Bionano Genomics Announces Peer-Reviewed Study Showing That Optical Genome Mapping Can Effectively Detect Oncogenic Structural Variants In Infant And Toddler T-cell Acute Lymphoblastic Leukemia

Bionano Genomics, Inc. (NASDAQ:BNGO) today announced a peer-reviewed publication from a team led by Manon Delafoy from the Institut Necker Enfants Malades (INEM) and colleagues from multiple French pediatric hematology centers showing how optical genome mapping (OGM) can be used to detect oncogenic structural variants (SVs) in clinical research of infant and toddler T-cell acute lymphoblastic leukemia (T-ALL). The publication shows that OGM can reveal distinct genetic drivers and prognostic subgroups that conventional cytogenetics failed to identify in a retrospective, national cohort of 27 T-ALL cases of infants and toddlers (<3 years) as part of a combined workflow of targeted sequencing, OGM, and RNA sequencing. Infants and toddlers can be a difficult segment of the population to analyze because their cancers are rare. The study conclusions support using OGM as a complementary tool to conventional assays to help accurately stratify samples from infants and toddlers according to prognostic risk.

Key OGM Findings based on Retrospective Analysis

• NKX2 rearrangements in one-third of cases: In the French cohort, 33% of cases (9 of 27) infant/toddler T‑ALL cases carried NKX2 family gene rearrangements. These events had not been previously characterized in this age group and frequently co‑occurred with MYB alterations (5/9) or complex chromothripsis-like events (3/9)
  
   
• Distinct genomic profile versus older pediatric subjects: Compared with a larger cohort of 245 cases aged 3-18 years, infant/toddler cases lacked TLX1/3 dysregulation but showed rates of TAL1/-like anomalies (30%), STAG2::LMO2 fusions (15%), ETS rearrangements (15%), and rarely, KMT2A rearrangements (7%)
  
   
• Comparable survival despite aggressive presentation: Despite higher rates of hyperleukocytosis and slower treatment response, these youngest subjects (infants and toddlers) achieved a 5-year overall survival (OS) of 75.4% (95% confidence interval [CI]: 60.0%–94.8%), closely matching the 75.2% (95% CI: 69.8%–81.1%) seen in the older pediatric subjects (p = 0.86) in the retrospective cohort
  
   
• Prognostic subgroups defined by structural variants in the retrospective analysis: Alterations in NKX2, KMT2A, and STAG2::LMO2 identified a subgroup with 100% overall survival (OS), whereas subjects with TAL1 or ETS dysregulation had less favorable outcomes. Findings were further supported by analysis of an independent cohort from the COG AALL0434 trial.
  
   
• Single‑workflow capability of OGM: OGM enabled detection and precise sizing of cryptic or complex rearrangements in a single assay, streamlining genomic profiling, compared to conventional or standard screening methods that may miss key variants or require multiple tests
  
   

"This study represents a significant collaborative effort across leading centers in France and offers a substantial leap forward for the pediatric leukemia community. Studying T-ALL in infants and young children is difficult because data are scarce and the genomic landscape is complex. Furthermore, standard approaches can often miss critical variants. OGM can provide a more complete view of the genome, revealing structural alterations that would otherwise remain hidden, uncovering drivers that can guide how we classify these cases, which may one day lead to better disease management and treatment," said Erik Holmlin, Bionano's President and CEO.