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
5444 - Analysis of the tumor microenvironment and tumor genotype through different stages of lung adenocarcinoma
Presenter: Peter Zink
Session: Poster Display session 1
Resources:
Abstract
3124 - Does Progress achieved in the Treatment of Patients with Metastatic Non-Small-Cell Lung Cancer (NSCLC) reach the Elderly Population?
Presenter: Jorune Suipyte
Session: Poster Display session 1
Resources:
Abstract
5142 - Prognostic factors for non-small cell lung cancer patients with driver mutation negative and brain metastases (HOT 1701)
Presenter: Yoshihito Ohhara
Session: Poster Display session 1
Resources:
Abstract
1580 - A novel risk classification system based on nomogram scores to predict survival of patients presenting with brain metastases at the first diagnosis of NSCLC
Presenter: Pengfei Cui
Session: Poster Display session 1
Resources:
Abstract
4442 - Comparison of real-world response rate (rwRR) to RECIST-based response rate in patients with advanced non-small cell lung cancer (aNSCLC)
Presenter: Xinran Ma
Session: Poster Display session 1
Resources:
Abstract
5405 - Estimating the cost and survival impact of new aNSCLC therapies in Canada with the iTEN model
Presenter: Parneet Kaur Cheema
Session: Poster Display session 1
Resources:
Abstract
1893 - SMARCA4 Deficient Non-Small Cell Lung Cancer (NSCLC): A Comprehensive Genomic Profiling (CGP) Study
Presenter: Stephen Graziano
Session: Poster Display session 1
Resources:
Abstract
5582 - Exploring Resistance to Nivolumab [NIV] applying an Immune Genomic Signature (IGS) in advanced pretreated NSCLC [PRINCiPe study]
Presenter: Sara Pilotto
Session: Poster Display session 1
Resources:
Abstract
1408 - DNA damage repair deficiency is associated with early resistance to crizotinib: whole-genome analysis in non-small cell lung cancer patients with ALK-fusion
Presenter: Dongyun He
Session: Poster Display session 1
Resources:
Abstract
5751 - Phase 3 ALTA-3 study of brigatinib (BRG) vs alectinib (ALC) in patients (pts) with advanced anaplastic lymphoma kinase (ALK)−positive non–small cell lung cancer (NSCLC) that progressed on crizotinib (CRZ)
Presenter: Sanjay Popat
Session: Poster Display session 1
Resources:
Abstract