Researchers have introduced a new diagnostic method that can more sensitively detect gene fusions in the most common childhood cancer, B-cell acute lymphoblastic leukemia (B-ALL), compared to other publicly available fusion detection algorithms. This tool is explained in detail in the following article: Molecular Diagnostic Journalis published by Elsevier and enables higher diagnostic yields from low-coverage, low-cost sequencing.
Current treatments for B-ALL are categorized according to risk level depending on age, white blood cell count, response to treatment, central nervous system status, and genomic subtype. Pediatric B-ALL is primarily caused by chromosomal abnormalities or structural mutations, which usually result in fused oncogenes that cause cancer cell growth and proliferation. Diagnosing B-ALL genomic subtypes is important for appropriate risk stratification treatment.
A new algorithm called FUSILLI (FUSions In Leukemia for Long-read sequencing Investigator) was developed to detect these fusion genes. It uses long-read sequencing from Oxford Nanopore Technologies (ONT). It interrogates larger DNA and RNA fragments and is easier to implement across different resource contexts compared to short-read sequencing technologies.
Researchers working on this new tool have previously demonstrated the use of nanopore RNA-seq to classify B-ALL. Now, the sensitive and accurate method for detecting gene fusion subtypes presented in FUSILLI fills a critical gap in the use of these data for clinical fusion detection.
“Long-read sequencing, and particularly nanopore sequencing, represents a new era in sequencing compared to more traditional short-read sequencing approaches. It has been around for about a decade, but is now maturing enough for clinical application,” said Jeremy R. Wang, Ph.D., a senior investigator in the University of North Carolina at Chapel Hill School of Medicine, Department of Genetics, Department of Pathology and Department of Pathology and Laboratory Medicine, and Lineberger Comprehensive Cancer Center.
Compared to traditional short-read next-generation sequencing, nanopore sequencing has dramatically lower capital and consumable costs and much faster turnaround times, making it particularly advantageous in resource-limited diagnostic settings. Our study builds on this technology and shows the potential to diagnose genomic subtypes of childhood cancers that have traditionally been resolved by several different assays that require extensive expertise and resources. ”
Jeremy R. Wang, University of North Carolina
The researchers took a supervised approach to determine what filtering parameters were needed to detect true B-ALL gene fusions compared to results obtained from clinical trials. Gene fusion detection can be subject to false positives resulting from both technical and computational artifacts.
“From our experience, we have observed sequence chimeras (artificial DNA sequences created during the sequencing process) that generate long reads that resemble true gene fusions. This is a rare occurrence. Careful filtering and sufficient sequencing depth distinguish these from true B-ALL gene fusions supported by at least two reads,” explains Dr. Wang.
This study further established detection limits and found that approximately 10 million reads per sample are required to reliably detect B-ALL fusions using this approach.
Furthermore, the researchers compared their results with other publicly available fusion callers (using default parameters) and demonstrated excellent sensitivity without significantly compromising specificity for clinically relevant fusion events. Also, by limiting the data to clinically relevant B-ALL gene fusions, the researchers achieved a much smaller search space and faster computational times.
Although in most cases the primary fusion that causes leukemia is the primary fusion detected, the researchers observed an unexpected number of suggestive secondary changes in the cohort’s data. “For example, what we are looking at is PAX5::ZCCHC7 In some cases, this is a known secondary change, but less is known about its clinical relevance. A deeper understanding of these lesser-known genomic events, which are not well captured by existing diagnostic tools, could further improve risk stratification and personalized medicine. ”
Dr. Wang concluded, “The development of FUSILLI demonstrates the potential to use a single, low-cost sequencing assay to diagnose gene fusion subtypes of B-ALL, reducing turnaround time. Modern genomic subtyping in pediatric B-ALL will inform risk stratification and targeted therapy, improve treatment response rates, and reduce unnecessary treatment-related toxicities.”
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Reference magazines:
Lin, J. others. (2026) Long-read whole transcriptome sequencing and selective gene panel profiling enables sensitive detection of fusion oncogenes in pediatric B-cell acute lymphoblastic leukemia. Molecular Diagnostic Journal. DOI: 10.1016/j.jmoldx.2026.01.007. https://www.jmdjournal.org/article/S1525-1578(26)00021-8/fulltext
