Introduction: Gastrointestinal stromal tumors (GIST) are the most common mesenchymal neoplasm of the gastrointestinal tract, the treatment of which represents a significant breakthrough in targeted cancer therapy. Given its overall rare nature, analysis of genomic differences and clinical implications between demographic groups has not been previously completed, but American Association for Cancer Research (AACR) Project GENIE makes such an analysis possible.
Methods: Anonymized demographic, clinical, and genomic data from 1,559 GIST patients was analyzed using cBioPortal and custom Python scripts, with no exclusions from the cohort. Data included patient demographics, genomic alterations, and co-occurrence information, and was classified according to clinical implications using the OncoKB database. Analysis involved Chi-squared tests for differences in genomic alterations across various demographic factors and mutual exclusivity analysis to identify co-mutation patterns.
Results: Male patients exhibited higher mutation rates at PDGFRA (14.56% vs 8.05%; p<0.001), while female patients had higher rates at NF1 (7.46% vs 3.23%; p=0.001). Asian patients showed higher alteration rates at KIT (85.59%; p=0.002). Co-occurrence analysis revealed KIT alterations frequently co-occurred with CDKN2A (q<0.001), MTAP (q=0.045), and PTEN (q=0.056), while showing mutual exclusivity with PDGFRA (q<0.001), NF1 (q<0.001), and BRAF (q=.015). CDKN2A alterations co-occurred with MTAP (q<0.001) and PIK3CA (q=.015), while being mutually exclusive with TP53 (q=.002) and NF1 (q=.007). Trends were similar among patients who had received no prior medical treatment. Imatinib-resistant mutations were more common in male patients (25.6% vs 18.9%; p=.0056) and those under 55 (27.3% vs 20.9%; p=.0228). Among patients with imatinib-resistant mutations, 77.78% had sunitinib resistance, while 70.25% maintained sensitivity to ripretinib.
Conclusion: Sex and race/ethnic differences in genomic alterations, as well as co-mutations, were prevalent among patients with GIST. Variations in mutational profiles highlight the importance of distinct genetic drivers that may be targeted to treat different patient populations.