Clinical Evaluation of Massively Parallel RNA Sequencing for Detecting Recurrent Gene Fusions in Hematologic Malignancies

The Journal of Molecular Diagnostics | Published online: September, 2018

Borahm Kim, Hyeonah Lee, Saeam Shin, Saeam ShinEmail the author Saeam Shin, Seung-Tae Lee, Seung-Tae LeeEmail the author Seung-Tae Lee, Jong Rak Choi

The application of next-generation sequencing (NGS) technology in clinical diagnostics should proceed with care. We have evaluated the clinical validity of two commercially available RNA fusion panels, the TruSight RNA fusion panel (Illumina®) and FusionPlex® Pan-Heme panel (ArcherDX, Inc.), to detect recurrent translocations in hematologic malignancies. Twenty-four bone marrow samples taken at the initial diagnosis of patients with acute leukemia and chronic myeloid leukemia were included. To assess the limit of detection, serial dilutions of BCR-ABL1 (e1a2) positive RNAs were prepared using a commercial reference material. Both NGS panels detected 19 cases with recurrent translocations identified with reverse transcription-PCR, as well as a case with KMT2A-AFF1 with false-negative results in reverse transcription-PCR. Two rare translocations, DDX3X-MLLT10 and NUP98-HOXC13, were additionally identified using NGS panels. The detection limit ranged from 10-1 to 10-2, which was not satisfactory for samples with low tumor burden. To conclude, RNA fusion panels were suitable for the initial diagnosis, however, for follow-up samples, conventional reverse transcription-PCR should be selected.

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