Whole exome sequencing of suspected mitochondrial patients in clinical practice.

Saskia B Wortmann,Lambert Den Van Heuvel,Richard J Rodenburg,Jan A Smeitink,David A Koolen

doi:10.1007/s10545-015-9823-y

Saskia B Wortmann, Lambert Den Van Heuvel + Show 3 more

Open Access

https://doi.org/10.1007/s10545-015-9823-y

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Abstract

Mitochondrial disorders are characterized by a broad clinical spectrum. Identical clinical signs and symptoms can be caused by mutations in different mitochondrial or nuclear genes. Vice versa, the same mutation can lead to different phenotypes. Genetic syndromes and neuromuscular disorders mimicking mitochondrial disorders further complicate the diagnostic process. Whole exome sequencing (WES) is the state of the art next generation sequencing technique to identify genetic defects in mitochondrial disorders. Until recently it has mainly been used as a research tool. In this study, the use of WES in routine diagnostics is described. The WES data of 109 patients, referred under the suspicion of a mitochondrial disorder, were examined in two steps. First, the data were filtered using a virtual gene panel of genes known to be associated with mitochondrial disease. If negative, the entire exome was examined. A molecular diagnosis was achieved in 39 % of the heterogeneous cohort, and in 57 % of the subgroup of 42 patients with the highest suspicion for a mitochondrial disease. In addition to mutations in genes known to be associated with mitochondrial disorders (e.g. TUFM, MTFMT, FBXL4), in the subgroup of patients with the lowest suspicion for a mitochondrial disorder we found mutations in several genes associated with neuromuscular disorders (e.g. SEPN1, ACTA1) and genetic syndrome (e.g. SETBP1, ARID1B). Our results show that WES technology has been successfully implemented as a state-of-the-art, molecular diagnostic test for mitochondrial disorders as well as for the mimicking disorders in daily clinical practice. It also illustrates that clinical and biochemical phenotyping is essential for successful application of WES to diagnose individual patients.

Highlights

The clinical spectrum of mitochondrial disorders (MD) is extremely broad and the underlying biochemical and genetic defects are heterogeneous (Koopman et al 2012)
In a proof principle study we have shown that diagnostic application of whole exome sequencing (WES), using a virtual gene panel of 211 genes known to be causative for MD for data filtering, in 44 suspected MD patients had a superior diagnostic yield when compared to standard Sanger sequencing (Neveling et al 2013)
We describe the results of the follow up analysis of these patients and an additional 65 patients (109 patients in total: 52 females, 57 males, aged 1.8 -27.8, median 10.8 years)

Summary

Introduction

The clinical spectrum of mitochondrial disorders (MD) is extremely broad and the underlying biochemical and genetic defects are heterogeneous (Koopman et al 2012). In classical mitochondrial disorders (MD), the primary biochemical defect is located in the oxidative phosphorylation system (OXPHOS). It consists of five multi-subunit enzyme complexes that perform the electron transport of reduction equivalents, generated from the oxidation of mitochondrial substrates, towards molecular oxygen, thereby generating a proton gradient that drives the phosphorylation of ADP into ATP. The genes encoding the subunits of these enzymes are distributed among the mitochondrial DNA (mtDNA) and the nuclear DNA. Mutations in these genes may result in a defect in the corresponding subunit, causing an isolated deficiency of one of the OXPHOS enzymes. A large number of defects outside the OXPHOS have been described that directly or

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