Clinical targeted next-generation sequencing panels for detection of somatic variants in gliomas

Hyemi Shin, Jason K. Sa, Joon Seol Bae, Harim Koo, Seonwhee Jin, Hee Jin Cho, Seung Won Choi, Jong Min Kyoung, Ja Yeon Kim, Yun Jee Seo, Je Gun Joung, Nayoung K.D. Kim, Dae Soon Son, Jongsuk Chung, Taeseob Lee, Doo Sik Kong, Jung Won Choi, Ho Jun Seol, Jung Il Lee, Yeon Lim SuhWoong Yang Park, Do Hyun Nam

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)41-50
Number of pages10
JournalCancer Research and Treatment
Volume52
Issue number1
DOIs
Publication statusPublished - 2020 Jan 1
Externally publishedYes

Keywords

  • Cancer panel
  • Glioma
  • Precision medicine
  • Targeted sequencing

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

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