Next-Generation Sequencing Germline Variant Confirmation

Publication Date: May 17, 2023

Summary of Recommendations

Clinical laboratories offering germline testing using NGS should establish a written policy regarding orthogonal confirmation of NGS results.

Laboratories' orthogonal confirmation policy should be overseen and approved by a qualified and appropriately certified medical professional with training and experience in NGS.

Laboratories' confirmatory methods, platforms, and associated bioinformatics should be validated and maintained under appropriate regulatory oversight, as for other aspects of the test.

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.

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.

Laboratories should clearly articulate their specific policies, criteria, and methods regarding orthogonal confirmation in written materials readily available on request.

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.

Special considerations apply to certain NGS-based test types and findings.

Recommendation Grading


The information in this patient summary should not be used as a substitute for professional medical care or advice. Contact a health care provider if you have questions about your health.



Next-Generation Sequencing Germline Variant Confirmation

Authoring Organizations

Publication Month/Year

May 17, 2023

Document Type


Country of Publication


Document Objectives

Clinical laboratory implementation of next-generation sequencing (NGS)-based constitutional genetic testing has been rapid and widespread. In the absence of widely adopted comprehensive guidance, there remains substantial variability among laboratories in the practice of NGS. One issue of sustained discussion in the field is whether and to what extent orthogonal confirmation of genetic variants identified by NGS is necessary or helpful. The Association for Molecular Pathology Clinical Practice Committee convened the NGS Germline Variant Confirmation Working Group to assess current evidence regarding orthogonal confirmation and to establish recommendations for standardizing orthogonal confirmation practices to support quality patient care. Based on the results of a survey of the literature, a survey of laboratory practices, and subject expert matter consensus, eight recommendations are presented, providing a common framework for clinical laboratory professionals to develop or refine individualized laboratory policies and procedures regarding orthogonal confirmation of germline variants detected by NGS.

Inclusion Criteria

Male, Female, Adolescent, Adult, Child, Infant, Older adult

Health Care Settings

Ambulatory, Laboratory services

Intended Users

Genetics, nurse, nurse practitioner, physician, physician assistant


Assessment and screening

Diseases/Conditions (MeSH)

D017421 - Sequence Analysis


Germline Testing, germline mutations, NGS, Next-Generation Sequencing, germline

Source Citation

Crooks KR, Farwell Hagman KD, Mandelker D, Santani A, Schmidt RJ, Temple-Smolkin RL, Lincoln SE. Recommendations for Next-Generation Sequencing Germline Variant Confirmation: A Joint Report of the Association for Molecular Pathology and National Society of Genetic Counselors. J Mol Diagn. 2023 May 17:S1525-1578(23)00103-4. doi: 10.1016/j.jmoldx.2023.03.012. Epub ahead of print. PMID: 37207865.