ArticlePLoS genetics2023
Long-read sequencing identifies novel structural variations in colorectal cancer.
Article in PLoS genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Resolving missing human polymorphic inversions and other complex variants from ultralong read data.Genome research · 2026Article
- SVScope improves somatic structural variations detection via graph-genome optimization.Genome biology · 2026Article
- NanoVar: a comprehensive workflow for structural variant detection to uncover the genome's hidden patterns.Nature protocols · 2026Review
- Critical assessment of intratumor and low-biomass microbiome using long-read sequencing.bioRxiv : the preprint server for biology · 2026Article
- Article
- Structural variation drives enhancer hijacking via 3D genome disruption in ccRCC.NPJ digital medicine · 2026Article
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- Long-read sequencing for cancer liquid biopsy: advancing precision oncology.Frontiers in oncology · 2026Review
- Recent advances in the detection technologies for balanced chromosomal rearrangements.Frontiers in genetics · 2026Review
- Decoding cancer dormancy: integrative genomic, phenotypic and live-cell imaging analysis to reveal the hidden cancer cell reservoir.Molecular cancer · 2025Review
- Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis.Genome research · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- The Cancer Genome in the Long Reads Era.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes.Cell genomics · 2024Article
- Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology.BMC genomics · 2024Article
- Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer.Science advances · 2024Article
- A new era of mutation rate analyses: Concepts and methods.Zoological research · 2024Review
- Digital telomere measurement by long-read sequencing distinguishes healthy aging from disease.Nature communications · 2024Article
- The Application of Long-Read Sequencing to Cancer.Cancers · 2024Review
- Long-read sequencing for brain tumors.Frontiers in oncology · 2024Review
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structural variations (SVs) are a key type of cancer genomic alterations, contributing to oncogenesis and progression of many cancers, including colorectal cancer (CRC). However, SVs in CRC remain difficult to be reliably detected due to limited SV-detection capacity of the commonly used short-read sequencing. This study investigated the somatic SVs in 21 pairs of CRC samples by Nanopore whole-genome long-read sequencing. 5200 novel somatic SVs from 21 CRC patients (494 SVs / patient) were identified. A 4.9-Mbp long inversion that silences APC expression (confirmed by RNA-seq) and an 11.2-kbp inversion that structurally alters CFTR were identified. Two novel gene fusions that might functionally impact the oncogene RNF38 and the tumor-suppressor SMAD3 were detected. RNF38 fusion possesses metastasis-promoting ability confirmed by in vitro migration and invasion assay, and in vivo metastasis experiments. This work highlighted the various applications of long-read sequencing in cancer genome analysis, and shed new light on how somatic SVs structurally alter critical genes in CRC. The investigation on somatic SVs via nanopore sequencing revealed the potential of this genomic approach in facilitating precise diagnosis and personalized treatment of CRC.
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