ArticleGenome research2011
RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Single cell spatial biology over developmental time can decipher pediatric brain pathologies.Neurobiology of disease · 2024Review
- Microsatellite break-induced replication generates highly mutagenized extrachromosomal circular DNAs.NAR cancer · 2024Article
- Microhomology-mediated repair machinery and its relationship with HPV-mediated oncogenesis.Journal of medical virology · 2024Review
- Improved detection of clinically relevant fusion transcripts in cancer by machine learning classification.BMC genomics · 2023Article
- Systematic investigation of the homology sequences around the human fusion gene breakpoints in pan-cancer - bioinformatics study for a potential link to MMEJ.Briefings in bioinformatics · 2023Article
- Progressive insights into fibrosarcoma diagnosis and treatment: leveraging fusion genes for advancements.Frontiers in cell and developmental biology · 2023Review
- HIV-1-Mediated Acceleration of Oncovirus-Related Non-AIDS-Defining Cancers.Biomedicines · 2022Review
- A rapidly reversible mutation generates subclonal genetic diversity and unstable drug resistance.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing.Nature communications · 2021Article
- Virus-Driven Carcinogenesis.Cancers · 2021Review
- A pilot radiogenomic study of DIPG reveals distinct subgroups with unique clinical trajectories and therapeutic targets.Acta neuropathologica communications · 2021Article
- Fusion Oncoproteins in Childhood Cancers: Potential Role in Targeted Therapy.The journal of pediatric pharmacology and therapeutics : JPPT : the official journal of PPAG · 2021Review
- Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.Nature genetics · 2020Article
- Detection of the KIAA1549-BRAF fusion gene in cells forming microvascular proliferations in pilocytic astrocytoma.PloS one · 2019Article
- Microhomology-mediated end joining: Good, bad and ugly.Mutation research · 2018Review
- RAD52 is required for RNA-templated recombination repair in post-mitotic neurons.The Journal of biological chemistry · 2018Article
- Review
- Break induced replication in eukaryotes: mechanisms, functions, and consequences.Critical reviews in biochemistry and molecular biology · 2017Review
- Identification of human papillomavirus (HPV) 16 DNA integration and the ensuing patterns of methylation in HPV-associated head and neck squamous cell carcinoma cell lines.International journal of cancer · 2017Article
- Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences.Nucleic acids research · 2016Article
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Authors and funding
11 authors.
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Abstract
Gene fusions involving members of the RAF family of protein kinases have recently been identified as characteristic aberrations of low-grade astrocytomas, the most common tumors of the central nervous system in children. While it has been shown that these fusions cause constitutive activation of the ERK/MAPK pathway, very little is known about their formation. Here, we present a detailed analysis of RAF gene fusion breakpoints from a well-characterized cohort of 43 low-grade astrocytomas. Our findings show that the rearrangements that generate these RAF gene fusions may be simple or complex and that both inserted nucleotides and microhomology are common at the DNA breakpoints. Furthermore, we identify novel enrichment of microhomologous sequences in the regions immediately flanking the breakpoints. We thus provide evidence that the tandem duplications responsible for these fusions are generated by microhomology-mediated break-induced replication (MMBIR). Although MMBIR has previously been implicated in the pathogenesis of other diseases and the evolution of eukaryotic genomes, we demonstrate here that the proposed details of MMBIR are consistent with a recurrent rearrangement in cancer. Our analysis of repetitive elements, Z-DNA and sequence motifs in the fusion partners identified significant enrichment of the human minisatellite conserved sequence/χ-like element at one side of the breakpoint. Therefore, in addition to furthering our understanding of low-grade astrocytomas, this study provides insights into the molecular mechanistic details of MMBIR and the sequence of events that occur in the formation of genomic rearrangements.
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