5. RNA-based fusion studies critically improves clinical management of acute leukemias

      Detection or exclusion of an increasing number of structural variants has become crucial to achieve accurate diagnosis and appropriate risk stratification, particularly in patients with acute leukemia. While RNA-based anchored multiplex PCR (AMP) can be used to identify gene fusion transcripts without a priori knowledge of the expected findings, the clinical utility when applied in conjunction with traditional cytogenetics has not been comprehensively characterized. Herein we describe an inter-institutional analysis of gene fusion detection via AMP-based studies and traditional cytogenetics across an unselected cohort of 108 acute myeloid and lymphoblastic leukemias. Fusion studies were concordant with cytogenetics in 81% (87/108) of cases evaluated. Discordances were seen in 19% of cases (21/108). A small fraction (4/21) were due to structural rearrangements detected by cytogenetics but not AMP studies as associated with enhancer hijacking and thus undetectable by this RNA-based approach. A larger fraction of discrepancies corresponding to 14% of cases across our cohort (15/108), were positive with RNA seq for a critical rearrangement which had been undetectable by cytogenetics.
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