FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data

We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements.

• Publication year

  2010

• Venue

  Genome Biology

• Publication date

  2010-10-21

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/gb-2010-11-10-r104PMID 20964841PMCID 3218660
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing.

  2011cited by this paper
• Global and unbiased detection of splice junctions from RNA-seq data

  2010influential reference
• Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

  2010cited by this paper
• FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data

  2010cited by this paper
• Fast and SNP-tolerant detection of complex variants and splicing in short reads

  2010cited by this paper
• Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

  2009influential reference
• Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line

  2009cited by this paper
• Transcriptome Sequencing to Detect Gene Fusions in Cancer

  2009cited by this paper
• Unlocking the secrets of the genome

  2009cited by this paper
• SLC45A3-ELK4 is a novel and frequent erythroblast transformation-specific fusion transcript in prostate cancer.

  2009cited by this paper
• PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

  2009influential reference
• Chimeric transcript discovery by paired-end transcriptome sequencing

  2009cited by this paper
• An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

  2009cited by this paper
• N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer.

  2009cited by this paper
• ETS gene fusions in prostate cancer: from discovery to daily clinical practice.

  2009cited by this paper
• Circos: an information aesthetic for comparative genomics.

  2009cited by this paper
• Massively parallel sequencing of the polyadenylated transcriptome of C. elegans.

  2009influential reference
• Implications of chimaeric non-co-linear transcripts

  2009cited by this paper
• RNA-Seq: a revolutionary tool for transcriptomics

  2009cited by this paper
• A transcriptional sketch of a primary human breast cancer by 454 deep sequencing

  2009cited by this paper
• Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer

  2008cited by this paper
• Identification of alternative splicing markers for breast cancer.

  2008cited by this paper
• A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

  2008cited by this paper
• Alternative Isoform Regulation in Human Tissue Transcriptomes

  2008cited by this paper
• A Neoplastic Gene Fusion Mimics Trans-Splicing of RNAs in Normal Human Cells

  2008cited by this paper
• The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

  2008influential reference
• Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

  2008cited by this paper
• Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

  2008cited by this paper
• A large genome center's improvements to the Illumina sequencing system

  2008cited by this paper
• Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry

  2008cited by this paper
• Pleiotropic biological activities of alternatively spliced TMPRSS2/ERG fusion gene transcripts.

  2008cited by this paper
• Mapping and quantifying mammalian transcriptomes by RNA-Seq

  2008influential reference
• Recurrent gene fusions in prostate cancer

  2008cited by this paper
• Detection of TMPRSS2-ERG translocations in human prostate cancer by expression profiling using GeneChip Human Exon 1.0 ST arrays.

  2008cited by this paper
• Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

  2007cited by this paper
• The impact of translocations and gene fusions on cancer causation

  2007cited by this paper
• Multiple genomic alterations on 21q22 predict various TMPRSS2/ERG fusion transcripts in human prostate cancers

  2007cited by this paper
• Completing the map of human genetic variation

  2007cited by this paper
• Identification of the transforming EML4–ALK fusion gene in non-small-cell lung cancer

  2007cited by this paper
• Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome

  2007cited by this paper
• TreeFam: 2008 Update

  2007cited by this paper
• Diversity of TMPRSS2-ERG fusion transcripts in the human prostate

  2007influential reference
• Human chromosome 11 DNA sequence and analysis including novel gene identification

  2006cited by this paper
• Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer.

  2006influential reference
• Expression of variant TMPRSS2/ERG fusion messenger RNAs is associated with aggressive prostate cancer.

  2006influential reference
• Fine-scale structural variation of the human genome

  2005cited by this paper
• TreeFam: a curated database of phylogenetic trees of animal gene families

  2005cited by this paper
• Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer

  2004cited by this paper
• End-sequence profiling: Sequence-based analysis of aberrant genomes

  2003cited by this paper
• The human genome browser at UCSC.

  2002cited by this paper
• BLAT--the BLAST-like alignment tool.

