Joanne G Ma, Matthew J O'Neill, Ebony Richardson, Kate L Thomson, Jodie Ingles, Ayesha Muhammad, Joseph F Solus, Giovanni Davogustto, Katherine C Anderson, M Benjamin Shoemaker, Andrew B Stergachis, Brendan J Floyd, Kyla Dunn, Victoria N Parikh, Henry Chubb, Mark J Perrin, Dan M Roden, Jamie I Vandenberg, Chai-Ann Ng, Andrew M Glazer
{"title":"判断 SCN5A Brugada 综合征相关变异的功能测定的多点验证。","authors":"Joanne G Ma, Matthew J O'Neill, Ebony Richardson, Kate L Thomson, Jodie Ingles, Ayesha Muhammad, Joseph F Solus, Giovanni Davogustto, Katherine C Anderson, M Benjamin Shoemaker, Andrew B Stergachis, Brendan J Floyd, Kyla Dunn, Victoria N Parikh, Henry Chubb, Mark J Perrin, Dan M Roden, Jamie I Vandenberg, Chai-Ann Ng, Andrew M Glazer","doi":"10.1161/CIRCGEN.124.004569","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Brugada syndrome is an inheritable arrhythmia condition that is associated with rare, loss-of-function variants in <i>SCN5A</i>. Interpreting the pathogenicity of <i>SCN5A</i> missense variants is challenging, and ≈79% of <i>SCN5A</i> missense variants in ClinVar are currently classified as variants of uncertain significance. Automated patch clamp technology enables high-throughput functional studies of ion channel variants and can provide evidence for variant reclassification.</p><p><strong>Methods: </strong>An in vitro <i>SCN5A</i>-Brugada syndrome automated patch clamp assay was independently performed at Vanderbilt University Medical Center and Victor Chang Cardiac Research Institute. The assay was calibrated according to ClinGen Sequence Variant Interpretation recommendations using high-confidence variant controls (n=49). Normal and abnormal ranges of function were established based on the distribution of benign variant assay results. Odds of pathogenicity values were derived from the experimental results according to ClinGen Sequence Variant Interpretation recommendations. The calibrated assay was then used to study <i>SCN5A</i> variants of uncertain significance observed in 4 families with Brugada syndrome and other arrhythmia phenotypes associated with <i>SCN5A</i> loss-of-function.</p><p><strong>Results: </strong>Variant channel parameters generated independently at the 2 research sites showed strong correlations, including peak <i>I</i><sub>Na</sub> density (<i>R</i><sup>2</sup>=0.86). The assay accurately distinguished benign controls (24/25 concordant variants) from pathogenic controls (23/24 concordant variants). Odds of pathogenicity values were 0.042 for normal function and 24.0 for abnormal function, corresponding to strong evidence for both American College of Medical Genetics and Genomics/Association for Molecular Pathology benign and pathogenic functional criteria (BS3 and PS3, respectively). Application of the assay to 4 clinical <i>SCN5A</i> variants of uncertain significance revealed loss-of-function for 3/4 variants, enabling reclassification to likely pathogenic.</p><p><strong>Conclusions: </strong>This validated high-throughput assay provides clinical-grade functional evidence to aid the classification of current and future <i>SCN5A</i>-Brugada syndrome variants of uncertain significance.</p>","PeriodicalId":10326,"journal":{"name":"Circulation: Genomic and Precision Medicine","volume":null,"pages":null},"PeriodicalIF":6.0000,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11335442/pdf/","citationCount":"0","resultStr":"{\"title\":\"Multisite Validation of a Functional Assay to Adjudicate <i>SCN5A</i> Brugada Syndrome-Associated Variants.\",\"authors\":\"Joanne G Ma, Matthew J O'Neill, Ebony Richardson, Kate L Thomson, Jodie Ingles, Ayesha Muhammad, Joseph F Solus, Giovanni Davogustto, Katherine C Anderson, M Benjamin Shoemaker, Andrew B Stergachis, Brendan J Floyd, Kyla Dunn, Victoria N Parikh, Henry Chubb, Mark J Perrin, Dan M Roden, Jamie I Vandenberg, Chai-Ann Ng, Andrew M Glazer\",\"doi\":\"10.1161/CIRCGEN.124.004569\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Brugada syndrome is an inheritable arrhythmia condition that is associated with rare, loss-of-function variants in <i>SCN5A</i>. Interpreting the pathogenicity of <i>SCN5A</i> missense variants is challenging, and ≈79% of <i>SCN5A</i> missense variants in ClinVar are currently classified as variants of uncertain significance. Automated patch clamp technology enables high-throughput functional studies of ion channel variants and can provide evidence for variant reclassification.</p><p><strong>Methods: </strong>An in vitro <i>SCN5A</i>-Brugada syndrome automated patch clamp assay was independently performed at Vanderbilt University Medical Center and Victor Chang Cardiac Research Institute. The assay was calibrated according to ClinGen Sequence Variant Interpretation recommendations using high-confidence variant controls (n=49). Normal and abnormal ranges of function were established based on the distribution of benign variant assay results. Odds of pathogenicity values were derived from the experimental results according to ClinGen Sequence Variant Interpretation recommendations. The calibrated assay was then used to study <i>SCN5A</i> variants of uncertain significance observed in 4 families with Brugada syndrome and other arrhythmia phenotypes associated with <i>SCN5A</i> loss-of-function.