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Clinical Targeted Next-Generation sequencing Panels for Detection of Somatic Variants in Gliomas
- Source :
- Cancer Research and Treatment : Official Journal of Korean Cancer Association
- Publication Year :
- 2019
- Publisher :
- Korean Cancer Association, 2019.
-
Abstract
- Purpose Targeted next-generation sequencing (NGS) panels for solid tumors have been useful in clinical framework for accurate tumor diagnosis and identifying essential molecular aberrations. However, most cancer panels have been designed to address a wide spectrum of pan-cancer models, lacking integral prognostic markers that are highly specific to gliomas. Materials and methods To address such challenges, we have developed a glioma-specific NGS panel, termed "GliomaSCAN," that is capable of capturing single nucleotide variations and insertion/deletion, copy number variation, and selected promoter mutations and structural variations that cover a subset of intron regions in 232 essential glioma-associated genes. We confirmed clinical concordance rate using pairwise comparison of the identified variants from whole exome sequencing (WES), immunohistochemical analysis, and fluorescence in situ hybridization. Results Our panel demonstrated high sensitivity in detecting potential genomic variants that were present in the standard materials. To ensure the accuracy of our targeted sequencing panel, we compared our targeted panel to WES. The comparison results demonstrated a high correlation. Furthermore, we evaluated clinical utility of our panel in 46 glioma patients to assess the detection capacity of potential actionable mutations. Thirty-two patients harbored at least one recurrent somatic mutation in clinically actionable gene. Conclusion We have established a glioma-specific cancer panel. GliomaSCAN highly excelled in capturing somatic variations in terms of both sensitivity and specificity and provided potential clinical implication in facilitating genome-based clinical trials. Our results could provide conceptual advance towards improving the response of genomically guided molecularly targeted therapy in glioma patients.
- Subjects :
- 0301 basic medicine
Male
Cancer Research
Cancer panel
DNA Copy Number Variations
medicine.medical_treatment
Computational biology
Genome
DNA sequencing
Targeted therapy
Diagnosis, Differential
03 medical and health sciences
0302 clinical medicine
Germline mutation
Gene Frequency
Exome Sequencing
medicine
Biomarkers, Tumor
Humans
Genetic Predisposition to Disease
Copy-number variation
Genetic Testing
Exome sequencing
Alleles
Genetic Association Studies
In Situ Hybridization, Fluorescence
medicine.diagnostic_test
business.industry
Precision medicine
Cancer
High-Throughput Nucleotide Sequencing
Glioma
Genomics
medicine.disease
Immunohistochemistry
030104 developmental biology
Oncology
030220 oncology & carcinogenesis
Mutation
Targeted sequencing
Original Article
Female
business
Fluorescence in situ hybridization
Subjects
Details
- Language :
- English
- ISSN :
- 20059256 and 15982998
- Volume :
- 52
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Cancer Research and Treatment : Official Journal of Korean Cancer Association
- Accession number :
- edsair.doi.dedup.....28d539a63be6cad8baa59ce79ac80c9e