Detecting and targetting oncogenic fusion proteins in the genomic era

Targetable Kinase-Activating Lesions in Ph-like Acute Lymphoblastic Leukemia

(2015) Kathryn G. Roberts et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2014) Francesco Abate et al.   BMC Systems Biology

BCR-ABL1 Compound Mutations Combining Key Kinase Domain Positions Confer Clinical Resistance to Ponatinib in Ph Chromosome-Positive Leukemia

(2014) Matthew S. Zabriskie et al.   CANCER CELL

Proteasome Inhibitors Evoke Latent Tumor Suppression Programs in Pro-B MLL Leukemias through MLL-AF4

(2014) Han Liu et al.   CANCER CELL

Two Novel ALK Mutations Mediate Acquired Resistance to the Next-Generation ALK Inhibitor Alectinib

(2014) R. Katayama et al.   CLINICAL CANCER RESEARCH

Dramatic Response to Crizotinib in ROS1 Fluorescent In Situ Hybridization- and Immunohistochemistry-Positive Lung Adenocarcinoma: A Case Series

(2014) Rita Chiari et al.   Clinical Lung Cancer

ChildSeq-RNA

(2014) Mohammed A. Qadir et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

The TPM3-NTRK1 rearrangement is a recurring event in colorectal carcinoma and is associated with tumor sensitivity to TRKA kinase inhibition

(2014) Elena Ardini et al.   Molecular Oncology

The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma

(2014) Gang Wu et al.   NATURE GENETICS

Acquired resistance to TKIs in solid tumours: learning from lung cancer

(2014) D. Ross Camidge et al.   Nature Reviews Clinical Oncology

First-Line Crizotinib versus Chemotherapy in ALK-Positive Lung Cancer

(2014) Benjamin J. Solomon et al.   NEW ENGLAND JOURNAL OF MEDICINE

Crizotinib in ROS1-Rearranged Non–Small-Cell Lung Cancer

(2014) Alice T. Shaw et al.   NEW ENGLAND JOURNAL OF MEDICINE

TMPRSS2:ERG blocks neuroendocrine and luminal cell differentiation to maintain prostate cancer proliferation

(2014) Z Mounir et al.   ONCOGENE

New Routes to Targeted Therapy of Intrahepatic Cholangiocarcinomas Revealed by Next-Generation Sequencing

(2014) J. S. Ross et al.   ONCOLOGIST

Identification of a Recurrent STRN/ALK Fusion in Thyroid Carcinomas

(2014) Gaëlle Pérot et al.   PLoS One

ERG expression in prostate cancer: The prognostic paradox

(2014) Michael Taris et al.   PROSTATE

RARAfusion genes in acute promyelocytic leukemia: a review

(2014) Etienne De Braekeleer et al.   Expert Review of Hematology

The landscape of kinase fusions in cancer

(2014) Nicolas Stransky et al.   Nature Communications

Kinase fusions are frequent in Spitz tumours and spitzoid melanomas

(2014) Thomas Wiesner et al.   Nature Communications

EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection

(2013) Hsueh-Ting Chu et al.   BIOINFORMATICS

Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data

(2013) Nameeta Shah et al.   BMC GENOMICS

ETV6-NTRK3 is a common chromosomal rearrangement in radiation-associated thyroid cancer

(2013) Rebecca J. Leeman-Neill et al.   CANCER

Identification ofROS1rearrangement in gastric adenocarcinoma

(2013) Jeeyun Lee et al.   CANCER

RETfusion gene: Translation to personalized lung cancer therapy

(2013) Takashi Kohno et al.   CANCER SCIENCE

Molecular Pathways: ROS1 Fusion Proteins in Cancer

(2013) K. D. Davies et al.   CLINICAL CANCER RESEARCH

Inflammatory myofibroblastic tumour of the lung with a novelPPFIBP1-ALKfusion variant

(2013) Akihiko Yoshida et al.   HISTOPATHOLOGY

Chaperones as thermodynamic sensors of drug-target interactions reveal kinase inhibitor specificities in living cells

(2013) Mikko Taipale et al.   NATURE BIOTECHNOLOGY

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma

(2013) David T W Jones et al.   NATURE GENETICS

Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas

(2013)   NATURE GENETICS

Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer

(2013) Aria Vaishnavi et al.   NATURE MEDICINE

Acquired Resistance to Crizotinib from a Mutation in CD74–ROS1

(2013) Mark M. Awad et al.   NEW ENGLAND JOURNAL OF MEDICINE

Crizotinib versus Chemotherapy in Advanced ALK-Positive Lung Cancer

(2013) Alice T. Shaw et al.   NEW ENGLAND JOURNAL OF MEDICINE

TMPRSS2–ERG gene fusions induce prostate tumorigenesis by modulating microRNA miR-200c

