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Well, What Does it Mean?

As part of a set of papers on clinical genomics testing published in the New England Journal of Medicine yesterday, the team behind the National Institutes of Health's Clinical Genome Resource program reports that different labs around the country sometimes have differing opinions as to the clinical significance of the same gene variant.

"We have very clear documentation that there are differences in what patients are getting" back when the same gene variants are interpreted by different labs, the Laboratory for Molecular Medicine at Partners HealthCare Personalized Medicine's Heidi Rehm tells the Associated Press.

ClinGen was established in 2013 as a means of building a genomic knowledge base to improve patient care. Its ClinVar database contains more than 145,300 unique sequence and structural variants spanning nearly 22,900 genes that were submitted by 314 users, as GenomeWeb notes.

As Rehm and her colleagues report, of the 118,169 unique variants with clinical interpretations, 11 percent have clinical interpretations submitted by more than one lab and of those, 17 percent were interpreted differently by the various contributors.

Further, 415 variants have such differing interpretations that they would likely lead to different clinical decisions.

"The magnitude of this problem is bigger than most people thought," Michael Watson, executive director of the American College of Medical Genetics and Genomics, tells the Associated Press.

ACMG worked with the sequence and structural-variant communities to develop standards for interpreting genetic variants, and the ClinVar team says it is now helping labs adopt these standards. It adds that these standards have already helped some labs resolve differences in interpretations.