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

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Fältnamn	Indikatorer	Metadata
000		12147naa a2201909 4500
001		oai:DiVA.org:umu-175470
003		SwePub
008		201002s2021 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
009		oai:lup.lub.lu.se:794cf9bb-4c42-4c75-8806-bf5585e45050
024	7	a https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1754702 URI
024	7	a https://doi.org/10.1038/s41436-020-00946-52 DOI
024	7	a https://lup.lub.lu.se/record/794cf9bb-4c42-4c75-8806-bf5585e450502 URI
040		a (SwePub)umud (SwePub)lu
041		a engb eng
042		9 SwePub
072	7	a ref2 swepub-contenttype
072	7	a art2 swepub-publicationtype
100	1	a Walsh, Roddyu Academic Medical Center of University of Amsterdam (AMC)4 aut
245	1 0	a Enhancing rare variant interpretation in inherited arrhythmias through quantitative analysis of consortium disease cohorts and population controls
264	1	b Nature Publishing Group,c 2021
338		a electronic2 rdacarrier
520		a 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.
650	7	a MEDICIN OCH HÄLSOVETENSKAPx Medicinska och farmaceutiska grundvetenskaperx Medicinsk genetik0 (SwePub)301072 hsv//swe
650	7	a MEDICAL AND HEALTH SCIENCESx Basic Medicinex Medical Genetics0 (SwePub)301072 hsv//eng
650	7	a LANTBRUKSVETENSKAPERx Bioteknologi med applikationer på växter och djurx Genetik och förädling inom lantbruksvetenskap0 (SwePub)404022 hsv//swe
650	7	a AGRICULTURAL SCIENCESx Agricultural Biotechnologyx Genetics and Breeding in Agricultural Sciences0 (SwePub)404022 hsv//eng
653		a variant interpretation
653		a LQTS
653		a Brugada
653		a ACMG/AMP guidelines
653		a ACMG/AMP guidelines
653		a Brugada
653		a LQTS
653		a variant interpretation
700	1	a Lahrouchi, Najimu Academic Medical Center of University of Amsterdam (AMC)4 aut
700	1	a Tadros, Rafiku Montreal Heart Institute4 aut
700	1	a Kyndt, Florenceu University of Nantes4 aut
700	1	a Glinge, Charlotteu Copenhagen University Hospital4 aut
700	1	a Postema, Pieter G.u Academic Medical Center of University of Amsterdam (AMC)4 aut
700	1	a Amin, Ahmad S.u Academic Medical Center of University of Amsterdam (AMC)4 aut
700	1	a Nannenberg, Eline A.u 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)4 aut
700	1	a Ware, James S.u Imperial College London,Royal Brompton and Harefield NHS Foundation Trust4 aut
700	1	a Whiffin, Nicolau Imperial College London,Royal Brompton and Harefield NHS Foundation Trust4 aut
700	1	a Mazzarotto, Francescou Imperial College London,Royal Brompton and Harefield NHS Foundation Trust,Careggi University Hospital,University of Florence4 aut
700	1	a Skoric-Milosavljevic, Dorisu Academic Medical Center of University of Amsterdam (AMC)4 aut
700	1	a Krijger, Christianu Academic Medical Center of University of Amsterdam (AMC)4 aut
700	1	a Arbelo, Elena4 aut
700	1	a Babuty, Dominiqueu University Hospital of Tours4 aut
700	1	a Barajas-Martinez, Hectoru Lankenau Institute for Medical Research4 aut
700	1	a Beckmann, Britt M.u German Center for Lung Research (DZL)4 aut
700	1	a Bezieau, Stephaneu University of Nantes4 aut
700	1	a Bos, J. Martijnu Mayo Clinic Minnesota4 aut
700	1	a Breckpot, Jeroenu University Hospitals Leuven4 aut
700	1	a Campuzano, Oscaru University of Barcelona,University of Girona,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV)4 aut
700	1	a Castelletti, Silviau Istituto Auxologico Italiano4 aut
700	1	a Celen, Candanu Ege University Medical School,Yukioka Hospital4 aut
700	1	a Clauss, Sebastianu German Center for Lung Research (DZL),German Centre for Cardiovascular Research,World Orthopaedic Concern4 aut
700	1	a Corveleyn, Annieku University Hospitals Leuven4 aut
700	1	a Crotti, Liau Istituto Auxologico Italiano,University of Milano-Bicocca4 aut
700	1	a Dagradi, Federicau Istituto Auxologico Italiano4 aut
700	1	a de Asmundis, Carlou Universitair Ziekenhuis Brussel4 aut
700	1	a Denjoy, Isabelleu Hopital Bichat-Claude-Bernard AP-HP4 aut
700	1	a Dittmann, Svenu University Hospital Münster4 aut
700	1	a Ellinor, Patrick T.u Massachusetts Institute of Technology,Massachusetts General Hospital4 aut
700	1	a Ortuno, Cristina Gilu Hospital Virgen de la Arrixaca4 aut
700	1	a Giustetto, Carlau Citta' della Salute e della Scienza Hospital-University of Turin4 aut
700	1	a Gourraud, Jean-Baptisteu University of Nantes4 aut
