Abstract 4419
Background
Neurofibromatosis type 1 (NF-1) is a tumor predisposition syndrome resulting from mutations in NF1 antioncogene. Differential diagnosis with genetic testing is essential in NF-1 diagnostics due to its clinical variability. Identifying of pathogenic mutations is challenging because of the gene size and structure, especially for low-level somatic mosaicism. Notably, patients with mosaic NF-1 demonstrate no less severe phenotype than those with classic form. Nowadays, NGS and Sanger sequencing are recognized diagnostics methods and they both are not sensitive enough to mosaic genotypes with small fractions of alternative alleles. We believe that this can be resolved with a special approach to sequencing data analysis.
Methods
In order to re-evaluate previously obtained NGS (Ion AmpliSeq technology) results for 275 probands with clinical diagnosis “NF-1” or “NF, unspecified” for whom germline mutations in NF1 and NF2 genes were not identified, we developed an improved data analysis pipeline to search for somatic mutations, which includes: (1) programmatic pool-based division of NGS reads, (2) elimination of out-of-design aligned reads, (3) exclusion of systematic sequencing errors, (4) variant calling with low stringency parameters (alternative allele frequency, AF ≥ 0.05; read depth, DP ≥ 20). Newly detected mutations were verified using Sanger sequencing and heteroduplex analysis. Sanger results were analysed using our in-house SeqBase software, highly sensitive to mosaic variants.
Results
Application of our NGS data reanalysis algorithm allowed us to detect 12 cases (4.3%) of somatic mosaic mutations among 275 probands otherwise lacking molecular verification of neurofibromatosis diagnosis. The majority of the identified mutations are nonsense or frameshift, with AF ranging from 0.051 to 0.296. Mutations were verified with alternative methods of molecular diagnostics.
Conclusions
Improved sequencing data analysis allows to detect NF-1 cases with mosaic genotype in cases unresolved by conventional analysis pipeline. Yet, success rate is strongly dependent upon the fraction of the mutant allele, thus alternative quantitative methods are required for exhaustive NF-1 molecular diagnosis.
Clinical trial identification
Editorial acknowledgement
Federal State Budgetary Institution "Research Centre for Medical Genetics"
Legal entity responsible for the study
Federal State Budgetary Institution "Research Centre for Medical Genetics".
Funding
The research was carried out within the state assignment of Ministry of Science and Higher Education of the Russian Federation.
Disclosure
All authors have declared no conflicts of interest.
Resources from the same session
5638 - Incidence of Vascular Thromboembolism Events in Cancer Patients Receiving Immunotherapy: A Single Institution Experience.
Presenter: Laura Gutiérrez Sainz
Session: Poster Display session 1
Resources:
Abstract
5182 - High Incidence of Venous Thromboembolic Events (VTE) in Patients with Diffuse Large B-Cell Lymphoma.
Presenter: Alaa Abufara
Session: Poster Display session 1
Resources:
Abstract
1504 - Weight Loss over Time in Non-Small Cell Lung Cancer: Results from a Landmark Analysis of 800+ Prospectively-Treated Patients
Presenter: Jennifer Le-rademacher
Session: Poster Display session 1
Resources:
Abstract
3972 - The prognostic significance of preoperative nutritional status in resected pancreatic ductal adenocarcinoma (PDAC).
Presenter: Salvatore Paiella
Session: Poster Display session 1
Resources:
Abstract
2313 - Impact of Timing and Technique of Gastrostomy Placement on the Outcome of Patients (pts) with Head and Neck Cancer (HNC)
Presenter: M Julia Lostes Bardaji
Session: Poster Display session 1
Resources:
Abstract
5219 - Clinical & nutritional determinants of quality of life in patients with incurable cancer
Presenter: Louise Daly
Session: Poster Display session 1
Resources:
Abstract
4075 - Loss of skeletal muscle mass during palliative chemotherapy is a poor prognostic factor in patients with advanced gastric cancer
Presenter: In Gyu Hwang
Session: Poster Display session 1
Resources:
Abstract
4159 - Impact of nutritional derangement on treatment outcome in advanced non-small-cell lung cancer (A-NSCLC) patients (pts).
Presenter: Ilaria Trestini
Session: Poster Display session 1
Resources:
Abstract
1210 - Sarcopenia and pretreatment anemia as prognostic factors for patients with localized muscle invasive bladder cancer treated by neoadjuvant chemotherapy and radical cystectomy
Presenter: Emilien Billon
Session: Poster Display session 1
Resources:
Abstract
2490 - Gender effect on the pharmacokinetics (PK) and pharmacodynamics (PD) of anamorelin (ANAM) in healthy volunteers and cancer patients with cachexia
Presenter: Stein Kaasa
Session: Poster Display session 1
Resources:
Abstract