Effectiveness of whole exome sequencing in unsolved patients with a clinical suspicion of a mitochondrial disorder in Estonia

Sanna Puusepp; Karit Reinson; Sander Pajusalu; Ülle Murumets; Eve Õiglane-Shlik; Reet Rein; Inga Talvik; Richard J Rodenburg; Katrin Õunap

doi:10.1016/j.ymgmr.2018.03.004

Effectiveness of whole exome sequencing in unsolved patients with a clinical suspicion of a mitochondrial disorder in Estonia

Mol Genet Metab Rep. 2018 Mar 15:15:80-89. doi: 10.1016/j.ymgmr.2018.03.004. eCollection 2018 Jun.

Authors

Sanna Puusepp^{1

2}, Karit Reinson^{1

2}, Sander Pajusalu^{1

2}, Ülle Murumets², Eve Õiglane-Shlik^{3

4}, Reet Rein³, Inga Talvik⁵, Richard J Rodenburg⁶, Katrin Õunap^{1

2}

Affiliations

¹ Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, 2 L. Puusepa Street, Tartu 51014, Estonia.
² Department of Clinical Genetics, United Laboratories, Tartu University Hospital, 2 L. Puusepa Street, Tartu 51014, Estonia.
³ Children's Clinic, Tartu University Hospital, 6 Lunini Street, Tartu 51014, Estonia.
⁴ Department of Pediatrics, Institute of Clinical Medicine, University of Tartu, 6 Lunini Street, Tartu 51014, Estonia.
⁵ Tallinn Children's Hospital, 28 Tervise Street, Tallinn 13419, Estonia.
⁶ Radboud Center for Mitochondrial Medicine, 830 Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.

Abstract

Objective: Reaching a genetic diagnosis of mitochondrial disorders (MDs) is challenging due to their broad phenotypic and genotypic heterogeneity. However, there is growing evidence that the use of whole exome sequencing (WES) for diagnosing patients with a clinical suspicion of an MD is effective (39-60%). We aimed to study the effectiveness of WES in clinical practice in Estonia, in patients with an unsolved, but suspected MD. We also show our first results of mtDNA analysis obtained from standard WES reads.

Methods: Retrospective cases were selected from a database of 181 patients whose fibroblast cell cultures had been stored from 2003 to 2013. Prospective cases were selected during the period of 2014-2016 from patients referred to a clinical geneticist in whom an MD was suspected. We scored each patient according to the mitochondrial disease criteria (MDC) (Morava et al., 2006) after re-evaluation of their clinical data, and then performed WES analysis.

Results: A total of 28 patients were selected to the study group. A disease-causing variant was found in 16 patients (57%) using WES. An MD was diagnosed in four patients (14%), with variants in the SLC25A4, POLG, SPATA5, and NDUFB11 genes. Other variants found were associated with a neuromuscular disease (SMN1, MYH2, and LMNA genes), neurodegenerative disorder (TSPOAP1, CACNA1A, ALS2, and SCN2A genes), multisystemic disease (EPG5, NKX1-2, ATRX, and ABCC6 genes), and one in an isolated cardiomyopathy causing gene (MYBPC3). The mtDNA point mutation was found in the MT-ATP6 gene of one patient upon mtDNA analysis.

Conclusions: The diagnostic yield of WES in our cohort was 57%, proving to be a very good effectiveness. However, MDs were found in only 14% of the patients. We suggest WES analysis as a first-tier method in clinical genetic practice for children with any multisystem, neurological, and/or neuromuscular problem, as nuclear DNA variants are more common in children with MDs; a large number of patients harbor disease-causing variants in genes other than the mitochondria-related ones, and the clinical presentation might not always point towards an MD. We have also successfully conducted analysis of mtDNA from standard WES reads, providing further evidence that this method could be routinely used in the future.

Keywords: Mitochondrial disorders; Muscle biopsy; Whole exome sequencing; mtDNA sequencing.