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, we show that targeted RNA sequencing (RNAseq) can overcome these limitations. First, we 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, we 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, we show that targeted RNAseq offers additional advantages by simultaneously measuring gene expression levels and profiling the immune-receptor repertoire. We anticipate that targeted RNAseq will improve clinical fusion gene detection, and its increasing use will provide a deeper understanding of fusion gene biology.The Australasian Leukaemia and Lymphoma Group Discovery Centre, funded by The Leukaemia Foundation of Australia and the Australian National Health and Medical Research Council (NHMRC), and the International Sarcoma Kindred Study, supported by the Rainbows for Kate Foundation, the Johanna Sewell Research Foundation, the ASSG and NHMRC grants APP1125042 and APP1103685. Funding provided by NHMRC grants APP1108254 (T.R.M. and J.B.) and APP1114016 (T.R.M.), NHMRC Project grant APP1103685 (E.E.H.), NHMRC PRF APP1104364 (D.M.T.), Cancer Institute NSW CDF171109 (M.L.B.), Cancer Institute NSW Early Career Fellowship 2018/ECF013 (I. W.D.), Australian Postgraduate Award scholarship (D.W.), National Breast Cancer Foundation (S.A.O.), Sydney Breast Cancer Foundation (S.A.O.), and philanthropic donations from the Paramor Family (T.R.M.), from the Tag family foundation, the O’Sullivan Family, ICAP and Mr David Paradice (S.A.O.), and in memory of Domenico Marrocco (T.R.M.).http://www.nature.com/ncommsam2019School of Health Systems and Public Health (SHSPH