Diversity of U1 small nuclear RNAs and Evaluation of Diagnostic Methods for their Mutations

U1 small nuclear RNA (snRNA) mutations are recurrent non-coding alterations found in various malignancies, including medulloblastoma, yet their identification has proven challenging due to their repetitive nature. To establish a robust DNA-based, and RNA-based method for detecting U1 snRNA mutations, we performed targeted DNA sequencing using our original gene panel for medulloblastoma and RNA-sequencing. As an RNA-based method, we developed a random forest classifier employing splicing patterns which were massively altered as a result of U1 snRNA mutations. By using both methods, we successfully detected U1 snRNA mutation in five DNA samples and four RNA samples.

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

2 Datasets 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000000971	RNA sequencing files that were used in our study. The cohort was composed of 39 cases of RNA sequencing data. RNA-seq library was prepared with rRNA depletion method, and the sequence was performed using DNBSEQ sequencer.	DNBSEQ-G400	39
EGAD50000000972	Targeted DNA sequencing files that were used in our study. The cohort was composed of 36 cases of tumor-only targeted DNA sequencing data. All files are UMI processed. The panel is designed with Agilent Sure Select and the sequence was performed using DNBSEQ sequencer.	DNBSEQ-G400	36

Publications	Citations
Diversity of U1 Small Nuclear RNAs and Diagnostic Methods for Their Mutations. Nakashima T, Miyauchi T, Takeuchi R, Sugihara Y, Funakoshi Y, Ohka F, Maeda S, Hirato J, Yoshioka T, Okita H, Narita Y, Kanemura Y, Kojima Y, Watanabe Y, Saito R, Suzuki H. Cancer Sci 116: 2025 2270-2280	0