Omicia Inc, Oakland, Calif, recently launched its American College of Medical Genetics (ACMG) scoring module for the Opal Clinical interpretation and reporting software platform. The functionality provides an intuitive interface and workflow for clinical testing labs to systematically assess the disease-causing potential of genetic variants using the evidence-based classification system defined in the 2015 Standards and Guidelines for the Interpretation of Sequence Variants.

Published as a joint consensus recommendation of ACMG, the Association for Molecular Pathology, and the College of American Pathologists, the guidelines were developed to standardize interpretation and reporting of genomic test results. Through systematic assessment of 28 weighted criteria, variants are ultimately classified on a five-point scale: benign, likely benign, uncertain significance, likely pathogenic, and pathogenic.

While recognized as a valuable framework to support consistency of reporting within and among clinical labs, several challenges have arisen for labs attempting to implement the ACMG guidelines for their genomic testing services, including gathering the pertinent evidence required to address each criterion; developing an efficient, repeatable workflow to assess the criteria; and automating the scoring and classification process for reliable, high-throughput reporting.

Opal Clinical’s scoring and classification system was developed to mitigate these challenges, enabling labs to adopt the ACMG guidelines and accelerate interpretation with a stepwise, guided assessment of each ACMG criterion. Opal integrates more than 90 public and proprietary data sources to compile the specific gene and variant annotations required to make an assessment of the indicated criterion, and provides a simple yes-or-no checkbox evaluation for scoring. As criteria evaluation progresses, Opal calculates an inferred classification that users can accept or override based on their evaluation of the evidence.

Jeanette McCarthy, MPH, PhD, Duke University.

Jeanette McCarthy, MPH, PhD, Duke University.

“Applying the ACMG guidelines using Opal Clinical software can improve consistency across interpreters because it represents a logical, systematic way to work through the criteria,” says Jeanette McCarthy, MPH, PhD, adjunct associate professor of community and family medicine at Duke University and a visiting associate professor of medicine at the University of California, San Francisco. “The Opal platform improves efficiency because it brings all the data sources needed for interpretation to the user, and the system captures decisions at every step.”

Opal Clinical features several timesaving functions for labs processing large numbers of clinical tests. A scoring history database is instantaneously updated as variants are classified within the platform. Variants that have been previously assessed are flagged, and historical classifications, notes, and citations can be used for bulk classification and automated reporting. These features are intended to speed lab test turnaround times, in an effort to make clinical testing with targeted sequencing panels, exomes, and whole genomes feasible at high throughput.

For more information, visit Omicia.