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Updated: Jul 26, 2025
11:02
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
19.5K
Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data
Yuichi Shiraishi1, Junji Koya2, Kenichi Chiba1
1Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.
Nucleic Acids Research
|June 19, 2023
Summary
We developed nanomonsv software to detect somatic structural variations (SVs) in cancer using long-read sequencing. It precisely identifies known and novel SVs, improving cancer genome analysis.
Area of Science:
- Genomics
- Bioinformatics
- Cancer Research
Background:
- Somatic structural variations (SVs) are crucial in cancer development.
- Accurate detection of SVs, especially complex ones, remains challenging.
- Long-read sequencing offers potential for high-resolution SV detection.
Purpose of the Study:
- Introduce nanomonsv, a novel software for detecting somatic SVs.
- Evaluate nanomonsv's performance using tumor and matched control long-read data.
- Characterize complex SVs, including mobile element insertions and repetitive element rearrangements.
Main Methods:
- Utilized tumor/control paired long-read sequencing data.
- Implemented two detection modules: Canonical SV and Single breakend SV.
- Developed a workflow for classifying mobile element insertions and their properties.
Main Results:
- nanomonsv achieved higher precision and recall for canonical SVs compared to existing methods.
- Successfully identified complex SVs, including those in repetitive regions and mediated by LINE1/viruses.
- Characterized mobile element insertions, detailing 5' truncations, internal inversions, and 3' transduction source sites.
Conclusions:
- nanomonsv accurately detects a wide range of somatic SVs with single-base resolution.
- The software enhances the analysis of complex genomic rearrangements in cancer.
- Provides insights into mutational processes and functional consequences of somatic SVs.
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