Minor Lesion Mutational Spectrum of the Entire NF1 Gene Does Not Explain Its High Mutability but Points to a Functional Domain Upstream of the GAP-Related Domain

Fahsold, Raimund; Hoffmeyer, Sven; Mischung, Claudia; Gille, Christoph; Ehlers, Christian; Kücükceylan, Nazan; Abdel-Nour, Maher; Gewies, Andreas; Peters, Hartmut; Kaufmann, Dieter; Buske, Annegret; Tinschert, Sigrid; Nürnberg, Peter

doi:10.1086/302809

Cited by 297 publications

(297 citation statements)

References 90 publications

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“…Interestingly, seventeen of the 32 (53%) recurrent mutation were due to a C>T or G>A transition at CpG dinucleotides. These data are in accordance to the earlier comprehensive study of Fahsold et al, (2000) in which 17% of alterations occurred within a CpG dinucleotide. We did not find a large number of splicing errors, as indicated by Ars et al, (2000).…”

Section: Discussionsupporting

confidence: 93%

“…Due to the large number of coding exons and the considerable mutational heterogeneity, the determination of the NF1 mutational spectrum has been complex. However, despite no true "hotspots" have been found in NF1 (Fahsold et al, 2000), recent data suggest that recurrence of several mutations are not so uncommon in NF1 patients (Ars et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

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Novel and recurrent mutations in theNF1 gene in Italian patients with neurofibromatosis type 1

et al. 2004

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Neurofibromatosis type 1 (NF1) is one of the most common autosomal dominant disorders in humans, affecting 1 in 3500 individuals. NF1 is a fully penetrant exhibiting a mutation rate some 10-fold higher compared to most other disease genes. As a consequence, a high number of cases (up to 50%) are sporadic. Mutation detection is complex due to the large size of NF1 gene, the presence of pseudogenes and the great variety of lesions. In the present study we attempted to delineate the NF1 mutational spectrum in the Italian population reporting four-year experience with the direct analysis of the whole NF1 coding region in 110 unrelated subjects affected by NF1. For each patient, the whole coding sequence and all splice sites were studied for mutations, either by the protein truncation test (PTT), or, most often, by denaturing high performance liquid chromatography (DHPLC). Mutations were identified in 75 (68%) patients. Twenty-two mutations were found to be novel. The detection rate for the different methods was 7/18 (39%) for PTT, and 68/103 (66%) for DHPLC. The mutations were evenly distributed along the NF1 coding sequence. Thirty-two of the 75 unrelated NF1 patients in which germline mutations were identified (32/75, 43%) harbour 23 different recurrent mutations. Fifteen sequence variants likely to represent nonpathogenic polymorphisms were observed at the NF1 locus. Genotype-phenotype analysis was unable to detect any obvious correlation.

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Section: Discussionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Novel and recurrent mutations in theNF1 gene in Italian patients with neurofibromatosis type 1

et al. 2004

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“…2007). Three patients were characterized by benign variants: the c.8436T>C variant (p.Asn2812Asn; NF1_248), reported in LOVD as a silent variation with unknown pathogenicity, and the c.5172G>A variant (p.K1724K; NF1_92 and NF1_181), a silent variation described by Fahsold et al 2000 at the DNA level and studied by Nementhova et al. at the RNA level (Fahsold et al.…”

