Toward the use of nanopore RNA sequencing technologies in the clinic: challenges and opportunities

Katopodi, Xanthi-Lida; Begik, Oguzhan; Novoa, Eva Maria

doi:http://dx.doi.org/10.1093/nar/gkaf128

Toward the use of nanopore RNA sequencing technologies in the clinic: challenges and opportunities

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Katopodi XL, Begik O, Novoa EM. Toward the use of nanopore RNA sequencing technologies in the clinic: challenges and opportunities. Nucleic Acids Res. 2025 Feb 27;53(5):gkaf128. DOI: 10.1093/nar/gkaf128

Abstract

RNA molecules have garnered increased attention as potential clinical biomarkers in recent years. While short-read sequencing and quantitative polymerase chain reaction have been the primary methods for quantifying RNA abundance, they typically fail to capture critical post-transcriptional regulatory elements, such as RNA modifications, which are often dysregulated in disease contexts. A promising cutting-edge technique sequencing method that addresses this gap is direct RNA sequencing, offered by Oxford Nanopore Technologies, which can simultaneously capture both RNA abundance and modification information. The rapid advancements in this platform, along with growing evidence of dysregulated RNA species in biofluids, presents a compelling clinical opportunity. In this review, we discuss the challenges and the emerging opportunities for the adoption of nanopore RNA sequencing technologies in the clinic, highlighting their potential to revolutionize personalized medicine and disease monitoring.