ArticlePloS one2015
A Systematic Assessment of Accuracy in Detecting Somatic Mosaic Variants by Deep Amplicon Sequencing: Application to NF2 Gene.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- SMARCB1-related schwannomatosis and other SMARCB1-associated phenotypes: clinical spectrum and molecular pathogenesis.Familial cancer · 2025Review
- Genetics of Primary Adrenal Insufficiency Beyond CAH in Saudi Arabian Population.Molecular genetics & genomic medicine · 2025Article
- SNV/indel hypermutator phenotype in biallelic RAD51C variant: Fanconi anemia.Human genetics · 2023Article
- SNV/indel hypermutator phenotype in biallelic RAD51C variant - Fanconi anemia.Research square · 2023Article
- Screening of potential novel candidate genes in schwannomatosis patients.Human mutation · 2022Article
- Clinical and genetic analyses of patients with lateralized overgrowth.BMC medical genomics · 2022Article
- Parental mosaicism for apparent de novo genetic variants: Scope, detection, and counseling challenges.Prenatal diagnosis · 2022Review
- Incidence of mosaicism in 1055 de novo NF2 cases: much higher than previous estimates with high utility of next-generation sequencing.Genetics in medicine : official journal of the American College of Medical Genetics · 2020Article
- Clinically-relevant postzygotic mosaicism in parents and children with developmental disorders in trio exome sequencing data.Nature communications · 2019Article
- Ultra-deep amplicon sequencing indicates absence of low-grade mosaicism with normal cells in patients with type-1 NF1 deletions.Human genetics · 2019Article
- Targeted next-generation sequencing for differential diagnosis of neurofibromatosis type 2, schwannomatosis, and meningiomatosis.Neuro-oncology · 2018Article
- Next Generation Sequencing Methods for Diagnosis of Epilepsy Syndromes.Frontiers in genetics · 2018Review
- Postzygotic single-nucleotide mosaicisms contribute to the etiology of autism spectrum disorder and autistic traits and the origin of mutations.Human mutation · 2017Article
- Pathogenic Variants and Allele Loss of the NF2 and LZTR1 Gene in Sporadic Vestibular Schwannoma.In vivo (Athens, Greece)Article
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13 authors.
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Abstract
The accurate detection of low-allelic variants is still challenging, particularly for the identification of somatic mosaicism, where matched control sample is not available. High throughput sequencing, by the simultaneous and independent analysis of thousands of different DNA fragments, might overcome many of the limits of traditional methods, greatly increasing the sensitivity. However, it is necessary to take into account the high number of false positives that may arise due to the lack of matched control samples. Here, we applied deep amplicon sequencing to the analysis of samples with known genotype and variant allele fraction (VAF) followed by a tailored statistical analysis. This method allowed to define a minimum value of VAF for detecting mosaic variants with high accuracy. Then, we exploited the estimated VAF to select candidate alterations in NF2 gene in 34 samples with unknown genotype (30 blood and 4 tumor DNAs), demonstrating the suitability of our method. The strategy we propose optimizes the use of deep amplicon sequencing for the identification of low abundance variants. Moreover, our method can be applied to different high throughput sequencing approaches to estimate the background noise and define the accuracy of the experimental design.
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