  2002influential reference
• The Ensembl genome database project

  2002cited by this paper
• Recurrent chromosome aberrations in cancer.

  2000cited by this paper
• Repbase update: a database and an electronic journal of repetitive elements.

  2000cited by this paper
• BIOINFORMATICS ORIGINAL PAPER Genome analysis The UCSC Known Genes

  year unknowncited by this paper
• Bioinformatics Applications Note Gene Expression Rseqtools: a Modular Framework to Analyze Rna-seq Data Using Compact, Anonymized Data Summaries

  year unknowncited by this paper

• Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events.

  2025cites this paper
• Semi-Supervised, Attention-Based Deep Learning for Predicting TMPRSS2:ERG Fusion Status in Prostate Cancer Using Whole Slide Images

  2024cites this paper
• Detecting Fusion Genes in Long-Read Transcriptome Sequencing Data with FUGAREC

  2024cites this paper
• A Protocol for the Detection of Fusion Transcripts Using RNA-Sequencing Data.

  2024cites this paper
• Molecular Mechanisms of Prostate Cancer Development in the Precision Medicine Era: A Comprehensive Review

  2024cites this paper
• Mechanistic Insights and Molecular Diagnostics of TMPRSS2-ERG: Overview of the Journey from Regulation of Signaling Landscape in Fusion Positive Prostate Cancer to Appraisal as a Diagnostic Marker.

  2024cites this paper
• Using Attention-based Deep Learning to Predict ERG:TMPRSS2 Fusion Status in Prostate Cancer from Whole Slide Images

  2022cites this paper
• Patterns of indolence in prostate cancer (Review)

  2022cites this paper
• Gene fusion as an important mechanism to generate new genes in the genus Oryza

  2022cites this paper
• Case Report: Giant Thyroid Angiolipoma—Challenging Clinical Diagnosis and Novel Genetic Alterations

  2022cites this paper
• ChiTaH: a fast and accurate tool for identifying known human chimeric sequences from high-throughput sequencing data

  2021cites this paper
• Re-Evaluate Fusion Genes in Prostate Cancer

  2021cites this paper
• Real-time quantification of fusion transcripts with ligase chain reaction by direct ligation of adjacent DNA probes at fusion junction.

  2020cites this paper
• Integrative multiplatform molecular profiling of benign prostatic hyperplasia identifies distinct subtypes

  2020cites this paper
• Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology

  2020cites this paper
• Targetable gene fusions and aberrations in genitourinary oncology

  2020cites this paper
• Fusions involving BCOR and CREBBP are rare events in infiltrating glioma

  2020cites this paper
• Enabling Precision Oncology Through Precision Diagnostics.

  2020cites this paper
• Overview of research on fusion genes in prostate cancer

  2020cites this paper
• Queryfuse is a sensitive algorithm for detection of gene-specific fusions

  2020cites this paper
• FusionScan: accurate prediction of fusion genes from RNA-Seq data

  2019influential citation
• Integrative genomic, transcriptomic, and epigenomic analyses of benign prostatic hyperplasia reveal new options for therapy

  2019cites this paper
• Targeting the epichaperome as an effective precision medicine approach in a novel PML-SYK fusion acute myeloid leukemia

  2018cites this paper
• Identification of novel enriched recurrent chimeric COL7A1-UCN2 in human laryngeal cancer samples using deep sequencing

  2018cites this paper
• Gene Fusion in Malignant Glioma: An Emerging Target for Next-Generation Personalized Treatment

  2018influential citation
• Recurrent RET Gene Rearrangements in Intraductal Carcinomas of Salivary Gland

  2017cites this paper
• Next-Generation Rapid Autopsies Enable Tumor Evolution Tracking and Generation of Preclinical Models.

