Comprehensive genetic evaluation in paediatric-onset mitochondrial diseases

Abstract

Background: Mitochondrial diseases (MD) are the commonest group of inborn errors of metabolism, characterized by defects in oxidative phosphorylation (OXPHOS). It is caused by mutations either in mitochondrial DNA (mtDNA) or nuclear DNA. Due to the phenotypic and genetic heterogeneity, a molecular diagnosis is crucial for disease management. MtDNA sequencing and whole exome sequencing (WES) are excellent diagnostic tools for MDs. In our study, we aim to investigate the clinical utility of mtDNA sequencing and WES in our cohort of patients with MDs. Methods: We recruited patients suspected to have paediatric-onset MDs with a minimal mitochondrial disease criteria (MDC) scoring of 3. Genetic tests were performed based on paediatric neurologist and clinical geneticist recommendation. They were performed in local settings (Clinical Genetics Services, Department of Health, and Paediatrics & Adolescent Medicine, HKU) and overseas laboratory (Genome Diagnostics Nijmegen). MtDNA result analysis was based on data from MitoMap. For WES, rare variants with population frequency ≤ 1% were interrogated for pathogenicity based on the ACMG guideline. Analysis of OXPHOS complexes was performed in Radboud Centre for Mitochondrial Medicine, Nijmegen. Results: Eighty-three subjects (male=54, female=29) with pre-biopsy MDC scoring range from 3 to 8 were recruited. CMA, targeted gene Sanger sequencing, mtDNA sequencing and WES was done in 2,3,46 and 75 patients respectively. 22q11.2 deletion was found in a pair of siblings by CMA. 3 pathogenic mutations and 2 variants of unknown significance (VUS) was found by mtDNA sequencing. 10 cases with disease-causing mutations were identified in MD-related genes (COQ4 (n=4), COQ7, GTPBP3, NDUFA9, NDUFS3, OPA1, SURF1), 19 cases with non-MDs related genes (ALDH5A1, AMACR, ATP1A3 (n=3, 2 from siblings), ARX, FA2H (n=2 from siblings), KCNT1, LDHD, NEFL, NKX2-2, PTRH2 (n=2 from siblings), SPG20, TAZ (n=2 from siblings), WAC, WFS1) and 4 cases of VUS was found in ERCC6 (n=2 from siblings), OPA1 and POLG using WES or Sanger sequencing. The overall diagnostic yield was 41% (34/83). Conclusion: MtDNA sequencing and WES are effective and promising tools in reaching the genetic diagnosis in our MD patients. As the majority of the disease-causing mutation was identified in nuclear DNA (37%, 31/83), and the ability of copy number variations and mtDNA analysis using WES data by enhanced bioinformatics pipeline, we suggest WES should be the first-tier testing in patients suspected to have MD.