These authors contributed equally.
An analysis of exome sequencing for diagnostic testing of the genes associated with muscle disease and spastic paraplegia†
Article first published online: 28 FEB 2012
© 2012 Wiley Periodicals, Inc.
Special Issue: Focus on the NIH Undiagnosed Diseases Program
Volume 33, Issue 4, pages 614–626, April 2012
How to Cite
Dias, C., Sincan, M., Cherukuri, P. F., Rupps, R., Huang, Y., Briemberg, H., Selby, K., Mullikin, J. C., Markello, T. C., Adams, D. R., Gahl, W. A. and Boerkoel, C. F. (2012), An analysis of exome sequencing for diagnostic testing of the genes associated with muscle disease and spastic paraplegia. Hum. Mutat., 33: 614–626. doi: 10.1002/humu.22032
For the Focus on the NIH Undiagnosed Diseases Program
- Issue published online: 12 MAR 2012
- Article first published online: 28 FEB 2012
- Accepted manuscript online: 6 FEB 2012 12:00AM EST
- Manuscript Accepted: 10 JAN 2012
- Manuscript Received: 18 AUG 2011
- This study was supported in part by the Rare Disease Foundation and by the Intramural Research Program of the National Human Genome Research Institute. CD is funded by the Child and Family Research Institute and the Canadian Child Health Clinician Scientist Program
- neuromuscular disorders;
- clinical genetic testing
In this study, we assess exome sequencing (ES) as a diagnostic alternative for genetically heterogeneous disorders. Because ES readily identified a previously reported homozygous mutation in the CAPN3 gene for an individual with an undiagnosed limb girdle muscular dystrophy, we evaluated ES as a generalizable clinical diagnostic tool by assessing the targeting efficiency and sequencing coverage of 88 genes associated with muscle disease (MD) and spastic paraplegia (SPG). We used three exome-capture kits on 125 individuals. Exons constituting each gene were defined using the UCSC and CCDS databases. The three exome-capture kits targeted 47–92% of bases within the UCSC-defined exons and 97–99% of bases within the CCDS-defined exons. An average of 61.2–99.5% and 19.1–99.5% of targeted bases per gene were sequenced to 20X coverage within the CCDS-defined MD and SPG coding exons, respectively. Greater than 95–99% of targeted known mutation positions were sequenced to ≥1X coverage and 55–87% to ≥20X coverage in every exome. We conclude, therefore, that ES is a rapid and efficient first-tier method to screen for mutations, particularly within the CCDS annotated exons, although its application requires disclosure of the extent of coverage for each targeted gene and supplementation with second-tier Sanger sequencing for full coverage. Hum Mutat 33:614–626, 2012. © 2012 Wiley Periodicals, Inc.