Consultation informs strategies for improving the use of functional evidence in variant classification

Rehan M Villani¹, Bronwyn Terrill², Emma Tudini³, Maddison E McKenzie¹, Corrina C Cliffe⁴, Christopher N Hahn⁵, Ben Lundie⁶, Tessa Mattiske⁷, Ebony Matotek⁸, Abbye E McEwen⁹, Sarah L Nickerson¹⁰, James Breen¹¹, Douglas M Fowler¹², John Christodoulou¹³, Lea Starita¹⁴, Alan F Rubin¹⁵, Amanda B Spurdle¹⁶

Affiliations

¹ QIMR Berghofer, Brisbane, QLD, Australia.
² Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Clinical Translation and Engagement Platform, Garvan Institute of Medical Research, Sydney, NSW, Australia; Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
³ QIMR Berghofer, Brisbane, QLD, Australia; Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
⁴ Douglass Hanly Moir Pathology, Macquarie Park, NSW, Australia.
⁵ Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia.
⁶ Pathology Queensland, Queensland Health, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia.
⁷ Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Australian Functional Genomics Network, Murdoch Children's Research Institute, Parkville, VIC, Australia.
⁸ Australian Functional Genomics Network, Murdoch Children's Research Institute, Parkville, VIC, Australia.
⁹ Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute, Seattle, WA, USA.
¹⁰ Department of Diagnostic Genomics, PathWest, QEII Medical Centre, Perth, WA, Australia; The University of Western Australia, Perth, WA, Australia.
¹¹ Black Ochre Data Labs (Indigenous Genomics), The Kids Research Institute Australia & Australian National University, Adelaide, SA, Australia; National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia.
¹² Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA.
¹³ Genomic Medicine Theme, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.
¹⁴ Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute, Seattle, WA, USA.
¹⁵ The Walter and Eliza Hall Institute of Medical Research, University of Melbourne, Melbourne, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia. Electronic address: alan.rubin@wehi.edu.au.
¹⁶ QIMR Berghofer, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia. Electronic address: amanda.spurdle@qimrb.edu.au.

PMID: 40480201
PMCID: PMC12256917 (available on 2025-12-05)
DOI: 10.1016/j.ajhg.2025.05.003

Consultation informs strategies for improving the use of functional evidence in variant classification

Rehan M Villani et al. Am J Hum Genet. 2025.

. 2025 Jun 5;112(6):1489-1495.

doi: 10.1016/j.ajhg.2025.05.003.

Authors

Affiliations

¹ QIMR Berghofer, Brisbane, QLD, Australia.
² Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Clinical Translation and Engagement Platform, Garvan Institute of Medical Research, Sydney, NSW, Australia; Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
³ QIMR Berghofer, Brisbane, QLD, Australia; Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
⁴ Douglass Hanly Moir Pathology, Macquarie Park, NSW, Australia.
⁵ Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia.
⁶ Pathology Queensland, Queensland Health, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia.
⁷ Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Australian Functional Genomics Network, Murdoch Children's Research Institute, Parkville, VIC, Australia.
⁸ Australian Functional Genomics Network, Murdoch Children's Research Institute, Parkville, VIC, Australia.
⁹ Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute, Seattle, WA, USA.
¹⁰ Department of Diagnostic Genomics, PathWest, QEII Medical Centre, Perth, WA, Australia; The University of Western Australia, Perth, WA, Australia.
¹¹ Black Ochre Data Labs (Indigenous Genomics), The Kids Research Institute Australia & Australian National University, Adelaide, SA, Australia; National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia.
¹² Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA.
¹³ Genomic Medicine Theme, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.
¹⁴ Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute, Seattle, WA, USA.
¹⁵ The Walter and Eliza Hall Institute of Medical Research, University of Melbourne, Melbourne, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia. Electronic address: alan.rubin@wehi.edu.au.
¹⁶ QIMR Berghofer, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia. Electronic address: amanda.spurdle@qimrb.edu.au.

PMID: 40480201
PMCID: PMC12256917 (available on 2025-12-05)
DOI: 10.1016/j.ajhg.2025.05.003

Abstract

When investigating whether a variant identified by diagnostic genetic testing is causal for disease, applied genetics professionals evaluate all available evidence to assign a clinical classification. Functional assays of higher and higher throughput are increasingly being generated and, when appropriate, can provide strong functional evidence for or against pathogenicity in variant classification. Despite functional assay data representing unprecedented value for genomic diagnostics, challenges remain around the application of functional evidence in variant curation. To investigate a growing gap articulated in recent international studies, we surveyed genetic diagnostic professionals in Australasia to assess their application of functional evidence in clinical practice. The survey results echo the universal difficulty in evaluating functional evidence but expand on this by indicating that even self-proclaimed expert respondents are not confident to apply functional evidence, mainly due to uncertainty around practice recommendations. Respondents also identified the need for support resources and educational opportunities, and in particular requested expert recommendations and updated practice guidelines to improve translation of experimental data to curation evidence. We then collated a list of 226 functional assays and the evidence strength recommended by 19 ClinGen Variant Curation Expert Panels. Specific assays for more than 45,000 variants were evaluated, but evidence recommendations were generally limited to lower throughput and strength. As an initial step, we provide our collated list of assay evidence as a source of international expert opinion on the evaluation of functional- evidence and conclude that these results highlight an opportunity to develop additional support resources to fully utilize functional evidence in clinical practice.

Keywords: ACMG/AMP guidelines; assay; clinical genomics; diagnostic genetics; education; functional evidence; pathogenicity assessment; variant classification.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Update of

Consultation informs strategies to improve functional evidence use in variant classification.
Villani RM, Terrill B, Tudini E, McKenzie ME, Cliffe CC, Hahn CN, Lundie B, Mattiske T, Matotek E, McEwen AE, Nickerson SL, Breen J, Fowler DM, Christodoulou J, Starita L, Rubin AF, Spurdle AB. Villani RM, et al. medRxiv [Preprint]. 2024 Dec 6:2024.12.04.24318523. doi: 10.1101/2024.12.04.24318523. medRxiv. 2024. Update in: Am J Hum Genet. 2025 Jun 5;112(6):1489-1495. doi: 10.1016/j.ajhg.2025.05.003. PMID: 39677445 Free PMC article. Updated. Preprint.

References

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Consultation informs strategies for improving the use of functional evidence in variant classification

Affiliations

Consultation informs strategies for improving the use of functional evidence in variant classification

Authors

Affiliations

Abstract

Conflict of interest statement

Update of

References

MeSH terms

LinkOut - more resources

Full Text Sources

Medical

Research Materials

Miscellaneous