RRC ID 52338
Author Reeser JW, Martin D, Miya J, Kautto EA, Lyon E, Zhu E, Wing MR, Smith A, Reeder M, Samorodnitsky E, Parks H, Naik KR, Gozgit J, Nowacki N, Davies KD, Varella-Garcia M, Yu L, Freud AG, Coleman J, Aisner DL, Roychowdhury S.
Title Validation of a Targeted RNA Sequencing Assay for Kinase Fusion Detection in Solid Tumors.
Journal J Mol Diagn
Abstract Kinase gene fusions are important drivers of oncogenic transformation and can be inhibited with targeted therapies. Clinical grade diagnostics using RNA sequencing to detect gene rearrangements in solid tumors are limited, and the few that are available require prior knowledge of fusion break points. To address this, we have analytically validated a targeted RNA sequencing assay (OSU-SpARKFuse) for fusion detection that interrogates complete transcripts from 93 kinase and transcription factor genes. From a total of 74 positive and 36 negative control samples, OSU-SpARKFuse had 93.3% sensitivity and 100% specificity for fusion detection. Assessment of repeatability and reproducibility revealed 96.3% and 94.4% concordance between intrarun and interrun technical replicates, respectively. Application of this assay on prospective patient samples uncovered OLFM4 as a novel RET fusion partner in a small-bowel cancer and led to the discovery of a KLK2-FGFR2 fusion in a patient with prostate cancer who subsequently underwent treatment with a pan-fibroblast growth factor receptor inhibitor. Beyond fusion detection, OSU-SpARKFuse has built-in capabilities for discovery research, including gene expression analysis, detection of single-nucleotide variants, and identification of alternative splicing events.
Volume 19(5)
Pages 682-696
Published 2017-9-1
DOI 10.1016/j.jmoldx.2017.05.006
PII S1525-1578(17)30114-9
PMID 28802831
PMC PMC5975628
MeSH Alternative Splicing Biomarkers, Tumor* Cell Line, Tumor Gene Expression Profiling Humans In Situ Hybridization, Fluorescence Neoplasms / diagnosis* Neoplasms / genetics* Oncogene Proteins, Fusion / genetics* Polymorphism, Single Nucleotide Protein Kinases / genetics* Proto-Oncogene Proteins c-ret / genetics Quality Control Receptor, Fibroblast Growth Factor, Type 2 / genetics Reproducibility of Results Reverse Transcriptase Polymerase Chain Reaction Sensitivity and Specificity Sequence Analysis, DNA Sequence Analysis, RNA / methods* Sequence Analysis, RNA / standards* Workflow
IF 4.88
Times Cited 24
Human and Animal Cells LC-2/ad(RCB0440)