</p><p><strong>Results: </strong>Variant channel parameters generated independently at the 2 research sites showed strong correlations, including peak <i>I</i><sub>Na</sub> density (<i>R</i><sup>2</sup>=0.86). The assay accurately distinguished benign controls (24/25 concordant variants) from pathogenic controls (23/24 concordant variants). Odds of pathogenicity values were 0.042 for normal function and 24.0 for abnormal function, corresponding to strong evidence for both American College of Medical Genetics and Genomics/Association for Molecular Pathology benign and pathogenic functional criteria (BS3 and PS3, respectively). Application of the assay to 4 clinical <i>SCN5A</i> variants of uncertain significance revealed loss-of-function for 3/4 variants, enabling reclassification to likely pathogenic.</p><p><strong>Conclusions: </strong>This validated high-throughput assay provides clinical-grade functional evidence to aid the classification of current and future <i>SCN5A</i>-Brugada syndrome variants of uncertain significance.</p>\",\"PeriodicalId\":10326,\"journal\":{\"name\":\"Circulation: Genomic and Precision Medicine\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":6.0000,\"publicationDate\":\"2024-08-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11335442/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Circulation: Genomic and Precision Medicine\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1161/CIRCGEN.124.004569\",\"RegionNum\":2,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/7/2 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q1\",\"JCRName\":\"CARDIAC & CARDIOVASCULAR SYSTEMS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Circulation: Genomic and Precision Medicine","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1161/CIRCGEN.124.004569","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/7/2 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"CARDIAC & CARDIOVASCULAR SYSTEMS","Score":null,"Total":0}
Multisite Validation of a Functional Assay to Adjudicate SCN5A Brugada Syndrome-Associated Variants.
Background: Brugada syndrome is an inheritable arrhythmia condition that is associated with rare, loss-of-function variants in SCN5A. Interpreting the pathogenicity of SCN5A missense variants is challenging, and ≈79% of SCN5A missense variants in ClinVar are currently classified as variants of uncertain significance. Automated patch clamp technology enables high-throughput functional studies of ion channel variants and can provide evidence for variant reclassification.
Methods: An in vitro SCN5A-Brugada syndrome automated patch clamp assay was independently performed at Vanderbilt University Medical Center and Victor Chang Cardiac Research Institute. The assay was calibrated according to ClinGen Sequence Variant Interpretation recommendations using high-confidence variant controls (n=49). Normal and abnormal ranges of function were established based on the distribution of benign variant assay results. Odds of pathogenicity values were derived from the experimental results according to ClinGen Sequence Variant Interpretation recommendations. The calibrated assay was then used to study SCN5A variants of uncertain significance observed in 4 families with Brugada syndrome and other arrhythmia phenotypes associated with SCN5A loss-of-function.
Results: Variant channel parameters generated independently at the 2 research sites showed strong correlations, including peak INa density (R2=0.86). The assay accurately distinguished benign controls (24/25 concordant variants) from pathogenic controls (23/24 concordant variants). Odds of pathogenicity values were 0.042 for normal function and 24.0 for abnormal function, corresponding to strong evidence for both American College of Medical Genetics and Genomics/Association for Molecular Pathology benign and pathogenic functional criteria (BS3 and PS3, respectively). Application of the assay to 4 clinical SCN5A variants of uncertain significance revealed loss-of-function for 3/4 variants, enabling reclassification to likely pathogenic.
Conclusions: This validated high-throughput assay provides clinical-grade functional evidence to aid the classification of current and future SCN5A-Brugada syndrome variants of uncertain significance.
期刊介绍:
Circulation: Genomic and Precision Medicine is a distinguished journal dedicated to advancing the frontiers of cardiovascular genomics and precision medicine. It publishes a diverse array of original research articles that delve into the genetic and molecular underpinnings of cardiovascular diseases. The journal's scope is broad, encompassing studies from human subjects to laboratory models, and from in vitro experiments to computational simulations.
Circulation: Genomic and Precision Medicine is committed to publishing studies that have direct relevance to human cardiovascular biology and disease, with the ultimate goal of improving patient care and outcomes. The journal serves as a platform for researchers to share their groundbreaking work, fostering collaboration and innovation in the field of cardiovascular genomics and precision medicine.