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

被引:14
作者
Cunha, Karin Soares [1 ,2 ,3 ]
Oliveira, Nathalia Silva [4 ]
Fausto, Anna Karoline [4 ]
de Souza, Carolina Cruz [5 ]
Gros, Audrey [6 ,7 ,8 ]
Bandres, Thomas [6 ]
Idrissi, Yamina [7 ,8 ]
Merlio, Jean-Philippe [6 ,7 ,8 ]
de Moura Neto, Rodrigo Soares [9 ]
Silva, Rosane [10 ]
Geller, Mauro [11 ,12 ]
Cappellen, David [6 ,7 ,8 ]
机构
[1] Univ Fed Fluminense, Sch Med, Grad Program Pathol, BR-24033900 Niteroi, RJ, Brazil
[2] Univ Fed Fluminense, Sch Med, Dept Pathol, BR-24033900 Niteroi, RJ, Brazil
[3] Neurofibromatosis Natl Ctr, BR-20011330 Rio De Janeiro, Brazil
[4] Univ Fed Fluminense, Hosp Univ Antanio Pedro, Serv Anat Pathol, BR-24033900 Niteroi, RJ, Brazil
[5] Univ Fed Fluminense, Sch Biomed, BR-24210130 Niteroi, RJ, Brazil
[6] Hop Haut Leveque, Ctr Hosp Univ Bordeaux, Serv Biol Tumeurs, F-33604 Pessac, France
[7] Bordeaux Res Translat Oncol BaRITON, Inserm Inst Natl Sante & Rech Med U1053, F-33076 Bordeaux, France
[8] Univ Bordeaux, F-33076 Bordeaux, France
[9] Univ Fed Rio de Janeiro, Inst Biol, BR-21941599 Rio De Janeiro, Brazil
[10] Univ Fed Rio de Janeiro, Carlos Chagas Filho Biophys Inst, BR-21941599 Rio De Janeiro, Brazil
[11] Ctr Univ Serra Orgaos, Sch Med, Dept Immunol & Microbiol, BR-25964004 Teresopolis, Brazil
[12] Univ Fed Rio de Janeiro, Martagao Gesteira Child Care & Pediat Inst, BR-21941912 Rio De Janeiro, Brazil
关键词
Neurofibromatosis; 1; NF1; gene; next generation sequencing; NEUROFIBROMATOSIS TYPE-1 GENE; MOLECULAR DIAGNOSIS; ENRICHMENT; DEFECTS; REVEALS; COMMON;
D O I
10.3390/genes7120133
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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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页数:14
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