High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency

• Published in: Nature genetics Vol. 42; no. 10; pp. 851 - 858
• Main Authors: Calvo, Sarah E, Tucker, Elena J, Compton, Alison G, Kirby, Denise M, Crawford, Gabriel, Burtt, Noel P, Rivas, Manuel, Guiducci, Candace, Bruno, Damien L, Goldberger, Olga A, Redman, Michelle C, Wiltshire, Esko, Wilson, Callum J, Altshuler, David, Gabriel, Stacey B, Daly, Mark J, Thorburn, David R, Mootha, Vamsi K
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.10.2010; Nature Publishing Group
• Subjects: 631/443/319/1642; Agriculture; Animal Genetics and Genomics; Awards & honors; Biological and medical sciences; Biomedical and Life Sciences; Biomedicine; Blotting, Western; Cancer Research; Case-Control Studies; DNA sequencing; Electron Transport Complex I - genetics; Fundamental and applied biological sciences. Psychology; Gene Dosage; Gene Function; Gene mutations; Genetic aspects; Genetic Association Studies; Genetic testing; Genetics; Genetics of eukaryotes. Biological and molecular evolution; Health aspects; Human Genetics; Human subjects; Humans; Methods; Mitochondrial diseases; Mitochondrial Diseases - genetics; Mitochondrial DNA; Mitochondrial Proteins - genetics; Mitochondrial Proteins - metabolism; Mutation; Mutation - genetics; Nucleotide sequencing; Project management; Reverse Transcriptase Polymerase Chain Reaction; Risk factors; RNA, Messenger - genetics; Sequence Analysis, DNA; Studies; Australia; Human; Identification; Pool; Mutation; Sequencing; Deficiency
• ISSN: 1061-4036; 1546-1718; 1546-1718
• DOI: 10.1038/ng.659

Vamsi Mootha and colleagues report high-throughput targeted sequencing of 103 candidate genes in 103 individuals with human mitochondrial complex I deficiency. They identify two genes newly associated with complex I deficiency and are able to provide genetic diagnoses in 22% of their previously unsolved cases. Discovering the molecular basis of mitochondrial respiratory chain disease is challenging given the large number of both mitochondrial and nuclear genes that are involved. We report a strategy of focused candidate gene prediction, high-throughput sequencing and experimental validation to uncover the molecular basis of mitochondrial complex I disorders. We created seven pools of DNA from a cohort of 103 cases and 42 healthy controls and then performed deep sequencing of 103 candidate genes to identify 151 rare variants that were predicted to affect protein function. We established genetic diagnoses in 13 of 60 previously unsolved cases using confirmatory experiments, including cDNA complementation to show that mutations in NUBPL and FOXRED1 can cause complex I deficiency. Our study illustrates how large-scale sequencing, coupled with functional prediction and experimental validation, can be used to identify causal mutations in individual cases.