| Literature DB >> 28471438 |
Christopher M Haggerty1, Cynthia A James2, Hugh Calkins2, Crystal Tichnell2, Joseph B Leader3, Dustin N Hartzel3, Christopher D Nevius1, Sarah A Pendergrass3, Thomas N Person3, Marci Schwartz4, Marylyn D Ritchie3, David J Carey5, David H Ledbetter4, Marc S Williams4, Frederick E Dewey6, Alexander Lopez6, John Penn6, John D Overton6, Jeffrey G Reid6, Matthew Lebo7,8, Heather Mason-Suares7,8, Christina Austin-Tse7, Heidi L Rehm7,8, Brian P Delisle9, Daniel J Makowski10, Vishal C Mehra10, Michael F Murray4, Brandon K Fornwalt1.
Abstract
PurposeArrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart disease. Clinical follow-up of incidental findings in ARVC-associated genes is recommended. We aimed to determine the prevalence of disease thus ascertained.MethodsIndividuals (n = 30,716) underwent exome sequencing. Variants in PKP2, DSG2, DSC2, DSP, JUP, TMEM43, or TGFβ3 that were database-listed as pathogenic or likely pathogenic were identified and evidence-reviewed. For subjects with putative loss-of-function (pLOF) variants or variants of uncertain significance (VUS), electronic health records (EHR) were reviewed for ARVC diagnosis, diagnostic criteria, and International Classification of Diseases (ICD-9) codes.ResultsEighteen subjects had pLOF variants; none of these had an EHR diagnosis of ARVC. Of 14 patients with an electrocardiogram, one had a minor diagnostic criterion; the rest were normal. A total of 184 subjects had VUS, none of whom had an ARVC diagnosis. The proportion of subjects with VUS with major (4%) or minor (13%) electrocardiogram diagnostic criteria did not differ from that of variant-negative controls. ICD-9 codes showed no difference in defibrillator use, electrophysiologic abnormalities or nonischemic cardiomyopathies in patients with pLOF or VUSs compared with controls.ConclusionpLOF variants in an unselected cohort were not associated with ARVC phenotypes based on EHR review. The negative predictive value of EHR review remains uncertain.Entities:
Mesh:
Year: 2017 PMID: 28471438 PMCID: PMC5671380 DOI: 10.1038/gim.2017.40
Source DB: PubMed Journal: Genet Med ISSN: 1098-3600 Impact factor: 8.822
Figure 1Overview of study design and patient group identities.
Details of variants database listed as “P/LP” and identified in 30,716 patients
| Gene | HGVS.c | HGVS.p | Variant Type | Patient count | Expert review |
|---|---|---|---|---|---|
| c.2587G>A | p.Gly863Arg | Missense | 30 | VUS | |
| c.2368_2370delGGA | p.Gly790del | Deletion | 1 | LB | |
| c.1048G>T | p.Asp350Tyr | Missense | 1 | VUS | |
| c.1034T>C | p.Ile345Thr | Missense | 16 | VUS | |
| c.394C>T | p.Arg132Cys | Missense | 1 | VUS | |
| c.4G>A | p.Glu2Lys | Missense | 15 | VUS | |
| c.260A>G | p.Tyr87Cys | Missense | 1 | VUS | |
| c.437G>A | p.Arg146His | Missense | 7 | VUS | |
| c.523+1G>A | Splice | 1 | LP | ||
| c.523+2T>C | Splice | 3 | LP | ||
| c.961T>A | p.Phe321Ile | Missense | 2 | VUS | |
| c.991G>A | p.Glu331Lys | Missense | 9 | VUS | |
| c.1520G>A | p.Cys507Tyr | Missense | 4 | VUS | |
| c.478C>T | p.Arg160* | Nonsense | 1 | LP | |
| c.688G>A | p.Asp230Asn | Missense | 9 | VUS | |
