Association of sampling method and FFPE storage duration with comprehensive genomic profiling success in gastrointestinal tract cancers

Abstract Purpose Comprehensive genomic profiling (CGP) is an essential tool in precision oncology, but CGP success can be influenced by pre-analytical factors. This study aimed to evaluate the impact of pre-analytical factors on CGP success using formalin-fixed, paraffin-embedded (FFPE) tissue samples from patients with gastrointestinal (GI) tract cancers. Methods We retrospectively analyzed 226 FFPE tissue samples from patients with GI tract cancers at our institution between June 2020 and July 2025. Sampling methods were categorized as endoscopic biopsy, primary surgery, or metastatic surgery. The associations between CGP success and pre-analytical factors were assessed using multivariate analysis. Results Endoscopic biopsy samples had a significantly lower success rate than the primary and metastatic surgery samples ( p = 0.0001). Prolonged FFPE storage was independently associated with reduced CGP success ( p < 0.0001). Logistic regression analysis demonstrated that the probability of CGP success decreased sharply with longer FFPE storage for endoscopic biopsy samples, falling to 50% at approximately 1.4 years, whereas surgical samples maintained over 50% success for more than 4 years. Primary tumor site ( p = 0.144), prior chemotherapy ( p = 0.855), and sample collection institution ( p = 0.778) were not significantly associated with CGP success. Conclusion Sampling method and FFPE storage duration were critical determinants of CGP success in GI tract cancers. Endoscopic biopsy samples were more susceptible to degradation than surgical resection samples, highlighting the need for optimal pre-analytical handling and timely submission to maximize the clinical utility of CGP.