Abstract 6: Applying Next-Generation Sequencing to Improve Pediatric Cancer Diagnosis in Mexico

Abstract

Abstract Purpose: In Mexico, cancer is the second leading cause of mortality among children between 4 to 15 years old. The overall cure rates remain below 50%, compared to >90% in the United States. This discrepancy is in part explained by the limited access to methods for accurate diagnosis and identification of appropriate therapies in Mexico. Only 48% of large hospitals across Mexico report having the capacity to perform some of the complex testing necessary for subclassification of pediatric cancers. Pan-cancer next generation sequencing (NGS) panels are not available in Mexico. We developed a strategy to perform clinical NGS in pediatric cancer patients in Mexico for identification of single nucleotide variants, copy number changes, and fusion events that are useful for risk stratification and adjusted therapy. Methods: We established collaborative agreements between UCSF and the National Institute for Genomic Medicine (INMEGEN) in Mexico City. We developed a pediatric cancer focused panel (IMOP) encompassing 200 genes and created a cloud-based bioinformatic and analysis pipeline for remote data interpretation. We established concordance by comparing the sequencing results of clinical cases obtained with the validated UCSF500 panel and the IMOP panel. Results: The results of 8 clinical samples previously sequenced using the clinically validated UCSF500 panel were compared to results obtained using the IMOP panel. Clinically relevant SNVs and fusions were successfully detected by the IMOP panel at similar variant allelic frequencies. The IMOP panel was shipped to INMEGEN where two samples with prior sequencing results were successfully sequenced. Re-sequencing of the 8 clinical samples to establish concordance at INMEGEN is pending. Conclusion: Our ongoing pilot proof-of-concept study shows feasibility of a strategy to implement clinical NGS testing in a middle-income country. We hypothesize that implementation of centralized NGS for pediatric cancers at INMEGEN will improve diagnostic accuracy. Moving forward, we plan to complete the clinical validation of the IMOP panel for routine sequencing of pediatric cancer patients. We will use the RE-AIM implementation science framework to assess the effectiveness of the assay in refining clinical diagnosis and treatment planning for pediatric cancer cases in Mexico. Citation Format: Roberto Ruiz-Cordero, Ela Alcantara, Ana Quintanar-Alfaro, Carlos A Espinoza-Mendez, Katherine Van Loon, Lindsay Breithaupt, Jorge Melendez Zajgla, Alejandro Sweet-Cordero. Applying Next-Generation Sequencing to Improve Pediatric Cancer Diagnosis in Mexico [abstract]. In: Proceedings of the 11th Annual Symposium on Global Cancer Research; Closing the Research-to-Implementation Gap; 2023 Apr 4-6. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(6_Suppl):Abstract nr 6.