Prevalence and Electronic Health Record-Based Phenotype of Loss-of-Function Genetic Variants in Arrhythmogenic Right Ventricular Cardiomyopathy-Associated Genes

Eric D. Carruth, Wilson Young, Dominik Beer, Cynthia A. James, Hugh Calkins, Linyuan Jing, Sushravya Raghunath, Dustin N. Hartzel, Joseph B. Leader, H. Lester Kirchner, Diane T. Smelser, David J. Carey, Melissa A. Kelly, Amy C. Sturm, Amro Alsaid, Brandon K. Fornwalt, Christopher M. Haggerty

Research output: Contribution to journalArticle

Abstract

BACKGROUND: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is associated with variants in desmosome genes. Secondary findings of pathogenic/likely pathogenic variants, primarily loss-of-function (LOF) variants, are recommended for clinical reporting; however, their prevalence and associated phenotype in a general clinical population are not fully characterized. METHODS: From whole-exome sequencing of 61 019 individuals in the DiscovEHR cohort, we screened for putative loss-of-function variants in PKP2, DSC2, DSG2, and DSP. We evaluated measures from prior clinical ECG and echocardiograms, manually over-read to evaluate ARVC diagnostic criteria, and performed a PheWAS (phenome-wide association study). Finally, we estimated expected penetrance using Bayesian inference. RESULTS: One hundred forty individuals (0.23%; 59±18 years old at last encounter; 33% male) had an ARVC variant (G+). None had an existing diagnosis of ARVC in the electronic health record, nor significant differences in prior ECG or echocardiogram findings compared with matched controls without variants. Several G+ individuals satisfied major repolarization (n=4) and ventricular function (n=5) criteria, but this prevalence matched controls. PheWAS showed no significant associations of other heart disease diagnoses. Combining our best genetic and disease prevalence estimates yields an estimated penetrance of 6.0%. CONCLUSIONS: The prevalence of ARVC loss-of-function variants is ≈1:435 in a general clinical population of predominantly European descent, but with limited electronic health record-based evidence of phenotypic association in our population, consistent with a low penetrance estimate. Prospective deep phenotyping and longitudinal follow-up of a large sequenced cohort is needed to determine the true clinical relevance of an incidentally identified ARVC loss-of-function variant.

Original languageEnglish (US)
Pages (from-to)e002579
JournalCirculation. Genomic and precision medicine
Volume12
Issue number11
DOIs
StatePublished - Nov 1 2019

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Arrhythmogenic Right Ventricular Dysplasia
Electronic Health Records
Phenotype
Penetrance
Genes
Electrocardiography
Population
Exome
Desmosomes
Inborn Genetic Diseases
Ventricular Function
Heart Diseases

Keywords

  • desmosomes
  • echocardiography
  • electronic health records
  • genomics
  • whole exome sequencing

ASJC Scopus subject areas

  • Genetics
  • Cardiology and Cardiovascular Medicine
  • Genetics(clinical)

Cite this

Prevalence and Electronic Health Record-Based Phenotype of Loss-of-Function Genetic Variants in Arrhythmogenic Right Ventricular Cardiomyopathy-Associated Genes. / Carruth, Eric D.; Young, Wilson; Beer, Dominik; James, Cynthia A.; Calkins, Hugh; Jing, Linyuan; Raghunath, Sushravya; Hartzel, Dustin N.; Leader, Joseph B.; Kirchner, H. Lester; Smelser, Diane T.; Carey, David J.; Kelly, Melissa A.; Sturm, Amy C.; Alsaid, Amro; Fornwalt, Brandon K.; Haggerty, Christopher M.

In: Circulation. Genomic and precision medicine, Vol. 12, No. 11, 01.11.2019, p. e002579.

Research output: Contribution to journalArticle

Carruth, ED, Young, W, Beer, D, James, CA, Calkins, H, Jing, L, Raghunath, S, Hartzel, DN, Leader, JB, Kirchner, HL, Smelser, DT, Carey, DJ, Kelly, MA, Sturm, AC, Alsaid, A, Fornwalt, BK & Haggerty, CM 2019, 'Prevalence and Electronic Health Record-Based Phenotype of Loss-of-Function Genetic Variants in Arrhythmogenic Right Ventricular Cardiomyopathy-Associated Genes', Circulation. Genomic and precision medicine, vol. 12, no. 11, pp. e002579. https://doi.org/10.1161/CIRCGEN.119.002579
Carruth, Eric D. ; Young, Wilson ; Beer, Dominik ; James, Cynthia A. ; Calkins, Hugh ; Jing, Linyuan ; Raghunath, Sushravya ; Hartzel, Dustin N. ; Leader, Joseph B. ; Kirchner, H. Lester ; Smelser, Diane T. ; Carey, David J. ; Kelly, Melissa A. ; Sturm, Amy C. ; Alsaid, Amro ; Fornwalt, Brandon K. ; Haggerty, Christopher M. / Prevalence and Electronic Health Record-Based Phenotype of Loss-of-Function Genetic Variants in Arrhythmogenic Right Ventricular Cardiomyopathy-Associated Genes. In: Circulation. Genomic and precision medicine. 2019 ; Vol. 12, No. 11. pp. e002579.
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abstract = "BACKGROUND: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is associated with variants in desmosome genes. Secondary findings of pathogenic/likely pathogenic variants, primarily loss-of-function (LOF) variants, are recommended for clinical reporting; however, their prevalence and associated phenotype in a general clinical population are not fully characterized. METHODS: From whole-exome sequencing of 61 019 individuals in the DiscovEHR cohort, we screened for putative loss-of-function variants in PKP2, DSC2, DSG2, and DSP. We evaluated measures from prior clinical ECG and echocardiograms, manually over-read to evaluate ARVC diagnostic criteria, and performed a PheWAS (phenome-wide association study). Finally, we estimated expected penetrance using Bayesian inference. RESULTS: One hundred forty individuals (0.23{\%}; 59±18 years old at last encounter; 33{\%} male) had an ARVC variant (G+). None had an existing diagnosis of ARVC in the electronic health record, nor significant differences in prior ECG or echocardiogram findings compared with matched controls without variants. Several G+ individuals satisfied major repolarization (n=4) and ventricular function (n=5) criteria, but this prevalence matched controls. PheWAS showed no significant associations of other heart disease diagnoses. Combining our best genetic and disease prevalence estimates yields an estimated penetrance of 6.0{\%}. CONCLUSIONS: The prevalence of ARVC loss-of-function variants is ≈1:435 in a general clinical population of predominantly European descent, but with limited electronic health record-based evidence of phenotypic association in our population, consistent with a low penetrance estimate. Prospective deep phenotyping and longitudinal follow-up of a large sequenced cohort is needed to determine the true clinical relevance of an incidentally identified ARVC loss-of-function variant.",
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T1 - Prevalence and Electronic Health Record-Based Phenotype of Loss-of-Function Genetic Variants in Arrhythmogenic Right Ventricular Cardiomyopathy-Associated Genes

