Evaluating the Potential and Limitations of Nanopore Adaptive Sampling for Targeted Transcriptome Sequencing

Authors

Nicole DeBruyne
Feng Wang
Yang Xu, Thomas Jefferson UniversityFollow
Lan Lin

Document Type

Article

Publication Date

10-9-2025

Comments

This article is the author’s final published version in Genome Biology, Volume 26, Issue 1, 2025, Article number 349.

The published version is available at https://doi.org/10.1186/s13059-025-03813-1. Copyright © he Author(s) 2025.

Abstract

Long-read RNA sequencing is a powerful technology for transcriptomics, but low throughput and high cost pose challenges. Adaptive sampling, a feature of Oxford Nanopore Technologies, offers real-time enrichment by selectively ejecting non-target molecules. We evaluate adaptive sampling for human transcriptome analysis. Adaptive sampling modestly enriches target transcripts (1.3 × for cDNA sequencing, 1.9 × for direct RNA sequencing) while preserving gene expression and splicing profiles, but is significantly less effective than cDNA hybridization capture. Short read lengths and low sequencing quality limit performance. Adaptive sampling on direct RNA sequencing can boost target yield (~ 20%) within fixed run times, potentially aiding time-constrained applications.

Recommended Citation

DeBruyne, Nicole; Wang, Feng; Xu, Yang; and Lin, Lan, "Evaluating the Potential and Limitations of Nanopore Adaptive Sampling for Targeted Transcriptome Sequencing" (2025). Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers. Paper 51.
https://jdc.jefferson.edu/ppcbfp/51

Creative Commons License

This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Language

English