Performances of targeted RNA sequencing for the analysis of fusion transcripts, gene mutation, and expression

RNA sequencing holds great promise to improve the diagnostic of hematological malignancies, because this technique enables to detect fusion transcripts, to look for somatic mutations in oncogenes, and to capture transcriptomic signatures of nosological entities. However, the analytical performances of targeted RNA sequencing have not been extensively described in diagnostic samples.

Using a targeted panel of 1385 cancer-related genes in a series of 100 diagnosis samples and 8 controls, researchers at Hôpital Lyon Sud detected all the already known fusion transcripts and also discovered unknown and/or unsuspected fusion transcripts in 12 samples. Regarding the analysis of transcriptomic profiles, the researchers show that targeted RNA sequencing is performant to discriminate acute lymphoblastic leukemia entities driven by different oncogenic translocations. Additionally, they show that 86% of the mutations identified at the DNA level are also detectable at the messenger RNA (mRNA) level, except for nonsense mutations that are subjected to mRNA decay. The researchers conclude that targeted RNA sequencing might improve the diagnosis of hematological malignancies. Standardization of the preanalytical steps and further refinements of the panel design and of the bioinformatical pipelines will be an important step towards its use in standard diagnostic procedures.

Description of the 3 new fusion transcripts discovered in this cohort

Schematic representation of the 3 new fusion transcripts identified by targeted RNA-seq: FUS-FEV from t(2;16) (A), EEA1-PDGFRB from t(5;12) (B), evolution of the eosinophil count of the platelet with the EEA1-PDGFRB fusion transcript under imatinib treatment (C), and VWC2-IKZF1 (D). For each fusion, transcript is provided a schematic representation of the translocation at the genomic level, a graphical representation of the coverage depth in the targeted RNA-seq, and a schematic representation of the protein fusion. RNA-seq = RNA sequencing.