(2013) J Kim et al.   ONCOGENE

Novel Targets in Non-Small Cell Lung Cancer: ROS1 and RET Fusions

(2013) J. F. Gainor et al.   ONCOLOGIST

Resistance to ROS1 Inhibition Mediated by EGFR Pathway Activation in Non-Small Cell Lung Cancer

(2013) Kurtis D. Davies et al.   PLoS One

Foretinib is a potent inhibitor of oncogenic ROS1 fusion proteins

(2013) M. A. Davare et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ALK inhibitors: a new targeted therapy in the treatment of advanced NSCLC

(2013) Francesca Casaluce et al.   Targeted Oncology

Response to Cabozantinib in Patients with RET Fusion-Positive Lung Adenocarcinomas

(2013) Alexander Drilon et al.   Cancer Discovery

Breakpoint Analysis of Transcriptional and Genomic Profiles Uncovers Novel Gene Fusions Spanning Multiple Human Cancer Types

(2013) Craig P. Giacomini et al.   PLoS Genetics

State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity

(2013) Matteo Carrara et al.   Biomed Research International

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

(2013) Wenlong Jia et al.   GENOME BIOLOGY

Fusion genes in solid tumors: an emerging target for cancer diagnosis and treatment

(2013) Brittany C. Parker et al.   Chinese Journal of Cancer

ETV6–NTRK3 as a therapeutic target of small molecule inhibitor PKC412

(2012) Hoang Thanh Chi et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model

(2012) F. Abate et al.   BIOINFORMATICS

Dissect: detection and characterization of novel structural alterations in transcribed sequences

(2012) D. Yorukoglu et al.   BIOINFORMATICS

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads

(2012) Ruping Sun et al.   BIOINFORMATICS

Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript

(2012) Matteo Benelli et al.   BIOINFORMATICS

Allosteric inhibition enhances the efficacy of ABL kinase inhibitors to target unmutated BCR-ABL and BCR-ABL-T315I

(2012) Afsar Ali Mian et al.   BMC CANCER

Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives

(2012) Q. Wang et al.   BRIEFINGS IN BIOINFORMATICS

The Growing Arsenal of ATP-Competitive and Allosteric Inhibitors of BCR-ABL

(2012) O. Hantschel et al.   CANCER RESEARCH

Identification of Anaplastic Lymphoma Kinase as a Potential Therapeutic Target in Ovarian Cancer

(2012) H. Ren et al.   CANCER RESEARCH

Analysis of Receptor Tyrosine Kinase ROS1-Positive Tumors in Non-Small Cell Lung Cancer: Identification of a FIG-ROS1 Fusion

(2012) V. M. Rimkunas et al.   CLINICAL CANCER RESEARCH

Mechanisms of Resistance to Crizotinib in Patients withALKGene Rearranged Non–Small Cell Lung Cancer

(2012) Robert C. Doebele et al.   CLINICAL CANCER RESEARCH

Identification of KIF5B-RET and GOPC-ROS1 Fusions in Lung Adenocarcinomas through a Comprehensive mRNA-Based Screen for Tyrosine Kinase Fusions

(2012) Y. Suehara et al.   CLINICAL CANCER RESEARCH

Recent Developments in the Third Generation Inhibitors of Bcr-Abl for Overriding T315I Mutation

(2012) X. Y. Lu et al.   CURRENT MEDICINAL CHEMISTRY

ALK1 Signaling Inhibits Angiogenesis by Cooperating with the Notch Pathway

(2012) Bruno Larrivée et al.   DEVELOPMENTAL CELL

Discovery of ALK-PTPN3 gene fusion from human non-small cell lung carcinoma cell line using next generation RNA sequencing

(2012) Yeonjoo Jung et al.   GENES CHROMOSOMES & CANCER

nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing

(2012) A. McPherson et al.   GENOME RESEARCH

Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies

(2012) Doron Lipson et al.   NATURE MEDICINE

RET, ROS1 and ALK fusions in lung cancer

(2012) Kengo Takeuchi et al.   NATURE MEDICINE

FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery

(2012) Rocco Piazza et al.   NUCLEIC ACIDS RESEARCH

KLC1-ALK: A Novel Fusion in Lung Cancer Identified Using a Formalin-Fixed Paraffin-Embedded Tissue Only

(2012) Yuki Togashi et al.   PLoS One

FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data

(2012) Richard W. Francis et al.   PLoS One

Escaping ALK Inhibition: Mechanisms of and Strategies to Overcome Resistance

(2012) C. M. Lovly et al.   Science Translational Medicine

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

(2012) Onur Sakarya et al.   PLoS Computational Biology

Mammary Analogue Secretory Carcinoma of the Salivary Glands With ETV6-NTRK3 Gene Fusion