| c.699G>A | p.Trp233* | Nonsense | 1 | LP | |
| c.1333A>G | p.Ile445Val | Missense | 2 | VUS | |
| c.2360A>G | p.Tyr787Cys | Missense | 1 | VUS | |
| c.2423G>A | p.Arg808His | Missense | 2 | VUS | |
| c.3764G>A | p.Arg1255Lys | Missense | 5 | VUS | |
| c.4117A>G | p.Thr1373Ala | Missense | 27 | VUS | |
| c.4961T>C | p.Leu1654Pro | Missense | 1 | VUS | |
| c.5513G>A | p.Arg1838His | Missense | 6 | VUS | |
| c.6496C>T | p.Arg2166* | Nonsense | 1 | VUS | |
| c.7622G>A | p.Arg2541Lys | Missense | 1 | VUS | |
| c.7784C>T | p.Thr2595Ile | Missense | 8 | VUS | |
| c.7916G>A | p.Arg2639Gln | Missense | 4 | B | |
| c.2078A>G | p.Tyr693Cys | Missense | 5 | VUS | |
| c.1280C>T | p.Thr427Met | Missense | 3 | VUS | |
| c.1219G>A | p.Val407Ile | Missense | 2 | VUS | |
| c.475G>T | p.Val159Leu | Missense | 6 | VUS | |
| c.56C>T | p.Thr19Ile | Missense | 4 | VUS | |
| c.2578-3A>G | Splice | 1 | VUS | ||
| c.2489+1G>A | Splice | 1 | P | ||
| c.2484C>T | Splice | 1 | VUS | ||
| c.2203C>T | p.Arg735* | Nonsense | 5 | LP | |
| c.2146-1G>C | Splice | 4 | LP | ||
| c.1904G>A | p.Arg635Gln | Missense | 3 | VUS | |
| c.1379-1G>A | Splice | 2 | VUS | ||
| c.1237C>T | p.Arg413* | Nonsense | 1 | P | |
| c.1093A>G | p.Met365Val | Missense | 8 | LB | |
| c.895C>T | p.Arg299Cys | Missense | 4 | VUS | |
| c.337-2A>T | Splice | 1 | LP | ||
| c.169G>A | p.Ala57Thr | Missense | 4 | VUS | |
| c.705+7G>A | Splice | 76 | LB |
re-classified as likely benign based on observed allele frequency; VUS – variant of uncertain significance; P/LP – pathogenic/likely pathogenic; B/LB – benign/likely benign; HGVS.c – Human Genome Variation Society cDNA change; HGVS.p – Human Genome Variation Society amino acid change.
Patient demographic details by group.
| Age (years) | Sex (% female) | |
|---|---|---|
| 59 ± 18 | 56 | |
| 62 ± 17 | 58 | |
| 61 ± 17 | 58 | |
| 41 ± 16 | 63 |
Summary findings of 2010 Task Force Criteria by Group
| pLOF (n =18) | Rare VUS (n = 184) | Variant-negative controls (n = 110) | p-value (VUS/Control) | ||
|---|---|---|---|---|---|
| 14 (78%) | 160 (87%) | 93 (85%) | 0.60 | ||
| 0 | 6 (4%) | 5 (5%) | 0.54 | ||
| 1 (7%) | 20 (13%) | 16 (17%) | 0.35 | ||
|
| |||||
| 8 (44%) | 109 (59%) | 63 (57%) | 0.81 | ||
| 0 | 1 (1%) | 2 (3%) | 0.56 | ||
| 0 | 2 (2%) | 0 | 0.53 | ||
|
| |||||
| 0 | 23 (13%) | 13 (12%) | 1 | ||
| 0 | 0 | 0 | N/A | ||
| 0 | 7 (30%) | 5 (38%) | 0.72 | ||
|
| |||||
| 0 | 1 (1%) | 1 (1%) | 1 | ||
| 0 | 2 (1%) | 2 (2%) | 0.60 | ||
Data presented as number (percentage);
Echo dysfunction (major) and repolarization findings from ECG (minor);
Subjects with multiple criteria were also separately accounted with the individual criteria;
Satisfies criteria for borderline diagnosis;
Repolarization (major) and depolarization (minor) criteria from ECG
Figure 2A) Prevalence of the composite ICD-9 categories within each study group. P-values denote Fisher’s exact test for a given category. AICD- automatic implantable cardioverter defibrillator. B) Kaplan-Meier survival estimates for each study group, showing that the pLOF group had significantly reduced survival by log-rank test.