Cancer Res Treat.  2020 Jan;52(1):41-50. 10.4143/crt.2019.036.

Clinical Targeted Next-Generation sequencing Panels for Detection of Somatic Variants in Gliomas

• Shin H
• Sa JK
• Bae JS
• Koo H
• Jin S
• Cho HJ
• Choi SW
• Kyoung JM
• Kim JY
• Seo YJ
• Joung JG
• Kim NKD
• Son DS
• Chung J
• Lee T
• Kong DS
• Choi JW
• Seol HJ
• Lee JI
• Suh YL
• Park WY
• Nam DH

• KMID: 2501200
• DOI: http://doi.org/10.4143/crt.2019.036

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.

Keyword

Glioma; Targeted sequencing; Precision medicine; Cancer panel

Figure

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  Fig. 1. Evaluation of GliomaSCAN sensitivity comparing with whole exome sequencing (WES) data. Concordance between the variant allelic frequency (VAF) value of single nucleotide variations/INDEL detected by WES and Brain TumorCAN. Sequenced results are highly correlated (Pearson coefficient=0.814). Blue represents higher density of VAF in two sequencing panels.

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  Fig. 2. Overview of alteration profile in therapeutic target genes. (A) Distribution of actionable alterations. Proportion (%) that cases with specific gene variants among the 46 cases. The cases are classified into three groups based on the importance of alterations. (B) Frequency of potentially actionable alterations. We show the most frequently mutated genes in 94 actionable genes.

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  Fig. 3. Landscape of recurrent alterations in diffuse gliomas. Oncoprint summarizing recurrently mutated genes detected by GliomaSCAN. Clinical profiles are represented above the Oncoprint. MGMT, O6-methylguanine-DNA methyltransferase; NA, not available. Bar plot provides the frequency of samples which are subdivided into two groups dependent on histologic grade (left plot). The Oncoprint shows a landscape of genomic alterations affecting individual cases. Single nucleotide variation s, inframe insertions or deletions are shown as green. Copy number amplifications or deletions are shown as blue and red, respectively.

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  Fig. 4. Possibility evaluation for clinical performances of the targeted sequencing panel. (A) Receiver operating characteristic curve describes accuracy of selected 20 genes for detecting chromosome 1p and 19q copy number deletions (area under curve [AUC]=0.929). (B) We applied validated gene-set to GliomaSCAN data. The result comparing GliomaSCAN and fluorescence in situ hybridization data shows high concordance rate (AUC=0.917). (C) Copy number alterations in the chromosomal levels are summarized for 1p/19q co-deleted and 1p/19q wild type samples. Upper plot shows targeted sequencing results and bottom plot shows whole exome sequencing (WES) results. WES and targeted sequencing data in an individual sample are well matched.

Reference

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