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Zhang X, Walsh R, Whiffin N, Buchan R, Midwinter W, Wilk A, Govind R, Li N, Ahmad M, Mazzarotto F, Roberts A, Theotokis PI, Mazaika E, Allouba M, de Marvao A, Pua CJ, Day SM, Ashley E, Colan SD, Michels M, Pereira AC, Jacoby D, Ho CY, Olivotto I, Gunnarsson GT, Jefferies JL, Semsarian C, Ingles J, O'Regan DP, Aguib Y, Yacoub MH, Cook SA, Barton PJR, Bottolo L, Ware JS. Disease-specific variant pathogenicity prediction significantly improves variant interpretation in inherited cardiac conditions. Genet Med 2021; 23:69-79. [PMID: 33046849 PMCID: PMC7790749 DOI: 10.1038/s41436-020-00972-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Accurate discrimination of benign and pathogenic rare variation remains a priority for clinical genome interpretation. State-of-the-art machine learning variant prioritization tools are imprecise and ignore important parameters defining gene-disease relationships, e.g., distinct consequences of gain-of-function versus loss-of-function variants. We hypothesized that incorporating disease-specific information would improve tool performance. METHODS We developed a disease-specific variant classifier, CardioBoost, that estimates the probability of pathogenicity for rare missense variants in inherited cardiomyopathies and arrhythmias. We assessed CardioBoost's ability to discriminate known pathogenic from benign variants, prioritize disease-associated variants, and stratify patient outcomes. RESULTS CardioBoost has high global discrimination accuracy (precision recall area under the curve [AUC] 0.91 for cardiomyopathies; 0.96 for arrhythmias), outperforming existing tools (4-24% improvement). CardioBoost obtains excellent accuracy (cardiomyopathies 90.2%; arrhythmias 91.9%) for variants classified with >90% confidence, and increases the proportion of variants classified with high confidence more than twofold compared with existing tools. Variants classified as disease-causing are associated with both disease status and clinical severity, including a 21% increased risk (95% confidence interval [CI] 11-29%) of severe adverse outcomes by age 60 in patients with hypertrophic cardiomyopathy. CONCLUSIONS A disease-specific variant classifier outperforms state-of-the-art genome-wide tools for rare missense variants in inherited cardiac conditions ( https://www.cardiodb.org/cardioboost/ ), highlighting broad opportunities for improved pathogenicity prediction through disease specificity.
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Affiliation(s)
- Xiaolei Zhang
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Roddy Walsh
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Nicola Whiffin
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Rachel Buchan
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - William Midwinter
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Alicja Wilk
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Risha Govind
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Nicholas Li
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Mian Ahmad
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Francesco Mazzarotto
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Angharad Roberts
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Pantazis I Theotokis
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Erica Mazaika
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Mona Allouba
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
| | - Antonio de Marvao
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | | | - Sharlene M Day
- Division of Cardiovascular Medicine and Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Euan Ashley
- Division of Cardiovascular Medicine, Stanford University Medical Center, Stanford, CA, USA
| | - Steven D Colan
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Michelle Michels
- Department of Cardiology, Thoraxcenter, Erasmus MC Rotterdam, Rotterdam, Netherlands
| | - Alexandre C Pereira
- Heart Institute (InCor), University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Daniel Jacoby
- Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Carolyn Y Ho
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Iacopo Olivotto
- Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy
| | | | - John L Jefferies
- The Cardiovascular Institute, University of Tennessee, Memphis, TN, USA
| | - Chris Semsarian
- Centenary Institute, The University of Sydney, Sydney, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Jodie Ingles
- Centenary Institute, The University of Sydney, Sydney, Australia
| | - Declan P O'Regan
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Yasmine Aguib
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
| | - Magdi H Yacoub
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
| | - Stuart A Cook
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
- National Heart Centre, Singapore, Singapore
- Duke-National University of Singapore, Singapore, Singapore
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.
- Alan Turing Institute, London, United Kingdom.
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom.
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS, Foundation Trust London, London, United Kingdom.
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom.
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Adalsteinsdottir B, Teekakirikul P, Maron BJ, Burke MA, Gudbjartsson DF, Holm H, Stefansson K, DePalma SR, Mazaika E, McDonough B, Danielsen R, Seidman JG, Seidman CE, Gunnarsson GT. Nationwide study on hypertrophic cardiomyopathy in Iceland: evidence of a MYBPC3 founder mutation. Circulation 2014; 130:1158-67. [PMID: 25078086 DOI: 10.1161/circulationaha.114.011207] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND The geographic isolation and homogeneous population of Iceland are ideally suited to ascertain clinical and genetic characteristics of hypertrophic cardiomyopathy (HCM) at the population level. METHODS AND RESULTS Medical records and cardiac imaging studies obtained between 1997 and 2010 were reviewed to identify Icelandic patients with HCM. Surviving patients were recruited for clinical and genetic studies. A previously identified Icelandic mutation, MYBPC3 c.927-2A>G, was genotyped, and mutation-negative samples were sequenced for HCM genes and other hypertrophic genes. Record review identified 180 patients with HCM. Genetic analyses of 151 patients defined pathogenic mutations in 101 (67%), including MYBPC3 c.927-2A>G (88 patients, 58%), 4 other MYBPC3 or MYH7 mutations (5 patients, 3.3%), and 2 GLA mutations (8 patients, 5.3%). Haplotype and genetic genealogical data defined MYBPC3 c.927-2A>G as a founder mutation, introduced into the Icelandic population in the 15th century, with a current population prevalence of 0.36%. MYBPC3 c.927-2A>G mutation carriers exhibited phenotypic diversity but were younger at diagnosis (42 versus 49 years; P=0.001) and sustained more adverse events (15% versus 2%; P=0.02) than mutation-negative patients. All-cause mortality for patients with HCM was similar to that of an age-matched Icelandic population (hazard ratio, 0.98; P=0.9). HCM-related mortality (0.78%/y) occurred at a mean age of 68 compared with 81 years for non-HCM-related mortality (P=0.02). CONCLUSIONS A founder MYBPC3 mutation that arose >550 years ago is the predominant cause of HCM in Iceland. The MYBPC3 c.927-2A>G mutation is associated with low adverse event rates but earlier cardiovascular mortality, illustrating the impact of genotype on outcomes in HCM.
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Affiliation(s)
- Berglind Adalsteinsdottir
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.).
| | - Polakit Teekakirikul
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
| | - Barry J Maron
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
| | - Michael A Burke
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
| | - Daniel F Gudbjartsson
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
| | - Hilma Holm
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
| | - Kari Stefansson
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
| | - Steven R DePalma
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
| | - Erica Mazaika
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
| | - Barbara McDonough
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
| | - Ragnar Danielsen
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
| | - Jonathan G Seidman
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
| | - Christine E Seidman
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
| | - Gunnar T Gunnarsson
- From Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland (B.A., R.D.); Faculty of Medicine (B.A., K.S., G.T.G.) and School of Engineering and Natural Sciences (D.F.G.), University of Iceland, Reykjavik, Iceland; Department of Genetics, Harvard Medical School, Boston, MA (P.T., M.A.B., S.R.D., E.M., B.M., J.G.S., C.E.S.); Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minneapolis, MN (B.J.M.); Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (M.A.B., C.E.S.); deCODE Genetics, Reykjavik, Iceland (D.F.G., H.H., K.S.); Howard Hughes Medical Institute, Boston, MA (C.E.S.); and Akureyri Hospital, Akureyri, Iceland (G.T.G.)
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