Enhancing rare variant interpretation in inherited arrhythmias through quantitative analysis of consortium disease cohorts and population controls.

Roddy Walsh, Najim Lahrouchi, Rafik Tadros, Florence Kyndt, Charlotte Glinge, Pieter G Postema, Ahmad S Amin, Eline A Nannenberg, James S Ware, Nicola Whiffin, Francesco Mazzarotto, Doris Škorić-Milosavljević, Christian Krijger, Elena Arbelo, Dominique Babuty, Hector Barajas-Martinez, Britt M Beckmann, Stéphane Bézieau, J Martijn Bos, Jeroen Breckpot, Oscar Campuzano, Silvia Castelletti, Candan Celen, Sebastian Clauss, Anniek Corveleyn, Lia Crotti, Federica Dagradi, Carlo de Asmundis, Isabelle Denjoy, Sven Dittmann, Patrick T Ellinor, Cristina Gil Ortuño, Carla Giustetto, Jean-Baptiste Gourraud, Daisuke Hazeki, Minoru Horie, Taisuke Ishikawa, Hideki Itoh, Yoshiaki Kaneko, Jørgen K Kanters, Hiroki Kimoto, Maria-Christina Kotta, Ingrid P C Krapels, Masahiko Kurabayashi, Julieta Lazarte, Antoine Leenhardt, Bart L Loeys, Catarina Lundin, Takeru Makiyama, Jacques Mansourati, Raphaël P Martins, Andrea Mazzanti, Stellan Mörner, Carlo Napolitano, Kimie Ohkubo, Michael Papadakis, Boris Rudic, Maria Sabater Molina, Frédéric Sacher, Hatice Sahin, Georgia Sarquella-Brugada, Regina Sebastiano, Sanjay Sharma, Mary N Sheppard, Keiko Shimamoto, M Benjamin Shoemaker, Birgit Stallmeyer, Johannes Steinfurt, Yuji Tanaka, David J Tester, Keisuke Usuda, Paul A van der Zwaag, Sonia Van Dooren, Lut Van Laer, Annika Winbo, Bo G Winkel, Kenichiro Yamagata, Sven Zumhagen, Paul G A Volders, Steven A Lubitz, Charles Antzelevitch, Pyotr G Platonov, Katja E Odening, Dan M Roden, Jason D Roberts, Jonathan R Skinner, Jacob Tfelt-Hansen, Maarten P van den Berg, Morten S Olesen, Pier D Lambiase, Martin Borggrefe, Kenshi Hayashi, Annika Rydberg, Tadashi Nakajima, Masao Yoshinaga, Johan B Saenen, Stefan Kääb, Pedro Brugada, Tomas Robyns, Daniela F Giachino, Michael J Ackerman, Ramon Brugada, Josep Brugada, Juan R Gimeno, Can Hasdemir, Pascale Guicheney, Silvia G Priori, Eric Schulze-Bahr, Naomasa Makita, Peter J Schwartz, Wataru Shimizu, Takeshi Aiba, Jean-Jacques Schott, Richard Redon, Seiko Ohno, Vincent Probst, Elijah R Behr, Julien Barc, Connie R Bezzina

Journal: Genetics in medicine : official journal of the American College of Medical Genetics 2021;23(1):47-58

PMID: 32893267

Abstract

PURPOSE

Stringent variant interpretation guidelines can lead to high rates of variants of uncertain significance (VUS) for genetically heterogeneous disease like long QT syndrome (LQTS) and Brugada syndrome (BrS). Quantitative and disease-specific customization of American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines can address this false negative rate.

METHODS

We compared rare variant frequencies from 1847 LQTS (KCNQ1/KCNH2/SCN5A) and 3335 BrS (SCN5A) cases from the International LQTS/BrS Genetics Consortia to population-specific gnomAD data and developed disease-specific criteria for ACMG/AMP evidence classes-rarity (PM2/BS1 rules) and case enrichment of individual (PS4) and domain-specific (PM1) variants.

RESULTS

Rare SCN5A variant prevalence differed between European (20.8%) and Japanese (8.9%) BrS patients (p = 5.7 × 10) and diagnosis with spontaneous (28.7%) versus induced (15.8%) Brugada type 1 electrocardiogram (ECG) (p = 1.3 × 10). Ion channel transmembrane regions and specific N-terminus (KCNH2) and C-terminus (KCNQ1/KCNH2) domains were characterized by high enrichment of case variants and >95% probability of pathogenicity. Applying the customized rules, 17.4% of European BrS and 74.8% of European LQTS cases had (likely) pathogenic variants, compared with estimated diagnostic yields (case excess over gnomAD) of 19.2%/82.1%, reducing VUS prevalence to close to background rare variant frequency.

CONCLUSION

Large case-control data sets enable quantitative implementation of ACMG/AMP guidelines and increased sensitivity for inherited arrhythmia genetic testing.

Address: Department of Clinical and Experimental Cardiology, Heart Centre, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands. [email protected].; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands. [email protected].; Department of Clinical and Experimental Cardiology, Heart Centre, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute and Faculty of Medicine, Université de Montréal, Montreal, QC, Canada.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.; National Heart and Lung Institute, Imperial College London, London, United Kingdom.; Cardiovascular Research Centre, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom.; MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom.; National Heart and Lung Institute, Imperial College London, London, United Kingdom.; Cardiovascular Research Centre, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom.; Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy.; Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.; Arrhythmia Section, Cardiology Department, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.; IDIBAPS, Institut d'Investigació August Pi i Sunyer (IDIBAPS), Barcelona, Spain.; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.; CHU Tours, Service de Cardiologie, Tours, France.; Lankenau Institute for Medical Research, Wynnewood, PA, USA.; Department of Internal Medicine I, LMU Klinikum, Klinikum der Ludwig Maximilians Universität München, München, Germany.; Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Mayo Clinic, Rochester, MN, USA.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium.; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.; Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain.; Medical Science Department, School of Medicine, University of Girona, Girona, Spain.; Biochemistry and Molecular Genetics Department, Hospital Clinic, University of Barcelona-IDIBAPS, Barcelona, Spain.; Istituto Auxologico Italiano, IRCCS-Center for Cardiac Arrhythmias of Genetic Origin, Milan, Italy.; Department of Cardiology, Ege University School of Medicine, Izmir, Turkey.; Department of Internal Medicine I, LMU Klinikum, Klinikum der Ludwig Maximilians Universität München, München, Germany.; German Centre for Cardiovascular Research (DZHK), Partner Site Munich, Munich Heart Alliance (MHA), Munich, Germany.; Walter Brendel Centre of Experimental Medicine, Ludwig-Maximilians University Munich (LMU), Munich, Germany.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium.; Istituto Auxologico Italiano, IRCCS-Center for Cardiac Arrhythmias of Genetic Origin, Milan, Italy.; Istituto Auxologico Italiano, IRCCS, Department of Cardiovascular, Neural and Metabolic Sciences, San Luca Hospital, Milan, Italy.; Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy.; Istituto Auxologico Italiano, IRCCS-Laboratory of Cardiovascular Genetics, Cusano Milanino, MI, Italy.; Heart Rhythm Management Center, Postgraduate program in Cardiac Electrophysiology and Pacing Universitair Ziekenhuis, Brussel-Vrije Universiteit Brussel, ERN Heart Guard Center, Brussels, Belgium.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; CNMR Maladies Cardiaques Héréditaires Rares, Hôpital Bichat, Université de Paris, Paris, France.; AP-HP, Service de Cardiologie, Hôpital Bichat, Paris, France.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Institute for Genetics of Heart Diseases, University Hospital Münster, Münster, Germany.; Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.; Cardiovascular Disease Initiative, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Cardiogenetic Laboratory, Inherited Cardiac Disease Unit, University Hospital Virgen de la Arrixaca-IMIB, Murcia, Spain.; Division of Cardiology, University of Torino, Department of Medical Sciences, "Città della Salute e della Scienza" Hospital, Torino, Italy.; Department of Pediatrics, Kagoshima City Hospital, Kagoshima, Japan.; Center for Epidemiologic Research in Asia, Shiga University of Medical Science, Seta-Tsukinowa-cho, Otsu, Japan.; Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan.; Division of Patient Safety, Hiroshima University Hospital, Minami-ku, Hiroshima, Japan.; Department of Cardiovascular Medicine, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan.; Laboratory of Experimental Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.; Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.; Istituto Auxologico Italiano, IRCCS-Center for Cardiac Arrhythmias of Genetic Origin, Milan, Italy.; Istituto Auxologico Italiano, IRCCS-Laboratory of Cardiovascular Genetics, Cusano Milanino, MI, Italy.; Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht, Netherlands.; Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.; Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.; Department of Clinical Genetics and Pathology, Lund University, Lund, Sweden.; Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.; CHU Brest, Service de Cardiologie, Brest, France.; Univ Rennes, CHU Rennes, INSERM, Rennes, France.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Molecular Cardiology, ICS Maugeri, IRCCS and Department of Molecular Medicine, University of Pavia, Pavia, Italy.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Centre for Cardiovascular Genetics, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden.; Department of Cardiovascular Medicine, Nihon University, Tokyo, Japan.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, United Kingdom.; Cardiology Clinical Academic Group, St. George's University Hospitals' NHS Foundation Trust, London, United Kingdom.; Department of Medicine, University Medical Center Mannheim, Mannheim, Germany.; German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Mannheim, Germany.; Hôpital Cardiologique du Haut-Lévêque, LIRYC Institute, Université Bordeaux, Bordeaux, France.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Medical Science Department, School of Medicine, University of Girona, Girona, Spain.; Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain.; Medical Genetics, San Luigi Univesity Hospital, Orbassano, TO, Italy.; Department of Cardiovascular Medicine, National Cerebral and Cardiovascular Center, Suita, Japan.; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.; Department of Cardiology and Angiology I, Heart Center University of Freiburg, Medical Faculty, Freiburg, Germany.; Department of Pediatrics, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan.; Department of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan.; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Centre for Medical Genetics, research group Reproduction and Genetics, research cluster Reproduction, Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium.; Department of Physiology, University of Auckland, Auckland, New Zealand.; Department of Cardiology, CARIM, Maastricht University Medical Center+, Maastricht, Netherlands.; Department of Cardiology, Clinical Sciences, Lund University, Lund, Sweden.; Department of Cardiology and Angiology I, Heart Center University of Freiburg, Medical Faculty, Freiburg, Germany.; Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA.; Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, ON, Canada.; Cardiac Inherited Disease Group, Starship Childrens Hospital, Auckland, New Zealand.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.; Department of Forensic Medicine, Faculty of Medical Sciences, University of Copenhagen, Copenhagen, Denmark.; Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.; Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Barts Heart Centre, Barts Health NHS Trust & Institute of Cardiovascular Science, University College London, London, United Kingdom.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Department of Clinical Sciences, Paediatrics, Umeå University, Umeå, Sweden.; Department of Cardiology, University of Antwerp, Antwerp University Hospital, Antwerp, Belgium.; Department of Internal Medicine I, LMU Klinikum, Klinikum der Ludwig Maximilians Universität München, München, Germany.; German Centre for Cardiovascular Research (DZHK), Partner Site Munich, Munich Heart Alliance (MHA), Munich, Germany.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Heart Rhythm Management Center, UZ Brussel-VUB, Brussels, Belgium.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Department of Cardiovascular Diseases, University Hospitals Leuven, Leuven, Belgium.; Medical Genetics, San Luigi Univesity Hospital, Orbassano, TO, Italy.; Medical Genetics Department, Clinical and Biological Sciences, Univestity of Torino, Orbassano, TO, Italy.; Hospital Trueta, CiberCV, University of Girona, IDIBGI, Girona, Spain.; Cardiovascular Institute, Hospital Clinic, University of Barcelona, Barcelona, Spain.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Inherited Cardiac Disease Unit, Cardiology Department, University Hospital Virgen de la Arrixaca, Murcia, Spain.; INSERM, Sorbonne University, UMRS 1166, Institute of Cardiometabolism and Nutrition (ICAN), Paris, France.; Department of Cardiovascular Medicine, Nippon Medical School, Tokyo, Japan.; Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Suita, Japan.; Member of the European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands.; Université de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France.
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