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At ACMG, Researchers Call for Improved Databases for Clinically Interpreting Genetic Variation

By Andrea Anderson

VANCOUVER, BRITISH COLUMBIA (GenomeWeb News) – A "clinical grade" database for sifting through mutations in the genome is needed to help realize the full potential of whole-genome analyses as a diagnostic tool, Mark Boguski argued at the American College of Medical Genetics meeting here this weekend.

Boguski, a pathology researcher affiliated with Harvard Medical School and the Beth Israel Deaconess Medical Center, discussed the potential that whole-genome analyses hold for improving the diagnosis, characterization, and treatment of cancer, arguing that medical genomics has the potential to produce disruptive change in the way pathologists and oncologists deal with disease.

In 2009, Boguski and his colleagues predicted that by 2020 medical sequencing would help clinicians make treatment decisions by uncovering information for reverse-engineering disease-related pathways, coming up appropriate treatments, and tracking patient response to these treatments.

Now, Boguski said, there's evidence that this change could come much more quickly. In particular, he pointed to a Genome Biology study published by British Columbia Cancer Agency researcher Marco Marra and colleagues last fall, in which researchers used genome and transcriptome sequencing to characterize a tongue adenocarcinoma from a 78-year old patient — information that was ultimately used to guide the individual's treatment.

Such treatment could become the standard of care in the relatively near future, Boguski said, noting that whole-genome analyses have the potential to become pathologists' new "microscope."

For that to happen, though, he says more refined and regulated databases are needed to discern between common variation in the genome and medically important mutations.

Boguski was not alone in this assessment, as other presenters discussing medical applications of genomics at the meeting echoed a similar sentiment.

For instance, Partners Healthcare and Harvard Medical School researcher Heidi Rehm highlighted the need for a centralized, accurate, open-access variant database with standardized nomenclature during a session on delivering genomic testing results to patients. Rehm said such a resource is needed to not only interpret genetic variation clinically, but to help in reporting medically relevant mutations back to clinicians and patients.

For her part, she is working with collaborators in Europe and elsewhere to take a crack at creating a resource dubbed MutaDATABASE to address some of these issue. That effort it still in its infancy, Rehm emphasized, but those involved are hopeful that it will eventually solve some of the problems associated with existing genetic variation and mutation databases.