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New gene test finds cause of sudden death more often and more rapidly

22 April 2013

Sudden death in a young person is the most dramatic outcome of heart disease (cardiomyopathy). So far, only about half the patients with an hereditary heart disease could actually be shown to have an error in their DNA. For the other half of the patients, no genetic susceptibility could be found. The Department of Genetics, UMCG, has now developed a technique (next-generation sequencing) which permits all the tens of known genetic mutations to be checked in one go. This reveals a defective ‘heart’ gene more often and more rapidly. This information is of crucial importance for the direct relatives, who have an increased chance of also developing hereditary heart disease. The Groningen researchers, under the leadership of Dr. Birgit Sikkema-Raddatz and Prof. Richard Sinke, have shown that their new method is not only faster but also technically very reliable. They published their findings in a paper in the authoritative journal Human Mutation last week.

Targeted Next-Generation Sequencing can Replace Sanger Sequencing in Clinical Diagnostics

Sikkema-Raddatz B, Johansson LF, de Boer EN, Almomani R, Boven LG, van den Berg MP, van Spaendonck-Zwarts KY, van Tintelen P, Sijmons RH, Jongbloed JD, Sinke, RJ.
Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands

Abstract

Mutation detection through Exome Sequencing (ES) allows simultaneous analysis of all coding sequences of genes. However, it cannot yet replace Sanger Sequencing (SS) in diagnostics because of incomplete representation and coverage of exons leading to missing clinically relevant mutations. Targeted Next-Generation Sequencing (NGS), in which a selected fraction of genes is sequenced, may circumvent these shortcomings. We aimed to determine whether the sensitivity and specificity of targeted NGS is equal to those of SS. We constructed a targeted enrichment kit that includes 48 genes associated with hereditary cardiomyopathies. In total, 84 individuals with cardiomyopathies were sequenced using 151 bp paired-end reads on an Illumina MiSeq sequencer. The reproducibility was tested by repeating the entire procedure for five patients. The coverage of ≥30 reads per nucleotide, our major quality criterion, was 99% and in total approx. 21,000 variants were identified. Confirmation with SS was performed for 168 variants (155 substitutions, 13 indels). All were confirmed, including a deletion of 18 bps and an insertion of 6 bps. The reproducibility was nearly 100%. We demonstrate that targeted NGS of a disease-specific subset of genes is equal to the quality of SS and it can therefore be reliably implemented as a stand-alone diagnostic test.

© 2013 Wiley Periodicals, Inc. Human Mutation, April 2013

Last modified:04 July 2014 9.36 p.m.
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