title: Use of whole-exome sequencing to determine the genetic basis of multiple mitochondrial respiratory chain complex deficiencies.
abstract: OBJECTIVE
  Mitochondrial disorders have emerged as a common cause of inherited disease, but their diagnosis remains challenging. Multiple respiratory chain complex defects are particularly difficult to diagnose at the molecular level because of the massive number of nuclear genes potentially involved in intramitochondrial protein synthesis, with many not yet linked to human disease.
  
  
  OBJECTIVE
  To determine the molecular basis of multiple respiratory chain complex deficiencies.
  
  
  METHODS
  We studied 53 patients referred to 2 national centers in the United Kingdom and Germany between 2005 and 2012. All had biochemical evidence of multiple respiratory chain complex defects but no primary pathogenic mitochondrial DNA mutation. Whole-exome sequencing was performed using 62-Mb exome enrichment, followed by variant prioritization using bioinformatic prediction tools, variant validation by Sanger sequencing, and segregation of the variant with the disease phenotype in the family.
  
  
  RESULTS
  Presumptive causal variants were identified in 28 patients (53%; 95% CI, 39%-67%) and possible causal variants were identified in 4 (8%; 95% CI, 2%-18%). Together these accounted for 32 patients (60% 95% CI, 46%-74%) and involved 18 different genes. These included recurrent mutations in RMND1, AARS2, and MTO1, each on a haplotype background consistent with a shared founder allele, and potential novel mutations in 4 possible mitochondrial disease genes (VARS2, GARS, FLAD1, and PTCD1). Distinguishing clinical features included deafness and renal involvement associated with RMND1 and cardiomyopathy with AARS2 and MTO1. However, atypical clinical features were present in some patients, including normal liver function and Leigh syndrome (subacute necrotizing encephalomyelopathy) seen in association with TRMU mutations and no cardiomyopathy with founder SCO2 mutations. It was not possible to confidently identify the underlying genetic basis in 21 patients (40%; 95% CI, 26%-54%).
  
  
  CONCLUSIONS
  Exome sequencing enhances the ability to identify potential nuclear gene mutations in patients with biochemically defined defects affecting multiple mitochondrial respiratory chain complexes. Additional study is required in independent patient populations to determine the utility of this approach in comparison with traditional diagnostic methods.
authors: Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, England.
authors: Robert W
authors: RW
authors: Taylor
authors: Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, England.
authors: Angela
authors: A
authors: Pyle
authors: Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, England.
authors: Helen
authors: H
authors: Griffin
authors: Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, England.
authors: Emma L
authors: EL
authors: Blakely
authors: Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, England.
authors: Jennifer
authors: J
authors: Duff
authors: Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, England.
authors: Langping
authors: L
authors: He
authors: Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, England.
authors: Tania
authors: T
authors: Smertenko
authors: Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, England.
authors: Charlotte L
authors: CL
authors: Alston
authors: Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, England.
authors: Vivienne C
authors: VC
authors: Neeve
authors: Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, England.
authors: Andrew
authors: A
authors: Best
authors: Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, England.
authors: John W
authors: JW
authors: Yarham
authors: Division of Neuropediatrics and Muscle Disorders, University Medical Center Freiburg, Freiburg, Germany.
authors: Janbernd
authors: J
authors: Kirschner
authors: Department of Neuropediatrics, University of Essen, Essen, Germany.
authors: Ulrike
authors: U
authors: Schara
authors: Department of Pediatrics, Hacettepe University, Ankara, Turkey.
authors: Beril
authors: B
authors: Talim
authors: Department of Pediatrics, Hacettepe University, Ankara, Turkey.
authors: Haluk
authors: H
authors: Topaloglu
authors: Department of Paediatrics, University Hospital Center Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia.
authors: Ivo
authors: I
authors: Baric
authors: Medical Genetics Center, Munich, Germany.
authors: Elke
authors: E
authors: Holinski-Feder
authors: Medical Genetics Center, Munich, Germany.
authors: Angela
authors: A
authors: Abicht
authors: Medical Genetics Center, Munich, Germany.
authors: Birgit
authors: B
authors: Czermin
authors: Medical Genetics Center, Munich, Germany.
authors: Stephanie
authors: S
authors: Kleinle
authors: Willink Biochemical Genetics Unit, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester, England.
authors: Andrew A M
authors: AA
authors: Morris
authors: Department of Paediatric Neurology, Central Manchester University Hospitals NHS Foundation Trust, Manchester, England.
authors: Grace
authors: G
authors: Vassallo
authors: Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, England.
authors: Grainne S
authors: GS
authors: Gorman
authors: Department of Paediatric Neurology, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, England.
authors: Venkateswaran
authors: V
authors: Ramesh
authors: Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, England.
authors: Douglass M
authors: DM
authors: Turnbull
authors: Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, England.
authors: Mauro
authors: M
authors: Santibanez-Koref
authors: Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, England10Department of Paediatric Neurology, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, En.
authors: Robert
authors: R
authors: McFarland
authors: Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, England.
authors: Rita
authors: R
authors: Horvath
authors: Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, England.
authors: Patrick F
authors: PF
authors: Chinnery
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D002675:Child, Preschool; D019295:Computational Biology; D004252:DNA Mutational Analysis; D059472:Exome; D005260:Female; D006239:Haplotypes; D006801:Humans; D007223:Infant; D008297:Male; D028361:Mitochondrial Diseases / Q000175:diagnosis* / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*