Combining multiplexed functional data to improve variant classification.ArXiv • April 08, 2025
Jeffrey Calhoun, Moez Dawood, Charlie Rowlands, Shawn Fayer, Elizabeth Radford, Abbye Mcewen, Clare Turnbull, Amanda Spurdle, Lea Starita, Sujatha Jagannathan
With the surge in the number of variants of uncertain significance (VUS) reported in ClinVar in recent years, there is an imperative to resolve VUS at scale. Multiplexed assays of variant effect (MAVEs), which allow the functional consequence of 100s to 1000s of genetic variants to be measured in a single experiment, are emerging as a source of evidence which can be used for clinical gene variant classification. Increasingly, there are multiple published MAVEs for the same gene, sometimes measuring different aspects of variant impact. Where multiple functional consequences may need to be considered to get a more complete understanding of variant effects for a given gene, combining data from multiple MAVEs may lead to the assignment of increased evidence strength which could impact variant classifications. Here, we provide guidance for combining such multiplexed functional data, incorporating a stepwise process from data curation and collection to model generation and validation. We illustrate the potential of this approach by showing the integration of multiplexed functional data from four MAVEs for the gene TP53. By following these steps, researchers can maximize the value of MAVEs, strengthen the functional evidence for clinical variant classification, reclassify more VUS, and potentially uncover novel mechanisms of pathogenicity for clinically relevant genes.
Validating data from multiplex assays of variant effect: A CanVIG-UK national survey of NHS clinical scientists.American Journal Of Human Genetics • February 04, 2025
Sophie Allen, Alice Garrett, Charlie Rowlands, Miranda Durkie, George Burghel, Rachel Robinson, Alison Callaway, Joanne Field, Bethan Frugtniet, Sheila Palmer Smith, Jonathan Grant, Judith Pagan, Trudi Mcdevitt, Katie Snape, Helen Hanson, Terri Mcveigh, David Adams, Gregory Findlay, Rehan Villani, Amanda Spurdle, Clare Turnbull
Advances in technology have made it possible for multiplex assays of variant effect (MAVEs) to systematically generate functional data for thousands of genetic variants. Robust clinical validation and accessible online resources for MAVE data have previously been identified as barriers to the clinical adoption of new MAVEs. We delivered a survey during the November 2024 Cancer Variant Interpretation Group UK (CanVIG-UK) meeting comprising National Health Service (NHS) clinical scientists and clinical geneticists and received 46 responses from individuals regularly performing variant classification for diagnostic reporting. Only 35% reported they would accept clinical validation of the MAVE provided by the authors who conducted the assay; 20% reported they would attempt clinical validation themselves, and 61% would await clinical validation by a trusted central body. 72% reported they would use MAVE data ahead of a formal peer-reviewed publication if reviewed and clinically validated by a trusted central body. When scoring central bodies on a scale of 1-5 for confidence in their review and validation of MAVEs, CanVIG-UK (median = 5), variant curation expert panels (VCEPs; median = 5), and ClinGen SVI Functional Working Group (median = 4) all scored highly. Participants supported making variant-level data accessible via a relevant web resource (although the majority of participants expressed that additional assay-level or variant-level information would have a low likelihood of altering validation scores provided by a trusted central body). These findings, from a comparatively homogeneous clinical diagnostic group operating in a resource-constrained healthcare setting, indicate that clinical application of new MAVEs for variant classification will be delayed unless robust clinical validations are performed by a trusted central body and made readily accessible.
Insights on improving accessibility and usability of functional data to unlock their potential for variant interpretation.American Journal Of Human Genetics • January 27, 2025
Min Park, Runjun Kumar, Cristian Ovadiuc, Andrew Folta, Abbye Mcewen, Ashley Snyder, Rehan Villani, Amanda Spurdle, Douglas Fowler, Alan Rubin, Brian Shirts, Lea Starita, Andrew Stergachis
Variant-level functional data are a core component of clinical variant classification and can aid in reinterpreting variants of uncertain significance (VUSs). However, the usage of functional data by genetics professionals is currently unknown. An online survey was developed and distributed in the spring of 2024 to individuals actively engaged in variant interpretation. Quantitative and qualitative methods were used to assess responses. 190 eligible individuals responded, with 93% reporting interpreting 26 or more variants per year. The median respondent reported 11-20 years of experience. The most common professional roles were laboratory medical geneticists (23%) and variant review scientists (23%). 77% reported using functional data for variant interpretation in a clinical setting, and overall, respondents felt confident assessing functional data. However, 67% indicated that functional data for variants of interest were rarely or never available, and 91% considered insufficient quality metrics or confidence in the accuracy of data as barriers to their use. 94% of respondents noted that better access to primary functional data and standardized interpretation of functional data would improve usage. Respondents also indicated that handling conflicting functional data is a common challenge in variant interpretation that is not performed in a systematic manner across institutions. The results from this survey showed a demand for a comprehensive database with reliable quality metrics to support the use of functional evidence in clinical variant interpretation. The results also highlight a need for guidelines regarding how putatively conflicting functional data should be used for variant classification.
Consultation informs strategies for improving the use of functional evidence in variant classification.American Journal Of Human Genetics • January 13, 2025
Rehan Villani, Bronwyn Terrill, Emma Tudini, Maddison Mckenzie, Corrina Cliffe, Christopher Hahn, Ben Lundie, Tessa Mattiske, Ebony Matotek, Abbye Mcewen, Sarah Nickerson, James Breen, Douglas Fowler, John Christodoulou, Lea Starita, Alan Rubin, Amanda Spurdle
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.
Consultation informs strategies to improve functional evidence use in variant classification.MedRxiv : The Preprint Server For Health Sciences • December 16, 2024
Rehan Villani, Bronwyn Terrill, Emma Tudini, Maddison Mckenzie, Corrina Cliffe, Christopher Hahn, Ben Lundie, Tessa Mattiske, Ebony Matotek, Abbye Mcewen, Sarah Nickerson, James Breen, Douglas Fowler, John Christodoulou, Lea Starita, Alan Rubin, Amanda Spurdle
To determine if a variant identified by diagnostic genetic testing is causal for disease, applied genetics professionals evaluate all available evidence to assign a clinical classification. Experimental assay data can provide strong functional evidence for or against pathogenicity in variant classification, but appears to be underutilised. We surveyed genetic diagnostic professionals in Australasia to assess their application of functional evidence in clinical practice. Results indicated that survey respondents are not confident to apply functional evidence, mainly due to uncertainty around practice recommendations. Respondents also identified need for support resources, educational opportunities, and in particular requested expert recommendations and updated practice guidelines to improve translation of experimental data to curation evidence. As an initial step, we have collated a list of functional assays recommended by 19 ClinGen Variant Curation Expert Panels as a source of international expert opinion on functional evidence evaluation. Additional support resources for diagnostic practice are in development.
