Collaborative development of pediatric cancer diagnostics in low-resource settings | LC 25

Biography

Thomas Alexander, MD, MPH, is a pediatric hematologist and oncologist at the University of North Carolina. His focus is combining cancer genomic sequencing with global health research to advance innovative, cost-effective sequencing approaches to expand access to comprehensive pediatric cancer diagnostics.

His research includes collaborations for technical and computational development using a nanopore sequencing approach, and implementation science approaches with qualitative researchers and clinicians.

Abstract

Successful treatment of pediatric cancer depends on the accurate classification of tissue and genomic subtypes. Appropriate diagnostic tools are not available in most of the world. Overcoming these diagnostic deficiencies requires new models of collaboration to develop resources and appropriate technical and organizational approaches. Based on our previously published nanopore whole-transcriptome sequencing (WTS) classification approaches for pediatric cancer, our teams at the University of North Carolina and St. Jude Children’s Research Hospital organized a research network with researchers at pediatric cancer centers in Malawi, Pakistan, India, Brazil, and Uganda.

This research program is based on remote training, commercially available non-targeted library preparation, local sequencing (without sample shipment), internet-based computational support, and iterative analytic improvement. We hold monthly virtual meetings to review the protocol, including specimen collection, library preparation, sequencing, data transfer, and analysis. These meetings included retraining, protocol updates, result review, troubleshooting, supply chain challenges, and peer learning and mentorship.

We have performed nanopore WTS on over 600 specimens of pediatric acute leukemia, with data transfer and central analysis. In 2025, we expect to double the number of collaborating centers. This growing database, generated in a distributed manner, is being utilized to train an updated classification model. Taking advantage of our established regulatory, logistical, training, and data-sharing processes, researchers in this network are performing WTS on pediatric solid tumors and WGS on pediatric leukemia specimens. This ‘crowdsourcing’ model of sequencing-based classification development is moving us closer to providing an accurate and comprehensive diagnosis for more children with cancer.