ArticleScientific reports2017
Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 34 citations in OpenAlex.
- Active Human Transposable Elements: Long-Read Sequencing Technologies, Computational Analysis, and Implications for Human Disease.Biomolecules · 2026Review
- Dynamic and Ongoing De Novo L1 Retrotransposition Contributes to Genome Plasticity and Intrapatient Heterogeneity in Ovarian Cancer.Cancer research · 2026Article
- Nanopore sequencing reveals hidden landscape of short L1 transductions in colorectal cancer.Communications biology · 2026Article
- Article
- Review
- LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunities.Genes & development · 2023Review
- Molecular methods for colorectal cancer screening: Progress with next-generation sequencing evolution.World journal of gastrointestinal oncology · 2023Review
- Targeted Nanopore Resequencing and Methylation Analysis of LINE-1 Retrotransposons.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- A Map of 3' DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes.Biology · 2022Article
- Ongoing endeavors to detect mobilization of transposable elements.BMB reports · 2022Review
- From telomere to telomere: The transcriptional and epigenetic state of human repeat elements.Science (New York, N.Y.) · 2022Article
- Nanopore sequencing technology, bioinformatics and applications.Nature biotechnology · 2021Review
- PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads.Genome biology · 2021Article
- A potential new mechanism for pregnancy loss: considering the role of LINE-1 retrotransposons in early spontaneous miscarriage.Reproductive biology and endocrinology : RB&E · 2020Review
- Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival.Nature communications · 2019Article
- NanoPipe-a web server for nanopore MinION sequencing data analysis.GigaScience · 2019Article
- Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome.Mobile DNA · 2019Article
- Diseases of the nERVous system: retrotransposon activity in neurodegenerative disease.Mobile DNA · 2019Review
- Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer.Nature protocols · 2018Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region by a process known as 3' transduction. L1 insertions can contribute to genome plasticity and cause potentially tumorigenic genomic instability. However, detecting the activity of a particular source L1 and identifying new insertions stemming from it is a challenging task with current methodological approaches. We developed a long-distance inverse PCR (LDI-PCR) based approach to monitor the mobility of active L1 elements based on their 3' transduction activity. LDI-PCR requires no prior knowledge of the insertion target region. By applying LDI-PCR in conjunction with Nanopore sequencing (Oxford Nanopore Technologies) on one L1 reported to be particularly active in human cancer genomes, we detected 14 out of 15 3' transductions previously identified by whole genome sequencing in two different colorectal tumour samples. In addition we discovered 25 novel highly subclonal insertions. Furthermore, the long sequencing reads produced by LDI-PCR/Nanopore sequencing enabled the identification of both the 5' and 3' junctions and revealed detailed insertion sequence information.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.