ArticleCell systems2021
A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery.
Article in Cell systems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 36 citations in OpenAlex.
- Article
- Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences.BioData mining · 2026Article
- Comparison of gene fusion detection algorithms reveals frequently overlooked driver fusions in hematologic malignancies.NPJ precision oncology · 2026Article
- RETRACTED: Endogenous Retroviruses as Regulators of Innate Immune Signaling and InflammationViruses · 2026Review
- Integrative Chimeric RNA Prediction with FASfuse.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Bioinformatic Discovery of Tumor-Specific Neoantigens Arising from Chimeric RNAs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Fusions4U: a resource of validated and annotated gene fusions in 328 cancer cell lines.BMC cancer · 2025Article
- Targeting PP2A in cancer: an underrated option.Journal of experimental & clinical cancer research : CR · 2025Review
- Computational methods and data resources for predicting tumor neoantigens.Briefings in bioinformatics · 2025Review
- Proteogenomic analysis reveals non-small cell lung cancer subtypes predicting chromosome instability, and tumor microenvironment.Nature communications · 2024Article
- A New Approach of DetectingCancers · 2024Article
- A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing.Life science alliance · 2024Article
- Discovery of a polymorphic gene fusion via bottom-up chimeric RNA prediction.Nucleic acids research · 2024Article
- 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
- mRNA Capture Sequencing and RT-qPCR for the Detection of Pathognomonic, Novel, and Secondary Fusion Transcripts in FFPE Tissue: A Sarcoma Showcase.International journal of molecular sciences · 2022Article
- In silico validation of RNA-Seq results can identify gene fusions with oncogenic potential in glioblastoma.Scientific reports · 2022Article
- Experimentally Deduced Criteria for Detection of Clinically Relevant Fusion 3' Oncogenes from FFPE Bulk RNA Sequencing Data.Biomedicines · 2022Article
- Accurate detection of tumor-specific gene fusions reveals strongly immunogenic personal neo-antigens.Nature biotechnology · 2022Article
- Target isoforms are an overlooked challenge and opportunity in chimeric antigen receptor cell therapy.Immunotherapy advances · 2022Article
Corrections and comments
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Authors and funding
30 authors at 7 institutions in 3 countries.
Funding
Abstract
The accurate identification and quantitation of RNA isoforms present in the cancer transcriptome is key for analyses ranging from the inference of the impacts of somatic variants to pathway analysis to biomarker development and subtype discovery. The ICGC-TCGA DREAM Somatic Mutation Calling in RNA (SMC-RNA) challenge was a crowd-sourced effort to benchmark methods for RNA isoform quantification and fusion detection from bulk cancer RNA sequencing (RNA-seq) data. It concluded in 2018 with a comparison of 77 fusion detection entries and 65 isoform quantification entries on 51 synthetic tumors and 32 cell lines with spiked-in fusion constructs. We report the entries used to build this benchmark, the leaderboard results, and the experimental features associated with the accurate prediction of RNA species. This challenge required submissions to be in the form of containerized workflows, meaning each of the entries described is easily reusable through CWL and Docker containers at https://github.com/SMC-RNA-challenge. A record of this paper's transparent peer review process is included in the supplemental information.
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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.