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Centralizing Clinical Variants

November 07, 2012

The National Center for Biotechnology Information's ClinVar database is proving useful for clinical labs trying to interpret genetic variants uncovered by next-gen sequencing, reports Nature.

ClinVar, designed to house information on the relationships between human variations and phenotypes, not only integrates clinical variation data from numerous publicly available resources, but "also provides, for the first time, a central place in which clinical testing laboratories can deposit their data," Nature says.

Clinical sequencing labs have to perform a considerable amount of analysis on novel variants to determine whether they are benign or pathogenic. But keeping this data in house means that many groups are duplicating their efforts.

"There is a growing recognition that a clinical lab may see a mutation once or never, so it’s better if all those data could be pooled,” says James Ostell, chief of the information engineering branch at NCBI.

“For everybody in the field, I think there will be a sigh of relief that this is finally happening,” adds Stephen Kingsmore of the Children’s Mercy Center for Pediatric Genome Medicine.

He says that when clinical labs share their data through ClinVar, “patients are going to be getting the best thinking of the community as opposed to an individual lab.”


Well...yes. Of course. But

Submitted by sherrib on Wed, 11/07/2012 - 14:39.

Well...yes. Of course. But the U41 grant application from Harvard, Emory, GeneDx, and other clinical labs that will support this effort to get clinical lab variants into ClinVar has yet to be funded. That is a must, or none of this will happen. Let us hope that there will be money available, and that the NIH finds this effort to be important enough to use the funds for that purpose. Otherwise ClinVar will be sitting pretty much empty.

(Disclaimer - I am a co-PI on that grant application).