(2011) André Fehr et al.   AMERICAN JOURNAL OF SURGICAL PATHOLOGY

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs

(2011) Marcus Kinsella et al.   BIOINFORMATICS

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data

(2011) Andrew McPherson et al.   BIOINFORMATICS

FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq

(2011) Yang Li et al.   BIOINFORMATICS

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution

(2011) Huanying Ge et al.   BIOINFORMATICS

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

(2011) Matthew K. Iyer et al.   BIOINFORMATICS

ALK1 as an emerging target for antiangiogenic therapy of cancer

(2011) S. I. Cunha et al.   BLOOD

The rise and fall of gatekeeper mutations? TheBCR-ABL1T315I paradigm

(2011) Don L. Gibbons et al.   CANCER

ALK Mutations Conferring Differential Resistance to Structurally Diverse ALK Inhibitors

(2011) J. M. Heuckmann et al.   CLINICAL CANCER RESEARCH

Characterization of a newly identified ETV6-NTRK3 fusion transcript in acute myeloid leukemia

(2011) Johanna M Kralik et al.   Diagnostic Pathology

Hereditary hemorrhagic telangiectasia: An overview of diagnosis, management, and pathogenesis

(2011) Jamie McDonald et al.   GENETICS IN MEDICINE

Targeting Oncogenic ALK: A Promising Strategy for Cancer Treatment

(2011) E. Grande et al.   MOLECULAR CANCER THERAPEUTICS

Towards systematic functional characterization of cancer genomes

(2011) Jesse S. Boehm et al.   NATURE REVIEWS GENETICS

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines

(2011) Yan W. Asmann et al.   NUCLEIC ACIDS RESEARCH

A tripartite complex composed of ETV6-NTRK3, IRS1 and IGF1R is required for ETV6-NTRK3-mediated membrane localization and transformation

(2011) C E Tognon et al.   ONCOGENE

Survey of Tyrosine Kinase Signaling Reveals ROS Kinase Fusions in Human Cholangiocarcinoma

(2011) Ting-Lei Gu et al.   PLoS One

Chromosome 3 Anomalies Investigated by Genome Wide SNP Analysis of Benign, Low Malignant Potential and Low Grade Ovarian Serous Tumours

(2011) Ashley H. Birch et al.   PLoS One

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

(2011) Andrew McPherson et al.   PLoS Computational Biology

Identification of fusion genes in breast cancer by paired-end RNA-sequencing

(2011) Henrik Edgren et al.   GENOME BIOLOGY

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

ETV6-NTRK3-Mediated Breast Epithelial Cell Transformation Is Blocked by Targeting the IGF1R Signaling Pathway

(2010) C. E. Tognon et al.   CANCER RESEARCH

Identification of a novel fusion, SQSTM1-ALK, in ALK-positive large B-cell lymphoma

(2010) K. Takeuchi et al.   HAEMATOLOGICA

Renal cell carcinoma with novel VCL–ALK fusion: new representative of ALK-associated tumor spectrum

(2010) Larisa V Debelenko et al.   MODERN PATHOLOGY

Anaplastic Lymphoma Kinase Inhibition in Non–Small-Cell Lung Cancer

(2010) Eunice L. Kwak et al.   NEW ENGLAND JOURNAL OF MEDICINE

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data

(2010) Andrea Sboner et al.   GENOME BIOLOGY

AP24534, a Pan-BCR-ABL Inhibitor for Chronic Myeloid Leukemia, Potently Inhibits the T315I Mutant and Overcomes Mutation-Based Resistance

(2009) Thomas O'Hare et al.   CANCER CELL

KIF5B-ALK, a Novel Fusion Oncokinase Identified by an Immunohistochemistry-based Diagnostic System for ALK-positive Lung Cancer

(2009) K. Takeuchi et al.   CLINICAL CANCER RESEARCH

On Trk--The TrkB Signal Transduction Pathway Is an Increasingly Important Target in Cancer Biology

(2009) C. J. Thiele et al.   CLINICAL CANCER RESEARCH

Exon Array Profiling Detects EML4-ALK Fusion in Breast, Colorectal, and Non-Small Cell Lung Cancers

(2009) E. Lin et al.   MOLECULAR CANCER RESEARCH

Perspectives on the development of imatinib and the future of cancer research

(2009) Brian J Druker   NATURE MEDICINE

Defining and targeting transcription factors in cancer

(2009) Aisling M Redmond et al.   GENOME BIOLOGY

Multiplex Reverse Transcription-PCR Screening for EML4-ALK Fusion Transcripts

(2008) K. Takeuchi et al.   CLINICAL CANCER RESEARCH

TMPRSS2:ERG Fusion Identifies a Subgroup of Prostate Cancers with a Favorable Prognosis

(2008) O. R. Saramaki et al.   CLINICAL CANCER RESEARCH

Quantitative phosphoproteomics by mass spectrometry: Past, present, and future

(2008) Aleksandra Nita-Lazar et al.   PROTEOMICS