Thomas Alexander from the University of North Carolina spoke at London Calling 2025 about “Collaborative development of pediatric cancer diagnostics in low-resource settings.” Alexander is a physician and focused on the use of Oxford Nanopore Technologies (ONT) to diagnose cancers. Diagnostic accuracy is foundational, and low-resource countries have worse outcomes, noted Alexander. Using a single assay, health care providers may be able to provide a lineage and diagnosis. Shallow Oxford Nanopore RNA sequencing protocols developed at UNC was used for leukemia diagnosis. The team used Jeremy Wang’s protocol and designed the Diagnostic Applications in Resource-limited Settings Using Global Advances in Nanopore Technologies (DARGAN) project to use established supply chain, existing local staff, and local sequencing as a model. Whole transcriptome sequencing with this approach has been performed in India, Brazil, Pakistan, and Uganda. Training was done primarily through monthly video group trainings and lab specific videos. At five sites, one-thousand sequencing runs were performed of shallow RNA sequencing. Alexander shared data from Malawi and India that indicated that most cases were correctly classified. Regulatory and data agreements and contracts have been time consuming. Supply chains require lead time for ordering that may be challenging. The gene expression-based program classification model will be trained with new results. The team is also working on optimizing RNA fusion detection using WTS. The use of shallow whole transcriptome sequencing and classifiers is promising in low-income countries!
