Sequencing Strategies for Fusion Gene Detection

Pan-cancer analysis of whole genomes

(2020)   NATURE

Diagnosis of fusion genes using targeted RNA sequencing

(2019) Erin E. Heyer et al.   Nature Communications

The genomic landscape of pediatric cancers: Implications for diagnosis and treatment

(2019) E. Alejandro Sweet-Cordero et al.   SCIENCE

A high-throughput SNP discovery strategy for RNA-seq data

(2019) Yun Zhao et al.   BMC GENOMICS

Performance of Oncomine Fusion Transcript kit for formalin‐fixed, paraffin‐embedded lung cancer specimens

(2019) Kazuko Sakai et al.   CANCER SCIENCE

Detecting disease‐defining gene fusions in unclassified round cell sarcomas using anchored multiplex PCR/targeted RNA next‐generation sequencing—Molecular and clinicopathological characterization of 16 cases

(2019) Jose G. Mantilla et al.   GENES CHROMOSOMES & CANCER

Immunogenic neoantigens derived from gene fusions stimulate T cell responses

(2019) Wei Yang et al.   NATURE MEDICINE

Long-Read Sequencing Emerging in Medical Genetics

(2019) Tuomo Mantere et al.   Frontiers in Genetics

Application of NanoString technologies in companion diagnostic development

(2019) Jennifer Mary Eastel et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

An Integrated Next-Generation Sequencing System for Analyzing DNA Mutations, Gene Fusions, and RNA Expression in Lung Cancer

(2019) Brian C. Haynes et al.   Translational Oncology

Rationale for targeting BCL6 in MLL-rearranged acute lymphoblastic leukemia

(2019) Christian Hurtz et al.   GENES & DEVELOPMENT

Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human

(2019) Ann M McCartney et al.   Genome Biology and Evolution

Novel and established EWSR1 gene fusions and associations identified by next generation sequencing and fluorescence in-situ hybridization

(2019) Melissa Krystel-Whittemore et al.   HUMAN PATHOLOGY

Comparison of in Situ and Extraction-Based Methods for the Detection of ROS1 Rearrangements in Solid Tumors

(2019) Carina Heydt et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Integrated genomic profiling expands clinical options for patients with cancer

(2019) Nike Beaubier et al.   NATURE BIOTECHNOLOGY

Newly identified LMO3-BORCS5 fusion oncogene in Ewing sarcoma at relapse is a driver of tumor progression

(2019) Célia Dupain et al.   ONCOGENE

1409PKnown and unknown gene fusion detection capabilities of solid tumour laboratories conducting next generation sequencing in 6 countries

(2019) S Finucane et al.   ANNALS OF ONCOLOGY

Fusion Transcripts of Adjacent Genes: New Insights into the World of Human Complex Transcripts in Cancer

(2019) Vincenza Barresi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Rapid detection of chromosomal translocation and precise breakpoint characterization in acute myeloid leukemia by nanopore long-read sequencing

(2019) Chun Hang Au et al.   Cancer Genetics

Targeted RNA‐sequencing assays: a step forward compared to FISH and IHC techniques?

(2019) Gaëlle Tachon et al.   Cancer Medicine

A New Next-Generation Sequencing Strategy for the Simultaneous Analysis of Mutations and Chromosomal Rearrangements at DNA Level in Acute Myeloid Leukemia Patients

(2019) M. Isabel Prieto-Conde et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Multiplexed Digital Detection of B-Cell Acute Lymphoblastic Leukemia Fusion Transcripts Using the NanoString nCounter System

(2019) Yunan Zhong et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

(2018) Maria Nattestad et al.   GENOME RESEARCH

Long reads: their purpose and place

(2018) Martin O Pollard et al.   HUMAN MOLECULAR GENETICS

Development and Evaluation of a Pan-Sarcoma Fusion Gene Detection Assay Using the NanoString nCounter Platform

(2018) Kenneth T.E. Chang et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

(2018) Simon Ardui et al.   NUCLEIC ACIDS RESEARCH

Molecular pathway activation – New type of biomarkers for tumor morphology and personalized selection of target drugs

(2018) Anton Buzdin et al.   SEMINARS IN CANCER BIOLOGY

Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion

(2018) Shanrong Zhao et al.   Scientific Reports

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

(2018) Qingsong Gao et al.   Cell Reports

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data

(2018) Chang Xu   Computational and Structural Biotechnology Journal

A nanopore sequencing–based assay for rapid detection of gene fusions

(2018) William R. Jeck et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Circular RNA F-circEA-2a derived from EML4-ALK fusion gene promotes cell migration and invasion in non-small cell lung cancer

(2018) Shuangyan Tan et al.   Molecular Cancer

Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors

(2018) Nathaniel D. Anderson et al.   SCIENCE

Validation of the Oncomine™ focus panel for next-generation sequencing of clinical tumour samples

(2018) Hannah L. Williams et al.   VIRCHOWS ARCHIV

CircBA9.3 supports the survival of leukaemic cells by up-regulating c-ABL1 or BCR-ABL1 protein levels

(2018) Yuming Pan et al.   BLOOD CELLS MOLECULES AND DISEASES

RNA-based analysis of ALK fusions in non-small cell lung cancer cases showing IHC/FISH discordance

(2018) Claudia Vollbrecht et al.   BMC CANCER

Design, Optimization, and Multisite Evaluation of a Targeted Next-Generation Sequencing Assay System for Chimeric RNAs from Gene Fusions and Exon-Skipping Events in Non–Small Cell Lung Cancer