  2017cites this paper
• High-confidence fusion gene detection in different tumor entities & biomarker discovery in breast cancer

  2017cites this paper
• Somatic mutations in tumors: their detection, generation mechanisms and implications

  2017cites this paper
• De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance

  2017cites this paper
• EWSR1 Fusions With CREB Family Transcription Factors Define a Novel Myxoid Mesenchymal Tumor With Predilection for Intracranial Location

  2017cites this paper
• An graph-based algorithm for prioritizing cancer susceptibility genes from gene fusion data

  2017cites this paper
• RNA-seq Based Transcription Characterization of Fusion Breakpoints as a Potential Estimator for Its Oncogenic Potential

  2017cites this paper
• Expanding the molecular signature of ossifying fibromyxoid tumors with two novel gene fusions: CREBBP‐BCORL1 and KDM2A‐WWTR1

  2017cites this paper
• GFusion: an Effective Algorithm to Identify Fusion Genes from Cancer RNA-Seq Data

  2017cites this paper
• ETV transcriptional upregulation is more reliable than RNA sequencing algorithms and FISH in diagnosing round cell sarcomas with CIC gene rearrangements

  2017cites this paper
• Recurrent SRF-RELA Fusions Define a Novel Subset of Cellular Myofibroma/Myopericytoma: A Potential Diagnostic Pitfall With Sarcomas With Myogenic Differentiation

  2017cites this paper
• Computational proteogenomic identification and functional interpretation of translated fusions and micro structural variations in cancer

  2017cites this paper
• Genomic integrative analysis to improve fusion transcript detection, liquid association and biclustering

  2017cites this paper
• Clinical Next-Generation Sequencing: Enabling Precision Medicine

  2017cites this paper
• ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data

  2016cites this paper
• Ewing sarcoma with ERG gene rearrangements: A molecular study focusing on the prevalence of FUS‐ERG and common pitfalls in detecting EWSR1‐ERG fusions by FISH

  2016influential citation
• High-throughput RNA sequencing: a step forward in transcriptome analysis

  2016cites this paper
• Novel fusion genes and chimeric transcripts in ependymal tumors

  2016cites this paper
• A primer on precision medicine informatics

  2016cites this paper
• Transcriptome Sequencing for the Detection of Chimeric Transcripts.

  2016cites this paper
• Recurrent NTRK1 Gene Fusions Define a Novel Subset of Locally Aggressive Lipofibromatosis-like Neural Tumors

  2016cites this paper
• Structural variation detection using next-generation sequencing data: A comparative technical review.

  2016cites this paper
• Discovering and understanding oncogenic gene fusions through data intensive computational approaches

  2016cites this paper
• Divergent clonal evolution of castration resistant neuroendocrine prostate cancer

  2016cites this paper
• InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data

  2016cites this paper
• ChimeRScope: a novel alignment-free algorithm for fusion gene prediction using paired-end short reads

  2016cites this paper
• A novel scoring estimator to screening for oncogenic chimeric transcripts in cancer transcriptome sequencing

  2016cites this paper
• Reproducible, Scalable Fusion Gene Detection from RNA-Seq.

  2016cites this paper
• Cancer Gene Profiling

  2016cites this paper
• Novel BCOR-MAML3 and ZC3H7B-BCOR Gene Fusions in Undifferentiated Small Blue Round Cell Sarcomas

  2016cites this paper
• Recurrent CIC Gene Abnormalities in Angiosarcomas: A Molecular Study of 120 Cases With Concurrent Investigation of PLCG1, KDR, MYC, and FLT4 Gene Alterations

  2016cites this paper
• Identifying fusion transcripts using next generation sequencing

  2016cites this paper
• Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

  2015cites this paper
• EWSR1‐PBX3: A novel gene fusion in myoepithelial tumors

  2015influential citation
• Characterization of Genome Rearrangements from Tumour Sequencing Data

  2015influential citation
• Altérations génétiques et épigénétiques dans la leucémie myélomonocytaire chronique - Modulation par les agents déméthylants

  2015cites this paper
• Resource The Molecular Taxonomy of Primary Prostate Cancer

