ArticleGenome biology2020
CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers, 1 of them a synthesis that pooled it.
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Who cites it
80 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic study of molecular diagnosis, treatment, and prognosis in infant-type hemispheric glioma: An individual patient data meta-analysis of 164 patients.Neuro-oncology · 2026Pooled it
- Cancer-associated fusion transcripts: mechanisms, functional roles, and clinical implications.Clinical and experimental medicine · 2026Review
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- Article
- Characteristics of fusion genes in breast cancer.Cancer cell international · 2026Review
- Therapy-Related Mutational Signatures in Subsequent Neoplasms among Survivors of Childhood Cancer.Cancer discovery · 2026Article
- Pitfalls and Challenges in the Detection of ZNF384 Rearrangements by Fluorescence in Situ Hybridization.Genes, chromosomes & cancer · 2026Article
- Article
- Developmental reprogramming underlies chemotherapy resistance in favorable-histology Wilms tumor.Cell reports · 2026Article
- PTPN11-related Noonan syndrome predisposes to multifocal low-grade CNS tumors harboring FGFR1 variants.Journal of neuro-oncology · 2026Article
- The GF-NEO discovery platform unveils a [KQE][DG] sequence motif within fusion neoantigens in pediatric cancer.iScience · 2026Article
- Article
- PTPN11-Related Noonan Syndrome Predisposes to Multifocal Low-Grade CNS Tumors Harboring FGFR1 Variants.Research square · 2026Article
- Genetic landscape of pediatric acute myeloid leukemia in Taiwan.Scientific reports · 2026Article
- Fast and sensitive detection of targeted gene fusions using frequency minimizers and fuzzy pattern matching with Fuzzion2.Cell reports methods · 2025Article
- Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia.Blood · 2025Article
- Clinical utility of targeted RNA sequencing in cancer molecular diagnostics.Nature medicine · 2025Article
- FOXR2 activation is not exclusive of CNS neuroblastoma.Neuro-oncology · 2025Article
- Establishment and characterization of a novel patient-derived TP63-rearranged anaplastic large-cell lymphoma model PTCL-S1.Human cell · 2025Article
- Oncogenic gene fusions in cancer: from biology to therapy.Signal transduction and targeted therapy · 2025Review
20 more citing papers are in PubMed but not listed here.
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Authors and funding
21 authors.
Funding
Abstract
To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ranking. CICERO outperforms commonly used methods, achieving a 95% detection rate for 184 independently validated driver fusions including internal tandem duplications and other non-canonical events in 170 pediatric cancer transcriptomes. Re-analysis of TCGA glioblastoma RNA-seq unveils previously unreported kinase fusions (KLHL7-BRAF) and a 13% prevalence of EGFR C-terminal truncation. Accessible via standard or cloud-based implementation, CICERO enhances driver fusion detection for research and precision oncology. The CICERO source code is available at https://github.com/stjude/Cicero.
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