Diagnosis of fusion genes using targeted RNA sequencing

Fusion genes are a major cause of cancer. Their rapid and accurate diagnosis can inform clinical action, but current molecular diagnostic assays are restricted in resolution and throughput. Here, researchers from the Garvan Institute of Medical Research show that targeted RNA sequencing (RNAseq) can overcome these limitations. First, they establish that fusion gene detection with targeted RNAseq is both sensitive and quantitative by optimising laboratory and bioinformatic variables using spike-in standards and cell lines. Next, they analyse a clinical patient cohort and improve the overall fusion gene diagnostic rate from 63% with conventional approaches to 76% with targeted RNAseq while demonstrating high concordance for patient samples with previous diagnoses. Finally, the researchers show that targeted RNAseq offers additional advantages by simultaneously measuring gene expression levels and profiling the immune-receptor repertoire. The researchers anticipate that targeted RNAseq will improve clinical fusion gene detection, and its increasing use will provide a deeper understanding of fusion gene biology.

Overview of targeted RNAseq and panel validation


a Schematic of targeted RNAseq process. b Scatterplot of targeted RNAseq enrichment for ERCCs included on (blue) or excluded from (orange) the blood panel. cAbundance of captured ERCCs before and after targeted sequencing on blood panel. d Metagene plot of K562 targeted RNAseq read coverage across all genes on the blood panel. TS=Transcript Start site; TE=Transcript End site

Heyer EE, Deveson IW, Wooi D, Selinger CI, Lyons RJ, Hayes VM, O’Toole SA, Ballinger ML, Gill D, Thomas DM, Mercer TR, Blackburn J. (2019) Diagnosis of fusion genes using targeted RNA sequencing. Nat Commun 10(1):1388. [article]

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