1Center for Human Genetic Research and Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Sixth Floor, Boston, MA 02114, USA.
2Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
3Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02141, USA.
4Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia.
5Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.
6Department of Neurology, Columbia University College of Physicians and Surgeons, 710 West 168th Street, New York, NY 10032, USA.
7Human Genetics Joint PhD Programme, University of Turin, 10125 Turin, Italy and University of Bologna, 40125 Bologna, Italy.
8Genetic Metabolic Disorders Research Unit, Children's Hospital at Westmead, 212 Hawkesbury Road, Westmead, NSW 2145, Australia.
9Disciplines of Paediatrics and Child Health and Genetic Medicine, University of Sydney, Sydney, NSW 2006, Australia.
10Department of Genetics and Molecular Pathology, 72 King William Road, North Adelaide, SW 5006, Australia.
11Discipline of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA 5005, Australia.
12Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, VIC 3052, Australia.
13Genetic Services of Western Australia, King Edward Memorial Hospital, University of Western Australia, Perth, WA 6009, Australia.
Advances in next-generation sequencing (NGS) promise to facilitate diagnosis of inherited disorders. Although in research settings NGS has pinpointed causal alleles using segregation in large families, the key challenge for clinical diagnosis is application to single individuals. To explore its diagnostic use, we performed targeted NGS in 42 unrelated infants with clinical and biochemical evidence of mitochondrial oxidative phosphorylation disease. These devastating mitochondrial disorders are characterized by phenotypic and genetic heterogeneity, with more than 100 causal genes identified to date. We performed "MitoExome" sequencing of the mitochondrial DNA (mtDNA) and exons of ~1000 nuclear genes encoding mitochondrial proteins and prioritized rare mutations predicted to disrupt function. Because patients and healthy control individuals harbored a comparable number of such heterozygous alleles, we could not prioritize dominant-acting genes. However, patients showed a fivefold enrichment of genes with two such mutations that could underlie recessive disease. In total, 23 of 42 (55%) patients harbored such recessive genes or pathogenic mtDNA variants. Firm diagnoses were enabled in 10 patients (24%) who had mutations in genes previously linked to disease. Thirteen patients (31%) had mutations in nuclear genes not previously linked to disease. The pathogenicity of two such genes, NDUFB3 and AGK, was supported by complementation studies and evidence from multiple patients, respectively. The results underscore the potential and challenges of deploying NGS in clinical settings.
Applying next-generation sequencing to 42 infants with mitochondrial disease highlights both the potential and the challenge of using this technology in clinical diagnosis.