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

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 mutat...

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Autores principales: Cunha, Karin Soares, Oliveira, Nathalia Silva, Fausto, Anna Karoline, de Souza, Carolina Cruz, Gros, Audrey, Bandres, Thomas, Idrissi, Yamina, Merlio, Jean-Philippe, de Moura Neto, Rodrigo Soares, Silva, Rosane, Geller, Mauro, Cappellen, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5192509/
https://www.ncbi.nlm.nih.gov/pubmed/27999334
http://dx.doi.org/10.3390/genes7120133
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author Cunha, Karin Soares
Oliveira, Nathalia Silva
Fausto, Anna Karoline
de Souza, Carolina Cruz
Gros, Audrey
Bandres, Thomas
Idrissi, Yamina
Merlio, Jean-Philippe
de Moura Neto, Rodrigo Soares
Silva, Rosane
Geller, Mauro
Cappellen, David
author_facet Cunha, Karin Soares
Oliveira, Nathalia Silva
Fausto, Anna Karoline
de Souza, Carolina Cruz
Gros, Audrey
Bandres, Thomas
Idrissi, Yamina
Merlio, Jean-Philippe
de Moura Neto, Rodrigo Soares
Silva, Rosane
Geller, Mauro
Cappellen, David
author_sort Cunha, Karin Soares
collection PubMed
description 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.
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spelling pubmed-51925092016-12-30 Hybridization Capture-Based Next-Generation Sequencing to Evaluate Coding Sequence and Deep Intronic Mutations in the NF1 Gene Cunha, Karin Soares Oliveira, Nathalia Silva Fausto, Anna Karoline de Souza, Carolina Cruz Gros, Audrey Bandres, Thomas Idrissi, Yamina Merlio, Jean-Philippe de Moura Neto, Rodrigo Soares Silva, Rosane Geller, Mauro Cappellen, David Genes (Basel) Article 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. MDPI 2016-12-17 /pmc/articles/PMC5192509/ /pubmed/27999334 http://dx.doi.org/10.3390/genes7120133 Text en © 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Cunha, Karin Soares
Oliveira, Nathalia Silva
Fausto, Anna Karoline
de Souza, Carolina Cruz
Gros, Audrey
Bandres, Thomas
Idrissi, Yamina
Merlio, Jean-Philippe
de Moura Neto, Rodrigo Soares
Silva, Rosane
Geller, Mauro
Cappellen, David
Hybridization Capture-Based Next-Generation Sequencing to Evaluate Coding Sequence and Deep Intronic Mutations in the NF1 Gene
title Hybridization Capture-Based Next-Generation Sequencing to Evaluate Coding Sequence and Deep Intronic Mutations in the NF1 Gene
title_full Hybridization Capture-Based Next-Generation Sequencing to Evaluate Coding Sequence and Deep Intronic Mutations in the NF1 Gene
title_fullStr Hybridization Capture-Based Next-Generation Sequencing to Evaluate Coding Sequence and Deep Intronic Mutations in the NF1 Gene
title_full_unstemmed Hybridization Capture-Based Next-Generation Sequencing to Evaluate Coding Sequence and Deep Intronic Mutations in the NF1 Gene
title_short Hybridization Capture-Based Next-Generation Sequencing to Evaluate Coding Sequence and Deep Intronic Mutations in the NF1 Gene
title_sort hybridization capture-based next-generation sequencing to evaluate coding sequence and deep intronic mutations in the nf1 gene
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5192509/
https://www.ncbi.nlm.nih.gov/pubmed/27999334
http://dx.doi.org/10.3390/genes7120133
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