Researchers have developed a novel diagnostics tool to detect gene fusions in pediatric B-cell acute lymphoblastic leukemia (B-ALL) with greater sensitivity than standard detection algorithms, according to findings from a study published in The Journal of Molecular Diagnostics.
The researchers have suggested that the tool, called FUSILLI (Fusions in Leukemia Long-Read Sequencing Investigator), offers a cheaper and more accessible sequencing-based molecular diagnostic platform for pediatric B-ALL.
“With the development of FUSILLI, we show the potential of using a single low-cost sequencing assay for diagnosing gene fusion subtypes of B-ALL, with faster turnaround time. Modern genomic subtyping in pediatric B-ALL informs risk-stratification and targeted therapy, improving treatment response rate and reducing unnecessary treatment-related toxicity,” stated senior investigator Jeremy R. Wang, PhD, Department of Genetics, Department of Pathology and Laboratory Medicine, and Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill.
Background and Study Methods
The researchers believed that long-read whole-transcriptome sequencing would be a more precise method for characterizing fusion oncogenes in B-ALL than current detection algorithms that do not fully explore sequencing depth and other analytical parameters in fusion transcripts.
Dr. Wang and his team developed their novel long-read fusion detection algorithm to explore targeted genomic subtyping in pediatric B-ALL.
The researchers evaluated FUSILLI against existing algorithms based on high-depth nanopore whole-transcriptome sequencing samples from 51 pediatric patients with B-ALL and low-depth sequencing samples from 68 patients (mean, 11.2 and 1.4 million reads, respectively).
“Long-read sequencing, and nanopore sequencing specifically, represent a new era of sequencing compared to more conventional short-read sequencing approaches. It has been around for about a decade but is now becoming mature enough for clinical applications,” Dr. Wang said. “Compared to traditional short-read next-generation sequencing, nanopore sequencing has dramatically lower capital and consumables costs and much faster turnaround time, making it particularly advantageous in resource-limited diagnostic settings. Our research builds on this technology to show the potential of diagnosing genomic subtypes of pediatric cancers, which are traditionally resolved through several different expertise- and resource-intensive assays.”
Key Findings
In the high-depth sequencing cohort, FUSILLI showed a sensitivity of 0.81 vs 0.63 with FusionSeeker, 0.76 with JAFFAL, and 0.70 with LongGF. FUSILLI also had a specificity of 0.92.
In the low-depth sequencing cohort, FUSILLI had a lower sensitivity of 0.27 that still outperformed the other fusion detection algorithms, which showed sensitivities of 0.09 to 0.16.
Computational down sampling suggested that 10 million reads was sufficient to sensitively detect gene fusions in B-ALL with FUSILLI. The limiting of data to just clinically relevant fusions allowed for a smaller search space and faster turnaround times.
The researchers also found an unexpected number of secondary alterations in the two cohorts. “For instance, we see PAX5::ZCCHC7 in several cases, which is a known secondary alteration, but less is known about its clinical relevance. A better understanding of these lesser-known genomic events that are not well captured by existing diagnostic tools has the potential to further improve risk stratification and personalized medicine.”
DISCLOSURES: This study was supported by the grants and awards from the National Cancer Institute of the NIH and National Institute of General Medical Sciences. Institutional and biobanking support was provided by UNC Lineberger Comprehensive Cancer Center, the University Cancer Research Fund, Hyundai Hope on Wheels, and Reelin’ for Research. For full disclosures of the study authors, visit jmdjournal.org.
