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

The Journal of Molecular Diagnostics : JMD
Kenneth Tou En ChangTony L Ng

Abstract

The NanoString nCounter assay is a high-throughput hybridization technique using target-specific probes that can be customized to test for numerous fusion transcripts in a single assay using RNA from formalin-fixed, paraffin-embedded material. We designed a NanoString assay targeting 174 unique fusion junctions in 25 sarcoma types. The study cohort comprised 212 cases, 96 of which showed fusion gene expression by the NanoString assay, including all 20 Ewing sarcomas, 11 synovial sarcomas, and 5 myxoid liposarcomas tested. Among these 96 cases, 15 showed fusion expression not identified by standard clinical assay, including EWSR1-FLI1, EWSR1-ERG, BCOR-CCNB3, ZC3H7B-BCOR, HEY1-NCOA2, CIC-DUX4, COL1A1-PDGFB, MYH9-USP6, YAP1-TFE3, and IRF2BP2-CDX1 fusions. There were no false-positive results; however, four cases were false negative when compared with clinically available fluorescence in situ hybridization or RT-PCR testing. When batched as six cases, the per-sample reagent cost was less than conventional techniques, such as fluorescence in situ hybridization, with technologist hands-on time of 1.2 hours per case and assay time of 36 hours. In summary, the NanoString nCounter Sarcoma Fusion CodeSet reliably and cost-effectively ide...Continue Reading

Citations

Jun 6, 2019·Expert Review of Molecular Diagnostics·Jennifer Mary EastelSze Chuen Cesar Wong
Jun 1, 2019·Epigenomics·Annalisa AstolfiAndrea Pession
Apr 23, 2019·Genes, Chromosomes & Cancer·Maribel D LacambraBrendan C Dickson
Jun 15, 2018·International Journal of Gynecological Pathology : Official Journal of the International Society of Gynecological Pathologists·Sorsiah MansorKenneth Tou En Chang
Aug 8, 2018·International Journal of Gynecological Pathology : Official Journal of the International Society of Gynecological Pathologists·Nicholas Wee Chong KohDerrick Wen Quan Lian
Jan 23, 2020·Genes, Chromosomes & Cancer·Wangzhao SongLéon C van Kempen
Apr 1, 2020·Cells·Carmen Salguero-ArandaEnrique de Álava
Apr 21, 2020·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Erin E Heyer, James Blackburn
Jul 1, 2019·Pathology Oncology Research : POR·Derek WongPoul H Sorensen
Aug 13, 2020·Nature Reviews. Cancer·Benjamin A NacevTorsten O Nielsen
Aug 10, 2018·Pediatric and Developmental Pathology : the Official Journal of the Society for Pediatric Pathology and the Paediatric Pathology Society·Javal ShethGino R Somers
Oct 28, 2019·Histopathology·Akihiko YoshidaTatsuhiro Shibata
Feb 13, 2020·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Lauren McConnellDavid Gonzalez
Jun 15, 2018·The American Journal of Surgical Pathology·Shamlal MangrayEvgeny Yakirevich
Oct 24, 2018·Genes, Chromosomes & Cancer·Brendan C Dickson, David Swanson
Mar 2, 2019·BMC Cancer·Sharon Y Y LowDavid C Y Low
Jun 14, 2019·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Ju-Yoon YoonCarlos Parra-Herran
Oct 30, 2020·Histopathology·Nissreen MohammadCheng-Han Lee
Apr 4, 2021·Cancers·Asle Charles HeslaPanagiotis Tsagkozis
Aug 7, 2021·The Journal of Molecular Diagnostics : JMD·Lisa HaleyChristopher D Gocke
Aug 10, 2021·Journal of Orthopaedic Research : Official Publication of the Orthopaedic Research Society·Farrah A MonibiScott A Rodeo
Jan 23, 2022·Genes, Chromosomes & Cancer·Xue Qi WangTorsten Owen Nielsen

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Applied Immunohistochemistry & Molecular Morphology : AIMM
Suzan E Ten HeuvelAlbert J H Suurmeijer
Pediatric and Developmental Pathology : the Official Journal of the Society for Pediatric Pathology and the Paediatric Pathology Society
Javal ShethGino R Somers
Journal of Cutaneous Pathology
Ana M Molina-Ruiz, Klaus J Busam
© 2022 Meta ULC. All rights reserved