Cardiogenetics research at the Department of Genetics, UMCG, focuses mainly on cardiomyopathies. In recent years we have identified several new genes and mutations for different types of this genetic condition. Using modern sequencing technologies like whole exome/genome sequencing and RNA sequencing, we aim to identify more genetic factors that contribute to this disease. We also carry out studies to better understand the pathophysiology of inherited cardiomyopathies and their variability and to predict the individual variation in the disease course. Staff in the Departments of Genetics and of Cardiology collaborate closely on these projects.
Since 2010, over 1,000 carriers of the PLN p.Arg14del founder mutation have been identified. With national and international collaborators, we are continuing our work on the most prevalent cause of arrhythmogenic and dilated cardiomyopathy in the Netherlands under the name PHORECAST (PHOspholamban RElated CArdiomyopathy STudy). Current projects include a multi-centre intervention study of asymptomatic mutation carriers with eplerenone (the iPHORECAST study), genetic studies of phenotypic extremes, and making animal models. More information at www.phorecast.nl
Next-Generation Sequencing (NGS) for cardiomyopathies
Cardiomyopathies have overlapping phenotypes and are genetically heterogeneous disorders, with mutations in over 50 disease genes having been identified. Many of these are observed to be involved in different types of the disease, hypertrophic (HCM), dilated (DCM), arrhythmogenic right ventricular (ARVC), left-ventricular non-compaction (LVNC) and restrictive (RCM) cardiomyopathies. Since there are a large number of genes associated with cardiomyopathies, and the number is still growing, cardiomyopathies are ideal candidate disorders for implementing NGS-based diagnostic tools. We have demonstrated that the sensitivity, specificity and robustness of targeted NGS for cardiomyopathies are equal to those of Sanger sequencing. We have constructed an improved kit targeting 55 cardiomyopathy genes and implemented this in routine clinical diagnostics. We are now investigating the outcome and yield of using this gene-panel-based approach in large cohorts of cardiomyopathy patients in routine clinical genetic diagnostics.
Genetic diagnosis through whole-exome sequencing. van der Zwaag PA, et al., N Engl J Med. 2014;370(11):1067.
Dilated cardiomyopathy (DCM) is the most common type of cardiomyopathy among children and infants. Previous work showed that only one-third of children had a known cause of DCM at diagnosis. Obtaining a genetic diagnosis is of great importance in determining the disease aetiology, course and prognosis and may lead to more rational therapeutic choices. In addition, an accurate diagnosis has major implications for family screening and offers insight into the recurrence risk. We perform SNP-array analysis and trio-based (parents and child) whole exome sequencing in paediatric DCM cases in order to evaluate the yield of genetic testing and to generate a suitable approach for genetic testing in these patients, while minimizing the chance of incidental findings and the number of variants of unknown significance.
Using homozygosity mapping and exome sequencing in two consanguineous families with idiopathic paediatric cardiomyopathy, we identified homozygous truncating mutations in a new disease gene: alpha-kinase 3 (ALPK3). This gene encodes a nuclear kinase essential for early differentiation of cardiomyocytes and is involved in important transcription factor pathways. A third family carrying mutated ALPK3 was identified during cohort screening. Patients with biallelic mutations presented with severe cardiomyopathy leading to early death or biventricular dysfunction in childhood. Some heterozygous family members showed adult-onset cardiomyopathy with atypically distributed hypertrophy, indicating that this gene may also play a role in dominantly inherited cardiomyopathies. We provided microscopic evidence of intercalated disc remodelling, as previously observed in Alpk3 knockout mice. Further functional experiments and studies on the role of the gene in adult-onset cardiomyopathies and cardiac hypertrophy are ongoing.
Biallelic Truncating Mutations in ALPK3 Cause Severe Pediatric Cardiomyopathy. Almomani R, et al. J Am Coll Cardiol . 2016;67(5):515-25
The ARVD/C Genetic Variants Database
Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiac disease characterized by myocardial atrophy, fibro-fatty replacement, and a high risk of ventricular arrhythmias that lead to sudden death. In 2009, genetic data from 57 publications were collected in the arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C) genetic variants database, which comprised 481 variants in 8 ACM-associated genes. In recent years, deep genetic sequencing has expanded what we know about the genetics of ACM and revealed a large spectrum of nucleotide variations for which the pathogenicity needs to be assessed. As of 2014, we have updated the ARVD/C database and it now contains more than 1,400 variants in 12 ACM-related genes (PKP2, DSP, DSC2, DSG2, JUP, TGFB3, TMEM43, LMNA, DES, TTN, PLN, CTNNA3) reported in >160 references. Of these, only 411 nucleotide variants have been reported as pathogenic, whereas the significance of the other approximately 1,000 variants is still unknown. This comprehensive collection of ACM genetic data represents a valuable source of information on the spectrum of ACM-associated genes and aims to facilitate the interpretation of genetic data and genetic counselling.
The ARVD/C genetic variants database: 2014 update. Lazzarini E, et al. Hum Mutat . 2015;36(4):403-10.
15% of congenital heart defects are left ventricular outflow tract obstructions (LVOTO). The prevalence of LVOTO in first-degree relatives is high (7-19%), but mutations in known genes (NOTCH1, Nkx2.5) are infrequent. In collaboration with the Departments of Paediatric Cardiology in Groningen, Rotterdam and Utrecht, we collected patients and families and screened all first-degree family members. In 148/428 patients (35%), left-sided congenital heart disease (LS-CHD) was found to be familial. Pathogenic mutations in NOTCH1 were identified in 7% of familial LS-CHD and in 1% of sporadic LS-CHD. The penetrance is high: a cardiovascular malformation was found in 75% of NOTCH1 mutation carriers.
Cardiovascular malformations caused by NOTCH1 mutations do not keep left: data on 428 probands with left-sided CHD and their families. Kerstjens-Frederikse WS et al., Genet Med . 2016;18(9):914-23.
In PREDICT, we apply fundamentally new approaches to study the genetic basis of sudden cardiac death (SCD) in large, well-characterized cohorts of SCD patients from the general population. We are studying susceptibility/modifier genes through genetic studies in large pedigrees with Mendelian, SCD-related diseases harbouring founder mutations, such as the PLN p.Arg14del mutation (see above) and mutations in PKP2 and SCN5A. We further aim to discover new genes underlying Mendelian rhythm disorders using an whole exome sequencing approach, with a particular focus on arrhythmogenic cardiomyopathy.
Recurrent and founder mutations in the Netherlands-Phospholamban p.Arg14del mutation causes arrhythmogenic cardiomyopathy. van der Zwaag PA, et al., Neth Heart J. 2013;21(6):286-93.
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