(2018) Richard A. Blidner et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

RNA-mediated gene fusion in mammalian cells

(2018) Sachin Kumar Gupta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Safety, pharmacokinetic, and pharmacodynamics of erdafitinib, a pan-fibroblast growth factor receptor (FGFR) tyrosine kinase inhibitor, in patients with advanced or refractory solid tumors

(2017) Tomohiro Nishina et al.   INVESTIGATIONAL NEW DRUGS

Validation of a Targeted RNA Sequencing Assay for Kinase Fusion Detection in Solid Tumors

(2017) Julie W. Reeser et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Fusions in solid tumours: diagnostic strategies, targeted therapy, and acquired resistance

(2017) Alison M. Schram et al.   Nature Reviews Clinical Oncology

Retinoic acid and arsenic trioxide in the treatment of acute promyelocytic leukemia: current perspectives

(2017) Derek McCulloch et al.   OncoTargets and Therapy

Multiplexed transcriptome analysis to detect ALK, ROS1 and RET rearrangements in lung cancer

(2017) Toni-Maree Rogers et al.   Scientific Reports

Integrated genomic DNA/RNA profiling of hematologic malignancies in the clinical setting

(2016) J. He et al.   BLOOD

Impact of RNA degradation on fusion detection by RNA-seq

(2016) Jaime I. Davila et al.   BMC GENOMICS

Lenvatinib: Role in thyroid cancer and other solid tumors

(2016) Maria E. Cabanillas et al.   CANCER TREATMENT REVIEWS

Oncogenic Role of Fusion-circRNAs Derived from Cancer-Associated Chromosomal Translocations

(2016) Jlenia Guarnerio et al.   CELL

NanoString, a novel digital color-coded barcode technology: current and future applications in molecular diagnostics

(2016) Hin-Fung Tsang et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Evolutionary Insights into RNA trans-Splicing in Vertebrates

(2016) Quan Lei et al.   Genome Biology and Evolution

Genomic complexity of multiple myeloma and its clinical implications

(2016) Salomon Manier et al.   Nature Reviews Clinical Oncology

Translating RNA sequencing into clinical diagnostics: opportunities and challenges

(2016) Sara A. Byron et al.   NATURE REVIEWS GENETICS

Discovering and understanding oncogenic gene fusions through data intensive computational approaches

(2016) Natasha S. Latysheva et al.   NUCLEIC ACIDS RESEARCH

Fusion transcriptome profiling provides insights into alveolar rhabdomyosarcoma

(2016) Zhongqiu Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FGFR3-TACC3 fusion in solid tumors: mini review

(2016) Ricardo Costa et al.   Oncotarget

The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing

(2016) Jongsuk Chung et al.   Scientific Reports

Identifying fusion transcripts using next generation sequencing

(2016) Shailesh Kumar et al.   Wiley Interdisciplinary Reviews-RNA

Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing

(2015) Lucia Cavelier et al.   BMC CANCER

The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing

(2015) Marcin Cieslik et al.   GENOME RESEARCH

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)

(2015) Donavan T. Cheng et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

ALK FISH and IHC: You Cannot Have One without the Other

(2015) Yasushi Yatabe   Journal of Thoracic Oncology

Comprehensive genomic profiles of small cell lung cancer

(2015) Julie George et al.   NATURE

Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data

(2015) Silvia Liu et al.   NUCLEIC ACIDS RESEARCH

Landscape of gene fusions in epithelial cancers: seq and ye shall find

(2015) Chandan Kumar-Sinha et al.   Genome Medicine

ChildSeq-RNA

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

Anchored multiplex PCR for targeted next-generation sequencing

(2014) Zongli Zheng et al.   NATURE MEDICINE

Variation in RNA-Seq Transcriptome Profiles of Peripheral Whole Blood from Healthy Individuals with and without Globin Depletion

(2014) Heesun Shin et al.   PLoS One

Next-Generation Sequencing of RNA and DNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal Tissue

(2014) Jakob Hedegaard et al.   PLoS One

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fusion genes and their discovery using high throughput sequencing

(2013) M.J. Annala et al.   CANCER LETTERS

Fibroblast growth factor receptor 2 tyrosine kinase fusions define a unique molecular subtype of cholangiocarcinoma

(2013) Yasuhito Arai et al.   HEPATOLOGY

Molecular Testing Guideline for Selection of Lung Cancer Patients for EGFR and ALK Tyrosine Kinase Inhibitors: Guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology

(2013) Neal I. Lindeman et al.   Journal of Thoracic Oncology

SS18-SSX fusion protein-induced Wnt/β-catenin signaling is a therapeutic target in synovial sarcoma

(2013) M Trautmann et al.   ONCOGENE

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

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

PAX3/FOXO1Fusion Gene Status Is the Key Prognostic Molecular Marker in Rhabdomyosarcoma and Significantly Improves Current Risk Stratification

(2012) Edoardo Missiaglia et al.   JOURNAL OF CLINICAL ONCOLOGY

RETFusions Define a Unique Molecular and Clinicopathologic Subtype of Non–Small-Cell Lung Cancer

(2012) Rui Wang et al.   JOURNAL OF CLINICAL ONCOLOGY

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study

(2011) S. Roychowdhury et al.   Science Translational Medicine

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Expression of Conjoined Genes: Another Mechanism for Gene Regulation in Eukaryotes

(2010) Tulika Prakash et al.   PLoS One

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS