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

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Walsh, RoddyAcademic Medical Center of University of Amsterdam (AMC) (author)

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

Article/chapterEnglish2021

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Nature Publishing Group,2021
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LIBRIS-ID:oai:DiVA.org:umu-175470
https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-175470URI
https://doi.org/10.1038/s41436-020-00946-5DOI
https://lup.lub.lu.se/record/794cf9bb-4c42-4c75-8806-bf5585e45050URI

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Language:English
Summary in:English

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Subject category:ref swepub-contenttype
Subject category:art swepub-publicationtype

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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 x 10(-18)) and diagnosis with spontaneous (28.7%) versus induced (15.8%) Brugada type 1 electrocardiogram (ECG) (p = 1.3 x 10(-13)). 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.

Subject headings and genre

MEDICIN OCH HÄLSOVETENSKAP Medicinska och farmaceutiska grundvetenskaper Medicinsk genetik hsv//swe
MEDICAL AND HEALTH SCIENCES Basic Medicine Medical Genetics hsv//eng
LANTBRUKSVETENSKAPER Bioteknologi med applikationer på växter och djur Genetik och förädling inom lantbruksvetenskap hsv//swe
AGRICULTURAL SCIENCES Agricultural Biotechnology Genetics and Breeding in Agricultural Sciences hsv//eng
variant interpretation
LQTS
Brugada
ACMG/AMP guidelines
ACMG/AMP guidelines
Brugada
LQTS
variant interpretation

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Lahrouchi, NajimAcademic Medical Center of University of Amsterdam (AMC) (author)
Tadros, RafikMontreal Heart Institute (author)
Kyndt, FlorenceUniversity of Nantes (author)
Glinge, CharlotteCopenhagen University Hospital (author)
Postema, Pieter G.Academic Medical Center of University of Amsterdam (AMC) (author)
Amin, Ahmad S.Academic Medical Center of University of Amsterdam (AMC) (author)
Nannenberg, Eline A.Academic Medical Center of University of Amsterdam (AMC),University of Barcelona,Institutd' Investigacions Biomèdiques August Pi iSunyer (IDIBAPS),Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV) (author)
Ware, James S.Imperial College London,Royal Brompton and Harefield NHS Foundation Trust (author)
Whiffin, NicolaImperial College London,Royal Brompton and Harefield NHS Foundation Trust (author)
Mazzarotto, FrancescoImperial College London,Royal Brompton and Harefield NHS Foundation Trust,Careggi University Hospital,University of Florence (author)
Skoric-Milosavljevic, DorisAcademic Medical Center of University of Amsterdam (AMC) (author)
Krijger, ChristianAcademic Medical Center of University of Amsterdam (AMC) (author)
Arbelo, Elena (author)
Babuty, DominiqueUniversity Hospital of Tours (author)
Barajas-Martinez, HectorLankenau Institute for Medical Research (author)
Beckmann, Britt M.German Center for Lung Research (DZL) (author)
Bezieau, StephaneUniversity of Nantes (author)
Bos, J. MartijnMayo Clinic Minnesota (author)
Breckpot, JeroenUniversity Hospitals Leuven (author)
Campuzano, OscarUniversity of Barcelona,University of Girona,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV) (author)
Castelletti, SilviaIstituto Auxologico Italiano (author)
Celen, CandanEge University Medical School,Yukioka Hospital (author)
Clauss, SebastianGerman Center for Lung Research (DZL),German Centre for Cardiovascular Research,World Orthopaedic Concern (author)
Corveleyn, AnniekUniversity Hospitals Leuven (author)
Crotti, LiaIstituto Auxologico Italiano,University of Milano-Bicocca (author)
Dagradi, FedericaIstituto Auxologico Italiano (author)
de Asmundis, CarloUniversitair Ziekenhuis Brussel (author)
Denjoy, IsabelleHopital Bichat-Claude-Bernard AP-HP (author)
Dittmann, SvenUniversity Hospital Münster (author)
Ellinor, Patrick T.Massachusetts Institute of Technology,Massachusetts General Hospital (author)
Ortuno, Cristina GilHospital Virgen de la Arrixaca (author)
Giustetto, CarlaCitta' della Salute e della Scienza Hospital-University of Turin (author)
Gourraud, Jean-BaptisteUniversity of Nantes (author)
Hazeki, DaisukeKagoshima City Hospital (author)
Horie, MinoruShiga University of Medical Science (author)
Ishikawa, TaisukeNational Cerebral and Cardiovascular Center (author)
Itoh, HidekiHiroshima University Hospital (author)
Kaneko, YoshiakiGunma University (author)
Kanters, Jorgen K.University of Copenhagen (author)
Kimoto, HirokiNagasaki University (author)
Kotta, Maria-ChristinaIstituto Auxologico Italiano (author)
Krapels, Ingrid P. C. (author)
Kurabayashi, MasahikoGunma University (author)
Lazarte, JulietaUniversity of Western Ontario (author)
Leenhardt, AntoineHopital Bichat-Claude-Bernard AP-HP (author)
Loeys, Bart L.Antwerp University Hospital (author)
Lundin, CatarinaLund University,Lunds universitet,Avdelningen för klinisk genetik,Institutionen för laboratoriemedicin,Medicinska fakulteten,Genetiska och epigenetiska studier av barnleukemi,Forskargrupper vid Lunds universitet,Division of Clinical Genetics,Department of Laboratory Medicine,Faculty of Medicine,Genetic and epigenetic studies of pediatric leukemia,Lund University Research Groups(Swepub:lu)klin-clu (author)
Makiyama, TakeruKyoto University (author)
Mansourati, Jacques (author)
Martins, Raphael P. (author)
Mazzanti, Andrea (author)
Mörner, StellanUmeå universitet,Avdelningen för medicin,Centre for Cardiovascular Genetics, Umeå University, Sweden, The European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands(Swepub:umu)stmo0005 (author)
Napolitano, Carlo (author)
Ohkubo, Kimie (author)
Papadakis, Michael (author)
Rudic, Boris (author)
Molina, Maria Sabater (author)
Sacher, Frederic (author)
Sahin, Hatice (author)
Sarquella-Brugada, Georgia (author)
Sebastiano, Regina (author)
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Sheppard, Mary N. (author)
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Volders, Paul G. A. (author)
Lubitz, Steven A. (author)
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Platonov, Pyotr G.Lund University,Lunds universitet,Kardiologi,Sektion II,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Electrocardiology Research Group - CIEL,Forskargrupper vid Lunds universitet,Cardiology,Section II,Department of Clinical Sciences, Lund,Faculty of Medicine,Lund University Research Groups(Swepub:lu)kard-ppl (author)
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Roberts, Jason D. (author)
Skinner, Jonathan R. (author)
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Olesen, Morten S. (author)
Lambiase, Pier D. (author)
Borggrefe, Martin (author)
Hayashi, Kenshi (author)
Rydberg, AnnikaUmeå universitet,Pediatrik,The European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands(Swepub:umu)anry0014 (author)
Nakajima, Tadashi (author)
Yoshinaga, Masao (author)
Saenen, Johan B. (author)
Kaeaeb, Stefan (author)
Brugada, Pedro (author)
Robyns, Tomas (author)
Giachino, Daniela F. (author)
Ackerman, Michael J. (author)
Brugada, Ramon (author)
Brugada, Josep (author)
Gimeno, Juan R. (author)
Hasdemir, Can (author)
Guicheney, Pascale (author)
Priori, Silvia G. (author)
Schulze-Bahr, Eric (author)
Makita, Naomasa (author)
Schwartz, Peter J. (author)
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Aiba, Takeshi (author)
Schott, Jean-Jacques (author)
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Probst, Vincent (author)
Behr, Elijah R. (author)
Barc, Julien (author)
Bezzina, Connie R. (author)
Academic Medical Center of University of Amsterdam (AMC)Montreal Heart Institute (creator_code:org_t)
Nantes Referral Center for inherited cardiac arrhythmia

