exactly in real time. Gerry says the team overseeing this initiative is "taking a conservative approach," and that means allowing patients to see only SNPs that are deemed reliable and medically actionable through lifestyle change or drug treatment. "The amount of information the participants will be able to view initially will be quite small," he says. An oversight board will meet twice a year to assess new sets of SNPs to determine whether they merit being shown to participants. Rules for what constitutes a "validated" SNP are still up in the air. "A SNP where there was a single small study in the literature with no replication or other data would not be a SNP that would be shown to the participants," Gerry says.

Part of the goal there is to ensure that patients understand what SNPs are and what it means to have one, says Courtney Sill, Coriell's director of communications. "We want to make sure participants understand what 'elevated risk' means," she says. Patients will have the option of sharing some or all of their data with their physician.

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