Gene fusions are an important feature of many blood cancers, including acute leukemia. Identifying these abnormal gene combinations helps physicians classify disease, choose appropriate treatments, and better understand a patient’s prognosis. While several laboratory methods are available to detect gene fusions, each has limitations, particularly when uncommon or previously unknown fusions are present.

Researchers at the Yonsei University College of Medicine investigated how well whole RNA sequencing performs for detecting gene fusions in patients with acute leukemia. Unlike targeted RNA sequencing, which looks for a predefined set of gene fusions, whole RNA sequencing examines the entire transcriptome, allowing researchers to identify both common and unexpected fusion events.

The team analyzed whole RNA sequencing data from 301 patients diagnosed with acute leukemia. Using the Arriba fusion detection algorithm, they identified clinically significant gene fusions in more than one-third of the patients. Importantly, whole RNA sequencing detected several pathogenic fusions that conventional laboratory methods failed to identify, including the rare UBTF::ATXN7L3 fusion.

The researchers also found that rearrangements involving the ZNF384 gene occurred more frequently than expected, highlighting the value of comprehensive transcriptome analysis. These findings demonstrate how whole RNA sequencing can provide a broader view of the genetic changes driving leukemia.

Another important goal was determining how much sequencing data is needed for reliable fusion detection. By repeatedly analyzing smaller subsets of sequencing reads, the investigators found that at least 100 million sequencing reads provided reliable detection of recurrent gene fusions with moderate confidence. Increasing sequencing depth to 300 million reads provided high confidence detection across all recurrent fusion events examined.

The results also showed strong agreement between whole RNA sequencing and traditional chromosome analysis while offering greater sensitivity for detecting clinically relevant rearrangements. Because whole transcriptome sequencing is not limited to known targets, it can identify novel or unexpected fusion events that targeted assays may miss.

As RNA sequencing becomes increasingly integrated into clinical laboratories, studies like this help establish practical guidelines for sequencing depth while demonstrating the advantages of comprehensive transcriptome analysis. Whole RNA sequencing may improve the diagnosis and classification of acute leukemia and help ensure that patients receive the most appropriate treatment based on the complete genetic profile of their disease.