Full-Length Original Research
Targeted capture and sequencing for detection of mutations causing early onset epileptic encephalopathy
Article first published online: 10 MAY 2013
Wiley Periodicals, Inc. © 2013 International League Against Epilepsy
Volume 54, Issue 7, pages 1262–1269, July 2013
How to Cite
Kodera, H., Kato, M., Nord, A. S., Walsh, T., Lee, M., Yamanaka, G., Tohyama, J., Nakamura, K., Nakagawa, E., Ikeda, T., Ben-Zeev, B., Lev, D., Lerman-Sagie, T., Straussberg, R., Tanabe, S., Ueda, K., Amamoto, M., Ohta, S., Nonoda, Y., Nishiyama, K., Tsurusaki, Y., Nakashima, M., Miyake, N., Hayasaka, K., King, M.-C., Matsumoto, N. and Saitsu, H. (2013), Targeted capture and sequencing for detection of mutations causing early onset epileptic encephalopathy. Epilepsia, 54: 1262–1269. doi: 10.1111/epi.12203
- Issue published online: 1 JUL 2013
- Article first published online: 10 MAY 2013
- Manuscript Accepted: 21 MAR 2013
- Ministry of Health, Labour and Welfare of Japan. Grant Numbers: 24133701, 11103577, 11103580, 11103340, 10103235
- Japan Society for the Promotion of Science. Grant Numbers: 12020465, 24591500, 10013428, 11001011
- Takeda Science Foundation
- Japan Science and Technology Agency
- Strategic Research Program for Brain Sciences. Grant Number: 11105137
- Scientific Research on Innovative Areas
- Ministry of Education, Culture, Sports, Science and Technology of Japan. Grant Number: 12024421
- Target capture;
- Copy number variation;
- Genetic testing
Early onset epileptic encephalopathies (EOEEs) are heterogeneous epileptic disorders caused by various abnormalities in causative genes including point mutations and copy number variations (CNVs). In this study, we performed targeted capture and sequencing of a subset of genes to detect point mutations and CNVs simultaneously.
We designed complementary RNA oligonucleotide probes against the coding exons of 35 known and potential candidate genes. We tested 68 unrelated patients, including 15 patients with previously detected mutations as positive controls. In addition to mutation detection by the Genome Analysis Toolkit, CNVs were detected by the relative depth of coverage ratio. All detected events were confirmed by Sanger sequencing or genomic microarray analysis.
We detected all positive control mutations. In addition, in 53 patients with EOEEs, we detected 12 pathogenic mutations, including 9 point mutations (2 nonsense, 3 splice-site, and 4 missense mutations), 2 frameshift mutations, and one 3.7-Mb microdeletion. Ten of the 12 mutations occurred de novo; the other two had been previously reported as pathogenic. The entire process of targeted capture, sequencing, and analysis required 1 week for the testing of up to 24 patients.
Targeted capture and sequencing enables the identification of mutations of all classes causing EOEEs, highlighting its usefulness for rapid and comprehensive genetic testing.