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Molecular and Immunologic Techniques in a Genetically Engineered Mouse Model of Gastrointestinal Stromal Tumor
Published on: May 2, 2022
Genetic Characterization of Molecular Targets in Korean Patients with Gastrointestinal Stromal Tumors
Joonhong Park1, Han Mo Yoo2, Hae Jung Sul3
1Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.
Purpose:
Gastrointestinal stromal tumors (GISTs) frequently harbor activating gene mutations in either KIT or platelet-derived growth factor receptor A (PDGFRA) and are highly responsive to several selective tyrosine kinase inhibitors. In this study, a targeted next-generation sequencing (NGS) assay with an Oncomine Focus Assay (OFA) panel was used for the genetic characterization of molecular targets in 30 Korean patients with GIST.
Materials And Methods:
Using the OFA that enables rapid and simultaneous detection of hotspots, single nucleotide variants (SNVs), insertion and deletions (Indels), copy number variants (CNVs), and gene fusions across 52 genes relevant to solid tumors, targeted NGS was performed using genomic DNA extracted from formalin-fixed and paraffin-embedded samples of 30 GISTs.
Results:
Forty-three hotspot/other likely pathogenic variants (33 SNVs, 8 Indels, and 2 amplifications) in 16 genes were identified in 26 of the 30 GISTs. KIT variants were most frequent (44%, 19/43), followed by 6 variants in PIK3CA, 3 in PDGFRA, 2 each in JAK1 and EGFR, and 1 each in AKT1, ALK, CCND1, CTNNB1, FGFR3, FGFR4, GNA11, GNAQ, JAK3, MET, and SMO. Based on the mutation types, majority of the variants carried missense mutations (60%, 26/43), followed by 8 frameshifts, 6 nonsense, 1 stop-loss, and 2 amplifications.
Conclusions:
Our study confirmed the advantage of using targeted NGS with a cancer gene panel to efficiently identify mutations associated with GISTs. These findings may provide a molecular genetic basis for developing new drugs targeting these gene mutations for GIST therapy.
Insights
Targeted next-generation sequencing identified frequent KIT and PDGFRA mutations in Korean gastrointestinal stromal tumor (GIST) patients. This genetic profiling aids in developing new targeted therapies for GIST.
Area of Science:
- Oncology
- Molecular Genetics
- Genomics
Background:
- Gastrointestinal stromal tumors (GISTs) often have activating mutations in KIT or PDGFRA genes.
- These mutations confer sensitivity to tyrosine kinase inhibitors.
Purpose of the Study:
- To genetically characterize molecular targets in 30 Korean GIST patients using targeted next-generation sequencing (NGS).
- To evaluate the utility of the Oncomine Focus Assay (OFA) panel for GIST mutation profiling.
Main Methods:
- Targeted NGS was performed on genomic DNA from 30 formalin-fixed, paraffin-embedded GIST samples.
- The Oncomine Focus Assay (OFA) panel was used for simultaneous detection of variants across 52 cancer-related genes.
Main Results:
- 16 genes with 43 likely pathogenic variants (33 SNVs, 8 Indels, 2 amplifications) were found in 26/30 GISTs.
- KIT variants were most common (44%), followed by PDGFRA and other cancer-related genes.
- Missense mutations constituted the majority (60%) of identified variants.
Conclusions:
- Targeted NGS with a cancer gene panel is efficient for identifying GIST-associated mutations.
- These genetic findings can inform the development of novel targeted therapies for GIST.
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