Section: Resultsmentioning

confidence: 99%

126 novel mutations in Italian patients with neurofibromatosis type 1

Bianchessi¹,

Morosini²,

Saletti³

et al. 2015

Molec Gen & Gen Med

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Genetic analysis of Neurofibromatosis type 1 (NF1) may facilitate the identification of patients in early phases of the disease. Here, we present an overview of our diagnostic research spanning the last 11 years, with a focus on the description of 225 NF1 mutations, 126 of which are novel, found in a series of 607 patients (513 unrelated) in Italy. Between 2003 and 2013, 443 unrelated patients were profiled by denaturing high pressure liquid chromatography (DHPLC) analysis of 60 amplicons derived from genomic NF1 DNA and subsequent sequencing of heterozygotic PCR products. In addition, a subset of patients was studied by multiplex ligation‐dependent probe amplification (MLPA) to identify any duplications, large deletions or microdeletions present at the locus. Over the last year, 70 unrelated patients were investigated by MLPA and sequencing of 22 amplicons spanning the entire NF1 cDNA. Mutations were found in 70% of the 293 patients studied by DHPLC, thereby fulfilling the NIH criterion for the clinical diagnosis of NF1 (detection rate: 70%); furthermore, 87% of the patients studied by RNA sequencing were genetically characterized. Mutations were also found in 36 of the 159 patients not fulfilling the NIH clinical criteria. We confirmed a higher incidence of intellectual disability in patients harboring microdeletion type 1 and observed a correlation between a mild phenotype and the small deletion c.2970_2972delAAT or the missense alteration in amino acid residue 1809 (p.Arg1809Cys). These data support the use of RNA‐based methods for genetic analysis and provide novel information for improving the management of symptoms in oligosymptomatic patients.

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“…It is comparable to the one obtained with previous screening methodologies including Sanger sequencing. 5,6,8,10,11 Of course, the single DNA sequencing can miss some NF1 alterations including deep intronic mutations that represent a weak proportion of the whole mutation types. 11 The distribution of the different types of mutations found by the NGS approach was the same than previously reported.…”

Section: Discussionmentioning

confidence: 99%

“…A huge number of different pathogenic NF1 mutations have been reported (Leiden Open Variation Database, LOVD: www.lovd.nl/NF1). [5][6][7][8][9][10][11] Over 1300 NF1 mutations have been reported by The Human Gene Mutation Database (HGMD, Institute of Medical Genetics, Cardiff, http://www.hgmd.org/). Among them, 5-10% are large 17q11.2 deletions encompassing the entire NF1 locus and neighbouring genes.…”

Section: Introductionmentioning

confidence: 99%

Neurofibromatosis type 1 molecular diagnosis: what can NGS do for you when you have a large gene with loss of function mutations?

et al. 2014

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Molecular diagnosis of neurofibromatosis type 1 (NF1) is challenging owing to the large size of the tumour suppressor gene NF1, and the lack of mutation hotspots. A somatic alteration of the wild-type NF1 allele is observed in NF1-associated tumours. Genetic heterogeneity in NF1 was confirmed in patients with SPRED1 mutations. Here, we present a targeted next-generation sequencing (NGS) of NF1 and SPRED1 using a multiplex PCR approach (230 amplicons of B150 bp) on a PGM sequencer. The chip capacity allowed mixing 48 bar-coded samples in a 4-day workflow. We validated the NGS approach by retrospectively testing 30 NF1-mutated samples, and then prospectively analysed 279 patients in routine diagnosis. On average, 98.5% of all targeted bases were covered by at least 20X and 96% by at least 100X. An NF1 or SPRED1 alteration was found in 246/279 (88%) and 10/279 (4%) patients, respectively. Genotyping throughput was increased over 10 times, as compared with Sanger, with B90h for consumables per sample. Interestingly, our targeted NGS approach also provided quantitative information based on sequencing depth allowing identification of multiexons deletion or duplication. We then addressed the NF1 somatic mutation detection sensitivity in mosaic NF1 patients and tumours.

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Minor Lesion Mutational Spectrum of the Entire NF1 Gene Does Not Explain Its High Mutability but Points to a Functional Domain Upstream of the GAP-Related Domain

Cited by 297 publications

References 90 publications

Novel and recurrent mutations in theNF1 gene in Italian patients with neurofibromatosis type 1

Novel and recurrent mutations in theNF1 gene in Italian patients with neurofibromatosis type 1

126 novel mutations in Italian patients with neurofibromatosis type 1

Neurofibromatosis type 1 molecular diagnosis: what can NGS do for you when you have a large gene with loss of function mutations?

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