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Genes (Basel). 2016 Dec 17;7(12). pii: E133. doi: 10.3390/genes7120133.

Hybridization Capture-Based Next-Generation Sequencing to Evaluate Coding Sequence and Deep Intronic Mutations in the NF1 Gene.

Author information

1
Graduate Program in Pathology, School of Medicine, Universidade Federal Fluminense, Niterói 24033-900, Brazil. karingcunha@gmail.com.
2
Department of Pathology, School of Medicine, Universidade Federal Fluminense, Niterói 24033-900, Brazil. karingcunha@gmail.com.
3
Neurofibromatosis National Center (Centro Nacional de Neurofibromatose), Rio de Janeiro 20011-330, Brazil. karingcunha@gmail.com.
4
Anatomy Pathology Service, Hospital Universitário Antônio Pedro, Universidade Federal Fluminense, Niterói 24033-900, Brazil. nsoliveira95@gmail.com.
5
Anatomy Pathology Service, Hospital Universitário Antônio Pedro, Universidade Federal Fluminense, Niterói 24033-900, Brazil. anna.karol@gmail.com.
6
School of Biomedicine, Universidade Federal Fluminense, Niterói 24210-130, Brazil. ccruz@id.uff.br.
7
Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac F-33604, France. audrey.gros@chu-bordeaux.fr.
8
Inserm (Institut National de la Santé et de la Recherche Médicale) U1053, Bordeaux Research in Translational Oncology (BaRITON) and University of Bordeaux, Bordeaux F-33076, France. audrey.gros@chu-bordeaux.fr.
9
Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac F-33604, France. thomas.bandres@chu-bordeaux.fr.
10
Inserm (Institut National de la Santé et de la Recherche Médicale) U1053, Bordeaux Research in Translational Oncology (BaRITON) and University of Bordeaux, Bordeaux F-33076, France. yamina.idrissi@u-bordeaux.fr.
11
Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac F-33604, France. jp.merlio@u-bordeaux.fr.
12
Inserm (Institut National de la Santé et de la Recherche Médicale) U1053, Bordeaux Research in Translational Oncology (BaRITON) and University of Bordeaux, Bordeaux F-33076, France. jp.merlio@u-bordeaux.fr.
13
Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil. rsmouraneto@gmail.com.
14
Carlos Chagas Filho Biophysics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil. silvaros@biof.ufrj.br.
15
Department of Immunology and Microbiology, School of Medicine, Centro Universitário Serra dos Órgãos, Teresópolis 25964-004, Brazil. maurogeller@gmail.com.
16
Martagão Gesteira Child Care and Pediatrics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-912, Brazil. maurogeller@gmail.com.
17
Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac F-33604, France. david.cappellen@u-bordeaux.fr.
18
Inserm (Institut National de la Santé et de la Recherche Médicale) U1053, Bordeaux Research in Translational Oncology (BaRITON) and University of Bordeaux, Bordeaux F-33076, France. david.cappellen@u-bordeaux.fr.

Abstract

Neurofibromatosis 1 (NF1) is one of the most common genetic disorders and is caused by mutations in the NF1 gene. NF1 gene mutational analysis presents a considerable challenge because of its large size, existence of highly homologous pseudogenes located throughout the human genome, absence of mutational hotspots, and diversity of mutations types, including deep intronic splicing mutations. We aimed to evaluate the use of hybridization capture-based next-generation sequencing to screen coding and noncoding NF1 regions. Hybridization capture-based next-generation sequencing, with genomic DNA as starting material, was used to sequence the whole NF1 gene (exons and introns) from 11 unrelated individuals and 1 relative, who all had NF1. All of them met the NF1 clinical diagnostic criteria. We showed a mutation detection rate of 91% (10 out of 11). We identified eight recurrent and two novel mutations, which were all confirmed by Sanger methodology. In the Sanger sequencing confirmation, we also included another three relatives with NF1. Splicing alterations accounted for 50% of the mutations. One of them was caused by a deep intronic mutation (c.1260 + 1604A > G). Frameshift truncation and missense mutations corresponded to 30% and 20% of the pathogenic variants, respectively. In conclusion, we show the use of a simple and fast approach to screen, at once, the entire NF1 gene (exons and introns) for different types of pathogenic variations, including the deep intronic splicing mutations.

KEYWORDS:

NF1 gene; Neurofibromatosis 1; next generation sequencing

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