AU - Carruth, Eric D.

AU - Young, Wilson

AU - Beer, Dominik

AU - James, Cynthia A.

AU - Calkins, Hugh

AU - Jing, Linyuan

AU - Raghunath, Sushravya

AU - Hartzel, Dustin N.

AU - Leader, Joseph B.

AU - Kirchner, H. Lester

AU - Smelser, Diane T.

AU - Carey, David J.

AU - Kelly, Melissa A.

AU - Sturm, Amy C.

AU - Alsaid, Amro

AU - Fornwalt, Brandon K.

AU - Haggerty, Christopher M.

PY - 2019/11/1

Y1 - 2019/11/1

N2 - BACKGROUND: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is associated with variants in desmosome genes. Secondary findings of pathogenic/likely pathogenic variants, primarily loss-of-function (LOF) variants, are recommended for clinical reporting; however, their prevalence and associated phenotype in a general clinical population are not fully characterized. METHODS: From whole-exome sequencing of 61 019 individuals in the DiscovEHR cohort, we screened for putative loss-of-function variants in PKP2, DSC2, DSG2, and DSP. We evaluated measures from prior clinical ECG and echocardiograms, manually over-read to evaluate ARVC diagnostic criteria, and performed a PheWAS (phenome-wide association study). Finally, we estimated expected penetrance using Bayesian inference. RESULTS: One hundred forty individuals (0.23%; 59±18 years old at last encounter; 33% male) had an ARVC variant (G+). None had an existing diagnosis of ARVC in the electronic health record, nor significant differences in prior ECG or echocardiogram findings compared with matched controls without variants. Several G+ individuals satisfied major repolarization (n=4) and ventricular function (n=5) criteria, but this prevalence matched controls. PheWAS showed no significant associations of other heart disease diagnoses. Combining our best genetic and disease prevalence estimates yields an estimated penetrance of 6.0%. CONCLUSIONS: The prevalence of ARVC loss-of-function variants is ≈1:435 in a general clinical population of predominantly European descent, but with limited electronic health record-based evidence of phenotypic association in our population, consistent with a low penetrance estimate. Prospective deep phenotyping and longitudinal follow-up of a large sequenced cohort is needed to determine the true clinical relevance of an incidentally identified ARVC loss-of-function variant.

AB - BACKGROUND: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is associated with variants in desmosome genes. Secondary findings of pathogenic/likely pathogenic variants, primarily loss-of-function (LOF) variants, are recommended for clinical reporting; however, their prevalence and associated phenotype in a general clinical population are not fully characterized. METHODS: From whole-exome sequencing of 61 019 individuals in the DiscovEHR cohort, we screened for putative loss-of-function variants in PKP2, DSC2, DSG2, and DSP. We evaluated measures from prior clinical ECG and echocardiograms, manually over-read to evaluate ARVC diagnostic criteria, and performed a PheWAS (phenome-wide association study). Finally, we estimated expected penetrance using Bayesian inference. RESULTS: One hundred forty individuals (0.23%; 59±18 years old at last encounter; 33% male) had an ARVC variant (G+). None had an existing diagnosis of ARVC in the electronic health record, nor significant differences in prior ECG or echocardiogram findings compared with matched controls without variants. Several G+ individuals satisfied major repolarization (n=4) and ventricular function (n=5) criteria, but this prevalence matched controls. PheWAS showed no significant associations of other heart disease diagnoses. Combining our best genetic and disease prevalence estimates yields an estimated penetrance of 6.0%. CONCLUSIONS: The prevalence of ARVC loss-of-function variants is ≈1:435 in a general clinical population of predominantly European descent, but with limited electronic health record-based evidence of phenotypic association in our population, consistent with a low penetrance estimate. Prospective deep phenotyping and longitudinal follow-up of a large sequenced cohort is needed to determine the true clinical relevance of an incidentally identified ARVC loss-of-function variant.

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KW - genomics

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