700	1	a Hazeki, Daisukeu Kagoshima City Hospital4 aut
700	1	a Horie, Minoruu Shiga University of Medical Science4 aut
700	1	a Ishikawa, Taisukeu National Cerebral and Cardiovascular Center4 aut
700	1	a Itoh, Hidekiu Hiroshima University Hospital4 aut
700	1	a Kaneko, Yoshiakiu Gunma University4 aut
700	1	a Kanters, Jorgen K.u University of Copenhagen4 aut
700	1	a Kimoto, Hirokiu Nagasaki University4 aut
700	1	a Kotta, Maria-Christinau Istituto Auxologico Italiano4 aut
700	1	a Krapels, Ingrid P. C.4 aut
700	1	a Kurabayashi, Masahikou Gunma University4 aut
700	1	a Lazarte, Julietau University of Western Ontario4 aut
700	1	a Leenhardt, Antoineu Hopital Bichat-Claude-Bernard AP-HP4 aut
700	1	a Loeys, Bart L.u Antwerp University Hospital4 aut
700	1	a Lundin, Catarinau Lund 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 Groups4 aut0 (Swepub:lu)klin-clu
700	1	a Makiyama, Takeruu Kyoto University4 aut
700	1	a Mansourati, Jacques4 aut
700	1	a Martins, Raphael P.4 aut
700	1	a Mazzanti, Andrea4 aut
700	1	a Mörner, Stellanu Umeå 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, Netherlands4 aut0 (Swepub:umu)stmo0005
700	1	a Napolitano, Carlo4 aut
700	1	a Ohkubo, Kimie4 aut
700	1	a Papadakis, Michael4 aut
700	1	a Rudic, Boris4 aut
700	1	a Molina, Maria Sabater4 aut
700	1	a Sacher, Frederic4 aut
700	1	a Sahin, Hatice4 aut
700	1	a Sarquella-Brugada, Georgia4 aut
700	1	a Sebastiano, Regina4 aut
700	1	a Sharma, Sanjay4 aut
700	1	a Sheppard, Mary N.4 aut
700	1	a Shimamoto, Keiko4 aut
700	1	a Shoemaker, M. Benjamin4 aut
700	1	a Stallmeyer, Birgit4 aut
700	1	a Steinfurt, Johannes4 aut
700	1	a Tanaka, Yuji4 aut
700	1	a Tester, David J.4 aut
700	1	a Usuda, Keisuke4 aut
700	1	a van der Zwaag, Paul A.4 aut
700	1	a Van Dooren, Sonia4 aut
700	1	a Van Laer, Lut4 aut
700	1	a Winbo, Annika4 aut
700	1	a Winkel, Bo G.4 aut
700	1	a Yamagata, Kenichiro4 aut
700	1	a Zumhagen, Sven4 aut
700	1	a Volders, Paul G. A.4 aut
700	1	a Lubitz, Steven A.4 aut
700	1	a Antzelevitch, Charles4 aut
700	1	a Platonov, Pyotr G.u 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 Groups4 aut0 (Swepub:lu)kard-ppl
700	1	a Odening, Katja E.4 aut
700	1	a Roden, Dan M.4 aut
700	1	a Roberts, Jason D.4 aut
700	1	a Skinner, Jonathan R.4 aut
700	1	a Tfelt-Hansen, Jacob4 aut
700	1	a van den Berg, Maarten P.4 aut
700	1	a Olesen, Morten S.4 aut
700	1	a Lambiase, Pier D.4 aut
700	1	a Borggrefe, Martin4 aut
700	1	a Hayashi, Kenshi4 aut
700	1	a Rydberg, Annikau Umeå universitet,Pediatrik,The European Reference Network for rare, low prevalence and/or complex diseases of the heart: ERN GUARD-Heart, Amsterdam, Netherlands4 aut0 (Swepub:umu)anry0014
700	1	a Nakajima, Tadashi4 aut
700	1	a Yoshinaga, Masao4 aut
700	1	a Saenen, Johan B.4 aut
700	1	a Kaeaeb, Stefan4 aut
700	1	a Brugada, Pedro4 aut
700	1	a Robyns, Tomas4 aut
700	1	a Giachino, Daniela F.4 aut
700	1	a Ackerman, Michael J.4 aut
700	1	a Brugada, Ramon4 aut
700	1	a Brugada, Josep4 aut
700	1	a Gimeno, Juan R.4 aut
700	1	a Hasdemir, Can4 aut
700	1	a Guicheney, Pascale4 aut
700	1	a Priori, Silvia G.4 aut
700	1	a Schulze-Bahr, Eric4 aut
700	1	a Makita, Naomasa4 aut
700	1	a Schwartz, Peter J.4 aut
700	1	a Shimizu, Wataru4 aut
700	1	a Aiba, Takeshi4 aut
700	1	a Schott, Jean-Jacques4 aut
700	1	a Redon, Richard4 aut
700	1	a Ohno, Seiko4 aut
700	1	a Probst, Vincent4 aut
700	1	a Behr, Elijah R.4 aut
700	1	a Barc, Julien4 aut
700	1	a Bezzina, Connie R.4 aut
710	2	a Academic Medical Center of University of Amsterdam (AMC)b Montreal Heart Institute4 org
710	2	a Nantes Referral Center for inherited cardiac arrhythmia
773	0	t Genetics in Medicined : Nature Publishing Groupg 23:1, s. 47-58q 23:1<47-58x 1098-3600x 1530-0366
856	4	u https://doi.org/10.1038/s41436-020-00946-5y Fulltext
856	4	u https://umu.diva-portal.org/smash/get/diva2:1472613/FULLTEXT02.pdfx primaryx Raw objecty fulltext:print
856	4	u https://www.nature.com/articles/s41436-020-00946-5.pdf
856	4	u http://dx.doi.org/10.1038/s41436-020-00946-5x freey FULLTEXT
856	4 8	u https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-175470
856	4 8	u https://doi.org/10.1038/s41436-020-00946-5
856	4 8	u https://lup.lub.lu.se/record/794cf9bb-4c42-4c75-8806-bf5585e45050

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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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