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Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes.
Genome Research · · Journal Article · Open access
Liu, Xia + more
Abstract ↗AI summary
The abstract is read at the publisher; the summary is JClub's.
Nanopore sequencing with SomaGauss-SV detects high-frequency somatic structural variations in 71.79% of LSCC patients, revealing recurrent genomic alterations.
- Why it matters: Understanding somatic mutations in LSCC is essential for insights into its development and progression, especially since conventional methods miss shared high-frequency variants that may drive tumorigenesis.
- What they did: The study developed SomaGauss-SV, a workflow utilizing nanopore long-read sequencing, and applied it to 15 paired LSCC samples, benchmarking its high precision and recall against five tumor cell line datasets.
- The result: A high-frequency somatic simple repeat expansion was found in 28 out of 39 patients, associated with upregulation of TP53BP2 and FBXO28, highlighting the method’s potential for biomarker discovery in LSCC.
The findingWhy it mattersWhat they didThe result
- Open access