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Genomic Variability of the HCT116 Cell Line Identified Using Oxford Nanopore Sequencing
Regina Mikheeva1,2, Pavel Leonov1,2, Maksim Koryukov1,2
1Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.
International Journal of Molecular Sciences
|July 15, 2026
Summary
This study identifies large genomic rearrangements (LGRs) and copy number variants (CNVs) in HCT116 colorectal cancer cells using Oxford Nanopore sequencing. Novel rearrangements in the CCSER1 gene were found, with distinct LGR mechanisms observed across samples.
Area of Science:
- Genomics and Molecular Biology
- Cancer Research
- Bioinformatics
Background:
- HCT116 is a widely used colorectal cancer cell line for anti-tumor drug development and eukaryotic cell molecular studies.
- While known for point mutations, its landscape of large genomic rearrangements (LGRs) and copy number variants (CNVs) remains incompletely characterized.
- Understanding genomic instability in HCT116 is crucial for accurate interpretation of experimental results.
Purpose of the Study:
- To comprehensively identify LGRs and CNVs in HCT116 cell line samples.
- To compare common and unique genomic variants across different HCT116 samples.
- To leverage Oxford Nanopore sequencing for detailed genomic structural variation analysis.
Main Methods:
- Utilized Oxford Nanopore sequencing technology on multiple HCT116 cell line samples, including public NCBI SRA data.
- Employed the eLaRodON tool for the identification and analysis of LGRs.
- Validated LGR findings using complementary copy number variant (CNV) analysis.
Main Results:
- Identified 22,666 common LGRs, with over 70% of large tandem duplications and deletions (>80 kb) confirmed by CNV analysis.
- Discovered two in-frame rearrangements within the CCSER1 gene (exons 4-6 deletion, exon 10 duplication), potentially impacting cell division regulation.
- Observed differential LGR mechanisms (ALR/Alpha vs. Alu repeats) in specific HCT116 samples, suggesting unique genomic instability pathways.
Conclusions:
- Oxford Nanopore sequencing effectively reveals a broad spectrum of LGRs and CNVs in the HCT116 cell line.
- The identified CCSER1 rearrangements may hold significance for future research due to its role in cell division and clinical relevance.
- Distinct genomic rearrangement patterns in different HCT116 samples highlight sample-specific mechanisms of genomic instability.
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