Genetic diagnosis of Cardiomyopathies

Circulation: Cardiovascular Genetics.
2011; 4: 110-122

Targeted Next-Generation Sequencing for the Molecular Genetic Diagnostics of Cardiomyopathies

Benjamin Meder, MD*, Jan Haas, MS*, Andreas Keller, PhD, Christiane Heid, MS, Steffen Just, PhD, Anne Borries, MS, Valesca Boisguerin, PhD, Maren Scharfenberger-Schmeer, PhD, Peer Stähler;, Markus Beier, PhD, Dieter Weichenhan, PhD, Tim M. Strom, MD, Arne Pfeufer, MD, PhD, Bernhard Korn, PhD, Hugo A. Katus, MD and Wolfgang Rottbauer, MD
+ Author Affiliations

From the Department of Internal Medicine III (B.M., J.H., C.H., S.J., H.A.K., W.R.), University of Heidelberg; Biomarker Discovery Center (A.K.); febit biomed gmbh (A.B., V.B., P.S., M.B.); and German Cancer Research Center (DKFZ) (M.S.-S., D.W., B.K.), Heidelberg, Germany; Institute of Human Genetics (T.M.S.), Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Human Genetics (A.P.), Klinikum rechts der Isar, Technische Universität München, Munich, Germany; and Department of Internal Medicine II (W.R.), University of Ulm, Ulm, Germany.

Abstract

Background— Today, mutations in more than 30 different genes have been found to cause inherited cardiomyopathies, some associated with very poor prognosis. However, because of the genetic heterogeneity and limitations in throughput and scalability of current diagnostic tools up until now, it is hardly possible to genetically characterize patients with cardiomyopathy in a fast, comprehensive, and cost-efficient manner.

Methods and Results— We established an array-based subgenomic enrichment followed by next-generation sequencing to detect mutations in patients with hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM). With this approach, we show that the genomic region of interest can be enriched by a mean factor of 2169 compared with the coverage of the whole genome, resulting in high sequence coverage of selected disease genes and allowing us to define the genetic pathogenesis of cardiomyopathies in a single sequencing run. In 6 patients, we detected disease-causing mutations, 2 microdeletions, and 4 point mutations. Furthermore, we identified several novel nonsynonymous variants, which are predicted to be harmful, and hence, might be potential disease mutations or modifiers for DCM or HCM.

Conclusions— The approach presented here allows for the first time a comprehensive genetic screening in patients with hereditary DCM or HCM in a fast and cost-efficient manner.

22q11 microdeletion

requency of 22q11.2 microdeletion in children with congenital heart defects in Western Poland

Anna Wozniak , Danuta Wolnik-Brzozowska , Marzena Wisniewska , Renata Glazar , Anna Materna-Kiryluk , Tomasz Moszura , Magdalena Badura-Stronka , Joanna Skolozdrzy , Maciej Krawczynski , Joanna Zeyland , Waldemar Bobkowski , Ryszard Slomski , Anna Latos-Bielenska and Aldona Siwinska

BMC Pediatrics 2010, 10:88doi:10.1186/1471-2431-10-88

Published:	6 December 2010

Abstract (provisional)

Background

The 22q11.2 microdeletion syndrome (22q11.2 deletion syndrome -22q11.2DS) refers to congenital abnormalities, including primarily heart defects and facial dysmorphy, thymic hypoplasia, cleft palate and hypocalcaemia. Microdeletion within chromosomal region 22q11.2 constitutes the molecular basis of this syndrome. The 22q11.2 microdeletion syndrome occurs in 1/4000 births. The aim of this study was to determine the frequency of 22q11.2 microdeletion in 87 children suffering from a congenital heart defect (conotruncal or non-conotruncal) coexisting with at least one additional 22q11.2DS feature and to carry out 22q11.2 microdeletion testing of the deleted children's parents. We also attempted to identify the most frequent heart defects in both groups and phenotypic traits of patients with microdeletion to determine selection criteria for at risk patients.

Methods

The analysis of microdeletions was conducted using fluorescence in situ hybridization (FISH) on metaphase chromosomes and interphase nuclei isolated from venous peripheral blood cultures. A molecular probe (Tuple) specific to the HIRA (TUPLE1, DGCR1) region at 22q11 was used for the hybridisation.

Results

Microdeletions of 22q11.2 region were detected in 13 children with a congenital heart defect (14.94% of the examined group). Microdeletion of 22q11.2 occurred in 20% and 11.54% of the conotruncal and non-conotruncal groups respectively. Tetralogy of Fallot was the most frequent heart defect in the first group of children with 22q11.2 microdeletion, while ventricular septal defect and atrial septal defect/ventricular septal defect were most frequent in the second group. The microdeletion was also detected in one of the parents of the deleted child (6.25%) without congenital heart defect, but with slight dysmorphism. In the remaining children, 22q11.2 microdeletion originated de novo.

Conclusions

Patients with 22q11.2DS exhibit wide spectrum of phenotypic characteristics, ranging from discreet to quite strong. The deletion was inherited by one child. Our study suggests that screening for 22q11.2 microdeletion should be performed in children with conotruncal and non-conotruncal heart defects and with at least one typical feature of 22q11.2DS as well as in the deleted children's parents.

Warfarin - Genotyping

Warfarin genotyping reduces hospitalization rates. Results from MM-WES (Medco-Mayo Warfarin Effectiveness Study).
Robert S. Epstein, et al. JACC 2010;55(25):2804-12.
Article
Editorial comments

Two genes have been shown in past decade to influence warfarin dosing.
One gene, CYP2C9 determines the activity of hepatic isoenzyme cytochrome P450 2C9 that plays a role in converting S-war-farin to its inactive form.
Second gene, VKORC1 - determines the activity of Vit K epoxide reductase that produces the active form of Vit K that is necessary for clotting.

CYP 2C9 & NKORC1 polymorphisms account for > 1/3rd of variations associated with variations in warfarin dosage. Warfarin sensitivity genotyping involves a test that simultaneously tests for allelic variation in both genes.

Genetic testing is not widely adopted due to lack of studies demonstrating the utility of these tests. This is the first national study on this.