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Updated: Dec 25, 2025
Molecular and Immunologic Techniques in a Genetically Engineered Mouse Model of Gastrointestinal Stromal Tumor
Published on: May 2, 2022
Mutational spectrum and classification of novel mutations in patients with metastatic gastrointestinal stromal
Alenka Bombac1, Branko Zakotnik2, Marina Bucic1
1Department of Molecular Diagnostics, Institute of Oncology, Ljubljana 1000, Slovenia.
Abstract:
In total, ~85% of malignant gastrointestinal stromal tumours (GISTs) harbour activating mutations in one of the genes KIT or PDGFRA, while 10‑15% of all GISTs have no detectable KIT or PDGFRA mutations, but could have alterations in genes of the succinate dehydrogenase complex or in BRAF, PIK3CA or rarely RAS family genes. The clinical benefit of tyrosine kinase inhibitors, such as imatinib, depends on the GIST genotype, therefore molecular characterization of GIST has a crucial role in overall management of GIST. The aim of the present study was to molecularly characterize a cohort of 70 patients with metastatic GISTs from the Slovenian Cancer Registry (National Cancer Registry) treated between January 2002 and December 2011. Exons 9, 11, 13 and 17 of the KIT gene and exons 12, 14 and 18 of the PDGFRA gene were analysed by direct Sanger sequencing. All KIT/PDGFRA wild‑type GISTs were tested for the presence of mutations in hot spot regions of KRAS, NRAS, BRAF, PIK3CA and AKT1 genes. Novel variants were characterized and classified using Cancer Genome Interpreter and according to The American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines. In total, 60 (85.7%) patients had mutations in KIT and 2 (2.9%) in PDGFRA. Whereas, 8 (11.4%) patients with GIST had no mutation in either of the analysed genes. The majority of GIST cases (n=52) had a mutation in KIT exon 11, where 40 different mutations were detected. Eight of the variants were novel: c.1652_1672del, c.1653_1660delinsAA, c.1665_1672delinsCC, c.1668_1686del, c.1676_1720del, c.1715_1756dup, c.1721_1765dup, and c.1722_1766dup. Mutation frequencies of KIT and PDGFRA genes observed in Slovenian patients are comparable with those in other European populations. In the present group of patients analysed, the most frequently mutated region was exon 11 in the KIT gene, responsible for coding juxtamembrane domain of KIT protein. In this region, eight novel mutations were identified and classified as likely pathogenic driver variants. In addition, the present study identified 6 patients with secondary KIT mutation and 1 patient with double mutant GIST, who had two different mutations in PDGFRA exon 14.
Insights
Molecular characterization of gastrointestinal stromal tumors (GISTs) in Slovenian patients revealed common KIT and PDGFRA mutations. Eight novel KIT exon 11 mutations were identified, impacting GIST treatment strategies.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Malignant gastrointestinal stromal tumors (GISTs) often harbor KIT or PDGFRA mutations, influencing treatment response to tyrosine kinase inhibitors.
- Understanding GIST genotype is crucial for effective patient management and personalized therapy.
- A significant subset of GISTs lack detectable KIT/PDGFRA mutations, suggesting alternative genetic alterations.
Purpose of the Study:
- To molecularly characterize a cohort of 70 metastatic GIST patients from Slovenia.
- To identify mutations in KIT, PDGFRA, and other relevant genes (KRAS, NRAS, BRAF, PIK3CA, AKT1) in GIST cases.
- To classify novel variants according to established guidelines for potential clinical significance.
Main Methods:
- Direct Sanger sequencing was employed to analyze specific exons of the KIT (9, 11, 13, 17) and PDGFRA (12, 14, 18) genes.
- KIT/PDGFRA wild-type GISTs underwent testing for mutations in hot spot regions of KRAS, NRAS, BRAF, PIK3CA, and AKT1.
- Novel variants were characterized and classified using Cancer Genome Interpreter and ACMG/AMP guidelines.
Main Results:
- Mutations in KIT were identified in 85.7% of patients (n=60), and in PDGFRA in 2.9% (n=2).
- KIT exon 11 mutations were most frequent (n=52), with 40 distinct mutations detected, including eight novel variants classified as likely pathogenic drivers.
- 11.4% of GIST cases (n=8) had no mutations in the analyzed KIT or PDGFRA genes. Secondary KIT mutations and a double PDGFRA mutation were also observed.
Conclusions:
- The mutation frequencies in Slovenian GIST patients align with those reported in other European populations.
- KIT exon 11 mutations are the predominant driver in this cohort, with newly identified variants potentially impacting therapeutic strategies.
- Comprehensive molecular profiling is essential for understanding GIST heterogeneity and guiding treatment decisions.
