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Updated: Oct 29, 2025

Comparative Lesions Analysis Through a Targeted Sequencing Approach
Published on: November 5, 2019
Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance
Marleen M Nieboer1,2, Luan Nguyen1,2, Jeroen de Ridder3,4
1Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands.
This study introduces svMIL2, a machine learning tool to identify pathogenic non-coding structural variants (SVs) in cancer genomes. It highlights the significant role of these non-coding SVs in disrupting gene regulation and driving cancer development.
Area of Science:
- Genomics
- Cancer Biology
- Bioinformatics
Background:
- Large-scale cancer genome sequencing projects have generated vast datasets.
- Focus has been on single nucleotide variants (SNVs), largely overlooking non-coding structural variants (SVs).
- Non-coding SVs can disrupt regulatory elements like TADs and CTCF loops, impacting gene expression.
Purpose of the Study:
- To introduce svMIL2, an improved machine learning method for analyzing somatic non-coding SVs.
- To assess the pathogenicity of non-coding SVs in 1646 cancer genomes.
- To identify novel driver genes and mechanisms affected by non-coding SVs.
Main Methods:
- Development and application of svMIL2, a Multiple Instance Learning-based tool.
- Analysis of somatic non-coding SVs in 1646 cancer genomes, focusing on disruptions of TADs and CTCF loops.
- Evaluation of svMIL2's predictive performance using AUC across 12 cancer types.
Main Results:
- svMIL2 achieved an average AUC of 0.86 in predicting pathogenic non-coding SVs across 12 cancer types.
- Identified non-coding SVs impacting known cancer driver genes.
- Disruption of active enhancers in open chromatin regions is a key pathogenic mechanism.
- Pathogenic non-coding SVs contribute significantly to gene disruption in ovarian and pancreatic cancers.
Conclusions:
- svMIL2 is a powerful tool for prioritizing pathogenic non-coding SVs and discovering driver genes.
- Non-coding SVs play a crucial role in cancer development, varying significantly by cancer type.
- Integrating non-coding SV analysis into cancer diagnostics is essential for comprehensive understanding and treatment.
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