Abstract 98: Custom Gene Fusion Assays for the Rapid Diagnosis of Pediatric Cancers in Low-Resourced Settings

Abstract

Abstract Purpose: Risk stratification and molecular targeting have been key to increasing cure rates for pediatric cancers in high-income countries. Precise diagnosis and successful treatment of pediatric cancer in low-resourced settings is often hindered by insufficient pathology infrastructure, including lack of laboratory platforms for molecular analysis. Given the high frequency of gene fusions in pediatric cancers, identifying such fusions would greatly aid cost-effective pediatric cancer diagnosis, risk stratification, and precision medicine in low-resourced settings. Methods: To allow for implementation of gene fusion detection at Global HOPE sites in Sub-Saharan Africa (SSA), methodologies were reviewed to consider minimal technical expertise required, the ability to utilize samples with sub-optimal RNA quality, and rapid turn-around-time. Literature review, clinical laboratory results, public databases, and large-scale genomic studies were used to obtain exact breakpoint sequence information for gene fusions associated with pediatric and adolescent cancers. Results: Two custom pediatric gene fusions panels were designed using the NanoString Elements technology. The hematologic malignancy panel was designed to detect 439 breakpoints for 223 non-IGH/TCR fusions reported in ALL, AML, lymphomas, and histiocytosis. The solid tumor panel was designed to detect 204 breakpoints for 436 fusions associated with pediatric sarcomas, brain tumors, and renal malignancies. Each panel was tested using 96 samples with known fusion status at Texas Children's Hospital to determine specificity, sensitivity, precision, and ease of workflow. Conclusions: The design, testing, and implementation of a rapid assay to detect gene fusions with diagnostic, prognostic, and therapeutic impact would be transformational in the care of pediatric cancer patients in low-resourced settings. The custom designed panels will allow for large-scale fusion detection in 2-3 days with only 15 minutes of technician time after RNA isolation. Additional steps are needed to identify and address any challenges upon initiation in SSA to fully realize the potential of such technology. Citation Format: Julie Gastier-Foster, Fredrick Lutwama, Joseph Lubega, Kevin Fisher, Dolores Lopez-Terrada, Angshumoy Roy, Nmazuo Ozuah, Jeremy Slone, Peter Wasswa, Carl Allen, David Poplack. Custom Gene Fusion Assays for the Rapid Diagnosis of Pediatric Cancers in Low-Resourced Settings [abstract]. In: Proceedings of the 9th Annual Symposium on Global Cancer Research; Global Cancer Research and Control: Looking Back and Charting a Path Forward; 2021 Mar 10-11. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2021;30(7 Suppl):Abstract nr 98.