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In:Genetics in Medicine: Nature Publishing Group23:1, s. 47-581098-36001530-0366

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By the author/editor: Walsh, Roddy; Lahrouchi, Najim; Tadros, Rafik; Kyndt, Florence; Glinge, Charlott ...; Postema, Pieter ...; show more...; Amin, Ahmad S.; Nannenberg, Elin ...; Ware, James S.; Whiffin, Nicola; Mazzarotto, Fran ...; Skoric-Milosavlj ...; Krijger, Christi ...; Arbelo, Elena; Babuty, Dominiqu ...; Barajas-Martinez ...; Beckmann, Britt ...; Bezieau, Stephan ...; Bos, J. Martijn; Breckpot, Jeroen; Campuzano, Oscar; Castelletti, Sil ...; Celen, Candan; Clauss, Sebastia ...; Corveleyn, Annie ...; Crotti, Lia; Dagradi, Federic ...; de Asmundis, Car ...; Denjoy, Isabelle; Dittmann, Sven; Ellinor, Patrick ...; Ortuno, Cristina ...; Giustetto, Carla; Gourraud, Jean-B ...; Hazeki, Daisuke; Horie, Minoru; Ishikawa, Taisuk ...; Itoh, Hideki; Kaneko, Yoshiaki; Kanters, Jorgen ...; Kimoto, Hiroki; Kotta, Maria-Chr ...; Krapels, Ingrid ...; Kurabayashi, Mas ...; Lazarte, Julieta; Leenhardt, Antoi ...; Loeys, Bart L.; Lundin, Catarina; Makiyama, Takeru; Mansourati, Jacq ...; Martins, Raphael ...; Mazzanti, Andrea; Mörner, Stellan; Napolitano, Carl ...; Ohkubo, Kimie; Papadakis, Micha ...; Rudic, Boris; Molina, Maria Sa ...; Sacher, Frederic; Sahin, Hatice; Sarquella-Brugad ...; Sebastiano, Regi ...; Sharma, Sanjay; Sheppard, Mary N ...; Shimamoto, Keiko; Shoemaker, M. Be ...; Stallmeyer, Birg ...; Steinfurt, Johan ...; Tanaka, Yuji; Tester, David J.; Usuda, Keisuke; van der Zwaag, P ...; Van Dooren, Soni ...; Van Laer, Lut; Winbo, Annika; Winkel, Bo G.; Yamagata, Kenich ...; Zumhagen, Sven; Volders, Paul G. ...; Lubitz, Steven A ...; Antzelevitch, Ch ...; Platonov, Pyotr ...; Odening, Katja E ...; Roden, Dan M.; Roberts, Jason D ...; Skinner, Jonatha ...; Tfelt-Hansen, Ja ...; van den Berg, Ma ...; Olesen, Morten S ...; Lambiase, Pier D ...; Borggrefe, Marti ...; Hayashi, Kenshi; Rydberg, Annika; Nakajima, Tadash ...; Yoshinaga, Masao; Saenen, Johan B.; Kaeaeb, Stefan; Brugada, Pedro; Robyns, Tomas; Giachino, Daniel ...; Ackerman, Michae ...; Brugada, Ramon; Brugada, Josep; Gimeno, Juan R.; Hasdemir, Can; Guicheney, Pasca ...; Priori, Silvia G ...; Schulze-Bahr, Er ...; Makita, Naomasa; Schwartz, Peter ...; Shimizu, Wataru; Aiba, Takeshi; Schott, Jean-Jac ...; Redon, Richard; Ohno, Seiko; Probst, Vincent; Behr, Elijah R.; Barc, Julien; Bezzina, Connie ...; show less...

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MEDICAL AND HEALTH SCIENCES: MEDICAL AND HEAL ...; and Basic Medicine; and Medical Genetics

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