NEW YORK (GenomeWeb) – Are public variant databases a collective good or are they a source of confusion and uncertainty that can harm patients?
Two new papers published last week added fresh data to a contentious debate over the use of public variant repositories, which are increasingly supported by regulators, the National Institutes of Health, guidelines bodies, peer-reviewed publications, and payors. And while a number of labs and pharma companies are openly sharing variant information in such databases, many are not, citing competitive reasons, patient privacy concerns, and the limitations of the repositories.
In a paper published by Invitae and collaborators last week in the Journal of Clinical Oncology – Precision Oncology, the authors demonstrated that among seven submitters of BRCA1 and BRCA2 gene variant classifications to an NIH-funded public repository, called ClinVar, their determinations agreed for 98.5 percent of around 2,000 variants. When they worked together to resolve the remaining discrepancies in rare variants, agreement was achieved for 99 percent of variants.
Pathogenic mutations in BRCA1/2 genes are known to increase risk for hereditary breast, ovarian, and other cancers, but the two genes are highly variable, and not all variations are potentially harmful. Working collaboratively to classify variants