ArticleGenome research2011
Transcriptional consequences of genomic structural aberrations in breast cancer.
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 52 papers.
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Who cites it
52 citing papers in PubMed.
- Characteristics of fusion genes in breast cancer.Cancer cell international · 2026Review
- GFSeeker: a splicing-graph-based approach for accurate gene fusion detection from long-read RNA sequencing data.Briefings in bioinformatics · 2026Article
- Article
- The genomic landscape of 2,023 colorectal cancers.Nature · 2024Article
- Decoding the Versatile Landscape of Autophagic Protein VMP1 in Cancer: A Comprehensive Review across Tissue Types and Regulatory Mechanisms.International journal of molecular sciences · 2024Review
- Gene Fusion Detection and Characterization in Long-Read Cancer Transcriptome Sequencing Data with FusionSeeker.Cancer research · 2023Article
- JAFFAL: detecting fusion genes with long-read transcriptome sequencing.Genome biology · 2022Article
- Analysis of Hi-C Data for Discovery of Structural Variations in Cancer.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing.RNA biology · 2021Article
- SVExpress: identifying gene features altered recurrently in expression with nearby structural variant breakpoints.BMC bioinformatics · 2021Article
- Protein-gene Expression Nexus: Comprehensive characterization of human cancer cell lines with proteogenomic analysis.Computational and structural biotechnology journal · 2021Article
- Hsa-miR-21-3p associates with breast cancer patient survival and targets genes in tumor suppressive pathways.PloS one · 2021Article
- Pan-Cancer Analysis Reveals the Diverse Landscape of Novel Sense and Antisense Fusion Transcripts.Molecular therapy. Nucleic acids · 2020Article
- FusionPro, a Versatile Proteogenomic Tool for Identification of Novel Fusion Transcripts and Their Potential Translation Products in Cancer Cells.Molecular & cellular proteomics : MCP · 2019Article
- Improved detection of gene fusions by applying statistical methods reveals oncogenic RNA cancer drivers.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Integrative molecular profiling identifies a novel cluster of estrogen receptor-positive breast cancer in very young women.Cancer science · 2019Article
- NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors.BMC bioinformatics · 2019Article
- High expression of the vacuole membrane protein 1 (VMP1) is a potential marker of poor prognosis in HER2 positive breast cancer.PloS one · 2019Article
- RhoGAP domain-containing fusions and PPAPDC1A fusions are recurrent and prognostic in diffuse gastric cancer.Nature communications · 2018Article
- Integrative detection and analysis of structural variation in cancer genomes.Nature genetics · 2018Article
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23 authors.
Funding
Abstract
Using a long-span, paired-end deep sequencing strategy, we have comprehensively identified cancer genome rearrangements in eight breast cancer genomes. Herein, we show that 40%-54% of these structural genomic rearrangements result in different forms of fusion transcripts and that 44% are potentially translated. We find that single segmental tandem duplication spanning several genes is a major source of the fusion gene transcripts in both cell lines and primary tumors involving adjacent genes placed in the reverse-order position by the duplication event. Certain other structural mutations, however, tend to attenuate gene expression. From these candidate gene fusions, we have found a fusion transcript (RPS6KB1-VMP1) recurrently expressed in ∼30% of breast cancers associated with potential clinical consequences. This gene fusion is caused by tandem duplication on 17q23 and appears to be an indicator of local genomic instability altering the expression of oncogenic components such as MIR21 and RPS6KB1.
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