ArticleNucleic acids research2011
A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- Trial
- High EVI1 expression is associated with MLL rearrangements and predicts decreased survival in paediatric acute myeloid leukaemia: a report from the children's oncology group.British journal of haematology · 2013Trial
- GFSeeker: a splicing-graph-based approach for accurate gene fusion detection from long-read RNA sequencing data.Briefings in bioinformatics · 2026Article
- Fusion Challenges in Solid Tumors: Shaping the Landscape of Cancer Care in Precision Medicine.JCO precision oncology · 2024Review
- Breaking paradigms: Long non-coding RNAs forming gene fusions with potential implications in cancer.Genes & diseases · 2024Review
- Fast and sensitive validation of fusion transcripts in whole-genome sequencing data.BMC bioinformatics · 2023Article
- Recent advances in cancer fusion transcript detection.Briefings in bioinformatics · 2023Review
- Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies.Genome biology · 2022Article
- Accurate detection of tumor-specific gene fusions reveals strongly immunogenic personal neo-antigens.Nature biotechnology · 2022Article
- Gene fusion as an important mechanism to generate new genes in the genus Oryza.Genome biology · 2022Article
- Article
- JAFFAL: detecting fusion genes with long-read transcriptome sequencing.Genome biology · 2022Article
- LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing.BMC genomics · 2020Article
- Tet2-mediated epigenetic drive for astrocyte differentiation from embryonic neural stem cells.Cell death discovery · 2020Article
- Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods.Genome biology · 2019Article
- Novel TG-FGFR1 and TRIM33-NTRK1 transcript fusions in papillary thyroid carcinoma.Genes, chromosomes & cancer · 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
- A fast detection of fusion genes from paired-end RNA-seq data.BMC genomics · 2018Article
- Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line.Genome research · 2018Article
- De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi.BMC genomics · 2017Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
SnowShoes-FTD, developed for fusion transcript detection in paired-end mRNA-Seq data, employs multiple steps of false positive filtering to nominate fusion transcripts with near 100% confidence. Unique features include: (i) identification of multiple fusion isoforms from two gene partners; (ii) prediction of genomic rearrangements; (iii) identification of exon fusion boundaries; (iv) generation of a 5'-3' fusion spanning sequence for PCR validation; and (v) prediction of the protein sequences, including frame shift and amino acid insertions. We applied SnowShoes-FTD to identify 50 fusion candidates in 22 breast cancer and 9 non-transformed cell lines. Five additional fusion candidates with two isoforms were confirmed. In all, 30 of 55 fusion candidates had in-frame protein products. No fusion transcripts were detected in non-transformed cells. Consideration of the possible functions of a subset of predicted fusion proteins suggests several potentially important functions in transformation, including a possible new mechanism for overexpression of ERBB2 in a HER-positive cell line. The source code of SnowShoes-FTD is provided in two formats: one configured to run on the Sun Grid Engine for parallelization, and the other formatted to run on a single LINUX node. Executables in PERL are available for download from our web site: http://mayoresearch.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm.
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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.