Performances of Targeted RNA Sequencing for the Analysis of Fusion Transcripts, Gene Mutation, and Expression in Hematological Malignancies

Abstract

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, we 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, we show that targeted RNA sequencing is performant to discriminate acute lymphoblastic leukemia entities driven by different oncogenic translocations. Additionally, we 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. We 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.

Classification and genetics of pediatric B-other acute lymphoblastic leukemia by targeted RNA sequencing

“…In hematologic malignancies, the TruSight Pan-Cancer was shown to detect 100% of fusions transcripts. 42 , 43 Regarding SNV, concordance between Pan-Cancer RNA sequencing and exome analysis was 86%, except for nonsense mutations likely subjected to messenger RNA decay. 42 Serial dilution of BCR-ABL1 + RNA into normal control RNA revealed a detection limit ranging from 1% to 10%.…”

“…NGS RNA sequencing circumvents this problem by providing the analysis of several loci at once and is particularly useful because it allows the identification of fusion transcripts derived from recurrent chromosomal translocations that are the hallmarks of ALL. 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 However, in the current diagnostics of ALL, NGS is used in addition to previous methods in intricate workflows. Our results suggest that targeted RNA sequencing might substitute FISH and RT-PCR methods, simplifying the current diagnostic strategy for ALL, while providing identification of both classical and modern subgroups of ALL, except for ploidy and copy number alterations.…”

Pan-Cancer Survival Classification With Clinicopathological and Targeted Gene Expression Features

“…Targeted gene expression panels facilitate multiplexed measurements of expression of select genes without having to perform whole transcriptome (WTX) sequencing and are anticipated to enter clinical oncology workflows. 8 Unlike targeted mutation profiling, which often has a binarized outcome, gene expression panels can provide dynamic information on tissue subtypes and states and can form the basis of more complex and quantitative predictive models.…”

Wholistic approach: Transcriptomic analysis and beyond using archival material for molecular diagnosis

“…Whole transcriptome and whole exome RNA sequencing are extremely powerful diagnostic techniques, as they allow exploring gene expression and comparing expression profiles. Several publications now describe RNA sequencing to improve the diagnosis of cancer in general, 54 glioma, 55 glioblastoma, 56 renal cell carcinoma, 57 breast carcinoma, [58][59][60][61][62] ovarian serous carcinoma, 63 lung idiopathic pulmonary fibrosis, 64 hematological malignancies, 65 and sarcoma 66 among others. WTS and WERS combine expression profiles and highthroughput detection of molecular biomarkers, including the detection of variations or small insertion/deletions.…”