Two studies published in March validate Oxford Nanopore Technologies' long-read sequencing platform for pediatric cancer classification and reproductive carrier screening, applying nanopore sequencing to workflows historically served by microarray and short-read technologies.
The first study, posted on medRxiv, describes TUCAN, a deep-learning classifier trained on 3,818 methylation profiles to classify pediatric solid tumors and lymphomas using nanopore sequencing. The authors report that nanopore-based methylation analysis enables rapid central nervous system tumor diagnosis, a capability the study says has not been previously explored for pediatric solid tumors and lymphomas. The medRxiv preprint has not undergone peer review.
The second study, published in The Journal of Molecular Diagnostics, validated a PCR/Nanopore assay for carrier screening of cystic fibrosis, spinal muscular atrophy, and fragile X syndrome. The assay assessed comprehensive variant detection across the CFTR, SMN1/SMN2, and FMR1 genes in a single nanopore workflow. Current carrier screening panels typically require multiple assay types to detect structural and repeat-expansion variants in these genes.
The studies arrive as Oxford Nanopore expands from research-use applications into regulated diagnostics. The company recently secured its first EU diagnostic approval, as previously reported by BaseCall.
Illumina's Infinium methylation arrays remain the reference standard for tumor classification, and its short-read chemistry underpins most clinical carrier screening pipelines. The TUCAN classifier's training set of 3,818 samples is substantial for proof-of-concept but smaller than the Heidelberg brain tumor classifier's reference cohort of over 80,000 profiles built on Illumina arrays.
Neither study disclosed Oxford Nanopore funding. Both used the company's commercially available sequencing devices and reagents.