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Kinase genotype analysis of gastric gastrointestinal stromal tumor cytology samples using targeted next-generation
Ferga C Gleeson1, Benjamin R Kipp2, Sarah E Kerr2
1Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
Abstract:
Gastric gastrointestinal stromal tumors (GISTs) usually contain the mast/stem cell growth factor receptor Kit gene (KIT) or platelet-derived growth factor receptor A (PDGFRA) mutations that can be targeted by, or mediate resistance to, imatinib. Diagnostic material often is obtained by endoscopic ultrasound-guided fine-needle aspiration, which often is unsuitable for molecular analysis. We investigated whether targeted next-generation sequencing (NGS) can be used in multiplex genotype analysis of cytology samples collected by endoscopic ultrasound-guided fine-needle aspiration. We used the Ion AmpliSeq V2 Cancer Hotspot NGS Panel (Life Technologies, Carlsbad, CA) to identify mutations in more than 2800 exons from 50 cancer-associated genes in GIST samples from 20 patients. We identified KIT mutations in 58% of samples (91% in exon 11 and 9% in exon 17) and PDGFRA mutations in 26% (60% in exon 18 and 40% in exon 12); 16% of samples had no mutations in KIT or PDGFRA. No pathogenic alterations were found in PIK3CA, BRAF, KRAS, NRAS, or FGFR3. We predicted that 32% of patients would have primary resistance to imatinib, based on mutations in exon 17 of KIT, exon 18 of PDGFRA (D842V), or no mutation in either gene. Targeted NGS of cytology samples from GISTs is feasible and provides clinically relevant data about kinase genotypes that can help guide individualized therapy.
Insights
Targeted next-generation sequencing (NGS) successfully analyzes mutations in gastrointestinal stromal tumors (GISTs) from cytology samples. This method aids in predicting imatinib resistance and guiding personalized GIST treatment.
Area of Science:
- Oncology
- Molecular Diagnostics
- Gastroenterology
Background:
- Gastrointestinal stromal tumors (GISTs) frequently harbor KIT or PDGFRA mutations, influencing imatinib therapy response.
- Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) is a common diagnostic method for GISTs, but samples are often unsuitable for molecular analysis.
- Identifying specific mutations is crucial for predicting treatment outcomes and guiding personalized therapy in GIST patients.
Purpose of the Study:
- To evaluate the feasibility of targeted next-generation sequencing (NGS) for multiplex genotype analysis of GIST cytology samples obtained via EUS-FNA.
- To identify common KIT and PDGFRA mutations in GISTs using NGS.
- To assess the potential of NGS findings in predicting primary resistance to imatinib therapy.
Main Methods:
- Utilized the Ion AmpliSeq V2 Cancer Hotspot NGS Panel to analyze over 2800 exons across 50 cancer-associated genes.
- Performed targeted NGS on cytology samples from 20 patients diagnosed with GIST.
- Correlated identified mutations with predicted imatinib resistance based on established mutation-resistance associations.
Main Results:
- KIT mutations were detected in 58% of samples (primarily in exon 11), and PDGFRA mutations in 26% (primarily in exon 18).
- 16% of samples showed no detectable KIT or PDGFRA mutations.
- Predicted primary imatinib resistance in 32% of patients based on specific mutations (KIT exon 17, PDGFRA D842V) or absence of targetable mutations.
Conclusions:
- Targeted NGS is a feasible method for molecular profiling of GIST cytology samples.
- NGS provides clinically relevant kinase genotype data, essential for guiding individualized imatinib therapy in GIST patients.
- This approach can help anticipate imatinib resistance, enabling proactive treatment strategy adjustments.
