TY - JOUR
T1 - The Use of Next-Generation Sequencing in Molecular Diagnosis of Neurofibromatosis Type 1
T2 - A Validation Study
AU - Maruoka, Ryo
AU - Takenouchi, Toshiki
AU - Torii, Chiharu
AU - Shimizu, Atsushi
AU - Misu, Kumiko
AU - Higasa, Koichiro
AU - Matsuda, Fumihiko
AU - Ota, Arihito
AU - Tanito, Katsumi
AU - Kuramochi, Akira
AU - Arima, Yoshimi
AU - Otsuka, Fujio
AU - Yoshida, Yuichi
AU - Moriyama, Keiji
AU - Niimura, Michihito
AU - Saya, Hideyuki
AU - Kosaki, Kenjiro
N1 - Publisher Copyright:
© 2014 Mary Ann Liebert Inc.. All rights reserved.
PY - 2014/11/1
Y1 - 2014/11/1
N2 - Aims: We assessed the validity of a next-generation sequencing protocol using in-solution hybridization-based enrichment to identify NF1 mutations for the diagnosis of 86 patients with a prototypic genetic syndrome, neurofibromatosis type 1. In addition, other causative genes for classic genetic syndromes were set as the target genes for coverage analysis. Results: The protocol identified 30 nonsense, 19 frameshift, and 8 splice-site mutations, together with 10 nucleotide substitutions that were previously reported to be pathogenic. In the remaining 19 samples, 10 had single-exon or multiple-exon deletions detected by a multiplex ligation-dependent probe amplification method and 3 had missense mutations that were not observed in the normal Japanese SNP database and were predicted to be pathogenic. Coverage analysis of the genes other than the NF1 gene included on the same diagnostic panel indicated that the mean coverage was 115-fold, a sufficient depth for mutation detection. Conclusions: The overall mutation detection rate using the currently reported method in 86 patients who met the clinical diagnostic criteria was 92.1% (70/76) when 10 patients with large deletions were excluded. The results validate the clinical utility of this next-generation sequencing-based method for the diagnosis of neurofibromatosis type 1. Comparable detection rates can be expected for other genetic syndromes, based on the results of the coverage analysis.
AB - Aims: We assessed the validity of a next-generation sequencing protocol using in-solution hybridization-based enrichment to identify NF1 mutations for the diagnosis of 86 patients with a prototypic genetic syndrome, neurofibromatosis type 1. In addition, other causative genes for classic genetic syndromes were set as the target genes for coverage analysis. Results: The protocol identified 30 nonsense, 19 frameshift, and 8 splice-site mutations, together with 10 nucleotide substitutions that were previously reported to be pathogenic. In the remaining 19 samples, 10 had single-exon or multiple-exon deletions detected by a multiplex ligation-dependent probe amplification method and 3 had missense mutations that were not observed in the normal Japanese SNP database and were predicted to be pathogenic. Coverage analysis of the genes other than the NF1 gene included on the same diagnostic panel indicated that the mean coverage was 115-fold, a sufficient depth for mutation detection. Conclusions: The overall mutation detection rate using the currently reported method in 86 patients who met the clinical diagnostic criteria was 92.1% (70/76) when 10 patients with large deletions were excluded. The results validate the clinical utility of this next-generation sequencing-based method for the diagnosis of neurofibromatosis type 1. Comparable detection rates can be expected for other genetic syndromes, based on the results of the coverage analysis.
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U2 - 10.1089/gtmb.2014.0109
DO - 10.1089/gtmb.2014.0109
M3 - Article
C2 - 25325900
AN - SCOPUS:84933518597
SN - 1945-0265
VL - 18
SP - 722
EP - 735
JO - Genetic testing and molecular biomarkers
JF - Genetic testing and molecular biomarkers
IS - 11
ER -