From innovation to global impact: adaptive genome sequencing for childhood leukemia | LC26

Abstract
Costs, lack of trained workforce, absent bioinformatics support, and complex supply chains remain barriers to improving global access to genomic diagnostics. We conducted a multicenter, quasi-independent, type-III hybrid implementation trial of an effective nanopore-based adaptive whole-genome sequencing (WGS) assay. A laboratory-developed test validation template was developed and implemented in clinical laboratories across four high- and low-income countries. Up to three samples were sequenced per PromethION Flow Cell to achieve on-target coverage ≥20x. Automated analysis reported digital karyotype, fusion detection, single nucleotide variants (SNVs), and internal tandem duplications (ITDs). Accuracy was measured by concordance with locally defined standard-of-care clinical testing. Two hundred and ninety-six leukemia specimens were sequenced across the four sites. In the unblinded phase, 221 cases (188 B-cell acute lymphoblastic leukemia [B-ALL], 25 acute myeloid leukemia [AML], 8 T-cell acute lymphoblastic leukemia [T-ALL]) were sequenced, with 75 samples reserved for blinded validation. In 23/23 (100%) AML cases within the unblinded cohort, adaptive results were concordant with conventionally identified driving fusion, SNV, FLT3-ITD, or UBTF-ITD. For B-ALL, samples were classified into one of 23 distinct genomic subtypes. Conventional testing identified a subtype in 133/188 (70.7%) unblinded B-ALL cases, while 55/188 (29.3%) cases were classified as B-other. Adaptive WGS was concordant with 133/133 (100%) conventionally determined cases, and added subtype-defining clarifications in 46/55 (83.6%) of B-other cases. Pharmacogenomic alleles in TMPT and NUDT15 were simultaneously detected. Blinded validation and integration of methylation calls is ongoing. Consumable costs ranged from $350 to $450 USD/multiplexed specimen. Real-world clinical use of adaptive WGS for comprehensive leukemia genomic classification and pharmacogenomics, with a single assay, is feasible across diverse resource settings without requiring compromising variations in implementation and yields value-added clinical data across all contexts.

Biography
Thomas Alexander, MD, MPH, is a pediatric oncologist working with global health research collaborators to integrate cancer genomic sequencing and expand access to accurate, affordable diagnostic testing for children with cancer.