AMP Releases Recommendations for NGS Germline Variant Confirmation

[seqadmin]

Next-generation sequencing (NGS) has truly revolutionized clinical molecular genetic testing, becoming the primary method in this field. However, there is considerable variability between laboratories and a lack of standardization for important methods. The Association for Molecular Pathology (AMP) has released a report aimed at establishing standardized practices for confirming germline variants detected through NGS, titled "Recommendations for Next-Generation Sequencing Germline Variant Confirmation: A Joint Report of the Association for Molecular Pathology and National Society of Genetic Counselors."

This manuscript provides guidelines to promote consistency, transparency, and quality improvement among laboratories. It offers eight recommendations based on an extensive review of published literature, empirical data, laboratory surveys, public feedback, and professional expertise.

The eight recommendations include:

1. Clinical laboratories offering germline testing using NGS should establish a written policy regarding orthogonal confirmation of NGS results.
2. Laboratories' orthogonal confirmation policy should be overseen and approved by a qualified and appropriately certified medical professional with training and experience in NGS.
3. Laboratories' confirmatory methods, platforms, and associated bioinformatics should be validated and maintained under appropriate regulatory oversight, as for other aspects of the test.
4. Laboratories' confirmatory methods should be orthogonal. Discrepant results between NGS and a confirmatory assay should be investigated and resolved, rather than accepting any one method to be always correct.
5. Laboratories should perform confirmatory testing for reported germline variants with significant clinical implications, except for variant calls meeting technical criteria rigorously demonstrated to ensure high positive predictive value from NGS alone.
6. Laboratories should clearly articulate their specific policies, criteria, and methods regarding orthogonal confirmation in written materials readily available on request.
7. Laboratories' clinical test reports should summarize orthogonal confirmation policy in every report, and when exceptions to the policy are made, these should be clearly indicated.
8. Special considerations apply to certain NGS-based test types and findings.

The evidence-based consensus recommendations in the report provide a framework for laboratories to develop policies for orthogonal confirmation of germline variants. The recommendations emphasize rigorous scientific study, uniform application within the laboratory, appropriate validation, and clear communication with ordering providers. Revisions will eventually be necessary as NGS technology and bioinformatics continue to evolve.