  2015cites this paper
• MAGI3–AKT3 fusion in breast cancer amended

  2015cites this paper
• Genomic analysis of head and neck endocrine glands

  2015cites this paper
• Next Generation Sequencing in Cancer Research, Volume 2

  2015cites this paper
• Molecular Characterization of Inflammatory Myofibroblastic Tumors With Frequent ALK and ROS1 Gene Fusions and Rare Novel RET Rearrangement

  2015cites this paper
• A genetic dichotomy between pure sclerosing epithelioid fibrosarcoma (SEF) and hybrid SEF/low‐grade fibromyxoid sarcoma: A pathologic and molecular study of 18 cases

  2015influential citation
• Data analytics for precision medicine : variation calling and copy number analysis for DNA sequencing

  2015cites this paper
• Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing

  2015cites this paper
• Dichotomy of Genetic Abnormalities in PEComas With Therapeutic Implications

  2015cites this paper
• The Molecular Taxonomy of Primary Prostate Cancer.

  2015cites this paper
• SimFuse: A Novel Fusion Simulator for RNA Sequencing (RNA-Seq) Data

  2015cites this paper
• Detecting and targetting oncogenic fusion proteins in the genomic era

  2015cites this paper
• A Molecular Study of Pediatric Spindle and Sclerosing Rhabdomyosarcoma: Identification of Novel and Recurrent VGLL2-related Fusions in Infantile Cases

  2015cites this paper
• Frequent FOS Gene Rearrangements in Epithelioid Hemangioma: A Molecular Study of 58 Cases With Morphologic Reappraisal

  2015cites this paper
• From chromosomes to genes

  2015cites this paper
• Next-Generation Sequencing in Cancer: Tools for Fusion Gene Detection

  2015cites this paper
• Next-Generation Sequencing (NGS) Tools and Impact in Plant Breeding

  2015cites this paper
• Applications of NGS to Screen FFPE Tumours for Detecting Fusion Transcripts

  2015cites this paper
• CRCDA—Comprehensive resources for cancer NGS data analysis

  2015cites this paper
• Landscape of gene fusions in epithelial cancers: seq and ye shall find

  2015cites this paper
• Clinical Applications of Next-Generation Sequencing of Formalin-Fixed Paraffin-Embedded Tumors

  2015cites this paper
• ZFP36‐FOSB fusion defines a subset of epithelioid hemangioma with atypical features

  2014influential citation
• Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer

  2014cites this paper
• Novel ZC3H7B‐BCOR, MEAF6‐PHF1, and EPC1‐PHF1 fusions in ossifying fibromyxoid tumors—molecular characterization shows genetic overlap with endometrial stromal sarcoma

  2014cites this paper
• Reference-free prediction of rearrangement breakpoint reads

  2014cites this paper
• Novel PRKD gene rearrangements and variant fusions in cribriform adenocarcinoma of salivary gland origin

  2014cites this paper
• RNA Sequencing and its Applications in Cancer Diagnosis and Targeted Therapy

  2014cites this paper
• Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq

  2014cites this paper
• Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency

  2014cites this paper
• Collection, integration and analysis of cancer genomic profiles: from data to insight.

  2014cites this paper
• Sequential combination of karyotyping and RNA-sequencing in the search for cancer-specific fusion genes.

  2014cites this paper
• NTRK1 Fusion in Glioblastoma Multiforme

  2014influential citation
• Next-Generation Sequencing of Translocation Renal Cell Carcinoma Reveals Novel RNA Splicing Partners and Frequent Mutations of Chromatin-Remodeling Genes

  2014cites this paper
• Detection and characterization of gene-fusions in breast and ovarian cancer using high-throughput sequencing

  2014cites this paper
• Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis

  2014cites this paper
• Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

  2014cites this paper
• Fusion Transcript Discovery in Formalin-Fixed Paraffin-Embedded Human Breast Cancer Tissues Reveals a Link to Tumor Progression

  2014cites this paper
• Novel MIR143‐NOTCH fusions in benign and malignant glomus tumors

  2013cites this paper