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Related Experiment Video

Updated: Aug 11, 2025

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
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Transcriptome profiling for precision cancer medicine using shallow nanopore cDNA sequencing.

Andreas Mock1,2,3, Melissa Braun1, Claudia Scholl4

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Portable nanopore sequencing offers a rapid, cost-effective method for tumor transcriptome profiling. This shallow nanopore RNA-seq approach, coupled with new bioinformatics tools, provides biologically meaningful data for precision cancer medicine.

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Area of Science:

  • Oncology
  • Genomics
  • Bioinformatics

Background:

  • Transcriptome profiling is crucial for translational cancer research and precision oncology.
  • Current bulk RNA sequencing (RNA-seq) methods face limitations in cost and turnaround time for clinical use.

Purpose of the Study:

  • To evaluate a portable nanopore long-read sequencing device (MinION) for tumor transcriptome profiling.
  • To assess the impact of lower sequencing coverage on data quality and utility compared to standard short-read RNA-seq.

Main Methods:

  • Compared shallow nanopore RNA-seq with Illumina short-read RNA-seq on ten tumor samples across four cancer types.
  • Utilized a new data processing pipeline, ShaNTi (Shallow Nanopore sequencing for Transcriptomics).
  • Investigated multiplexing strategies for cost-efficiency and assessed data utility for various bioinformatics analyses.

Main Results:

  • Achieved a rapid five-day turnaround time with the nanopore platform and ShaNTi pipeline.
  • Demonstrated high correlation (r=0.89) between MinION nanopore RNA-seq and Illumina data, outperforming Flongle flow cells (r=0.24).
  • Multiplexing four samples per flow cell maintained high correlation (r=0.56-0.86) with Illumina data.
  • Shallow nanopore RNA-seq proved effective for inferring pathway activity, identifying kinase targets, analyzing tumor microenvironment, and detecting fusion genes.

Conclusions:

  • Shallow nanopore RNA-seq is a viable method for rapid, cost-effective, and biologically meaningful transcriptome profiling of tumors.
  • This technology shows promise for applications in precision cancer medicine and warrants further investigation.