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Transcriptome profiling for precision cancer medicine using shallow nanopore cDNA sequencing

Transcriptome profiling is a mainstay of translational cancer research and is increasingly finding its way into precision oncology. While bulk RNA sequencing (RNA-seq) is widely available, high investment costs and long data return time are limiting factors for clinical applications. We investigated...

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Bibliographische Detailangaben
Hauptverfasser: Mock, Andreas (VerfasserIn) , Braun, Melissa (VerfasserIn) , Scholl, Claudia (VerfasserIn) , Fröhling, Stefan (VerfasserIn) , Erkut, Cihan (VerfasserIn)
Dokumenttyp: Article (Journal)
Sprache:Englisch
Veröffentlicht: 09 February 2023
In: Scientific reports
Year: 2023, Jahrgang: 13, Pages: 1-11
ISSN:2045-2322
DOI:10.1038/s41598-023-29550-8
Online-Zugang:Verlag, kostenfrei, Volltext: https://doi.org/10.1038/s41598-023-29550-8
Verlag, kostenfrei, Volltext: https://www.nature.com/articles/s41598-023-29550-8
Volltext
Verfasserangaben:Andreas Mock, Melissa Braun, Claudia Scholl, Stefan Fröhling & Cihan Erkut
Beschreibung
Zusammenfassung:Transcriptome profiling is a mainstay of translational cancer research and is increasingly finding its way into precision oncology. While bulk RNA sequencing (RNA-seq) is widely available, high investment costs and long data return time are limiting factors for clinical applications. We investigated a portable nanopore long-read sequencing device (MinION, Oxford Nanopore Technologies) for transcriptome profiling of tumors. In particular, we investigated the impact of lower coverage than that of larger sequencing devices by comparing shallow nanopore RNA-seq data with short-read RNA-seq data generated using reversible dye terminator technology (Illumina) for ten samples representing four cancer types. ...
Beschreibung:Gesehen am 30.11.2023
Beschreibung:Online Resource
ISSN:2045-2322
DOI:10.1038/s41598-023-29550-8

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