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Genome Interpretation Database, Quality Effort Underway

DNA illustration

(National Heart, Lung, and Blood Institute, NIH)

28 May 2015. A program to improve diagnostics and research based on genomic variations is underway that collects genetic data and implements standards for their interpretation. A description of the Clinical Genome Resource or ClinGen program appears in yesterday’s issue of the New England Journal of Medicine.

ClinGen is a collaborative effort of  public, academic, and private institutions to produce more consistency and accuracy in genomic interpretation, for the diagnosis of disorders in individuals and understanding of relationships between genomic variations and disease. The program collects genetic data and supporting evidence from labs and individuals, then stores the data — with identifying items removed — in a database. Before storing the data, however, expert working groups review and analyze the submissions for accuracy and consistency in their interpretation of genomic variations.

The standards for interpreting the data are a product of American College of Medical Genetics and Genomics for analyzing genetic variants. Under those standards, working groups with members from 75 organizations check for consistent naming of genomic variations and their accurate mapping with the human genome sequence reference, as well as accurate terms for describing their clinical significance. After depositing data, each lab receives a report noting any discrepancies between its original interpretations and those already in the database.

The database, known as ClinVar, now has more than 172,000 genomic variations representing some 22,800 different genes from 314 sources. Contributors to ClinVar include other disease-specific genomic databases, medical and research labs, expert consortia, professional associations, health care providers, and individual patients. ClinGen established a patient registry known as GenomeConnect for health care providers and individuals to contribute their genetic data.

The journal article reports on the scale of differences in interpretation of genomic variants already found through this process. The authors report more than 118,000 unique variations are identified in ClinVar with clinical interpretations. Of that number, 24,725 — about 1 in 5 — are variants of uncertain significance. In addition, nearly 13,000 of these identified variations were reported by different labs, of which more than 2,200 variants had different interpretations, including different assessments of potential danger to the patient.

Providing more consistent and accurate interpretation of genomic variations has immediate benefits for individual patients, say the authors, but also for advancing the adoption of precision medicine and improving recruitment for clinical trials. ClinVar is maintained at National Center for Biotechnology Information, part of National Institutes of Health that funds the ClinGen project.

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