Optical genome mapping detects additional genetic variants in nearly 20% of individuals with acute leukemia

New research assessing the efficacy of optical genome mapping (OGM) in a group of patients with acute leukemia has demonstrated that OGM provided reliable and robust analytical performance with high sensitivity and specificity in detecting genetic alterations. In nearly 20% of cases, additional genetic variants were found that standard tests had missed. Although these current standard assays retain value in the diagnostic workflow, the study, published in The Journal of Molecular Diagnostics, shows that OGM offers an exceptional complement and can replace certain elements of the current testing algorithm.

When an individual is diagnosed with acute leukemia, clinicians rely on genetic testing to determine the exact subtype of disease, the best course of treatment, and the anticipated outcome. Current standard-of-care tests include the use of multiple testing methods that are run in parallel and, once combined, reveal the diagnostic picture for many cases, but not all. The current study addresses these gaps in the routine testing workflow.

OGM visualizes the entire genome in a comprehensive and unbiased way to detect a wide range of alteration sizes and types, overcoming many limitations that are pervasive in historical testing approaches. The investigators of this study recognized the pivotal role that OGM could play in painting a more comprehensive clinical diagnostic picture.

Lead investigator Tara Spence, Ph.D., FCCMG, FACMG, Cytogenomics Laboratory, Department of Pathology and Laboratory Medicine, Vancouver General Hospital; and Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, explains, “Our large Canadian tertiary care facility launched OGM as a new diagnostic test for adult individuals with acute leukemia alongside existing standard-of-care workflows. We analyzed the yield of this test in the first 200 patients and found that OGM offered remarkable utility, refining diagnosis or risk stratification in nearly 20% of cases by identifying critical genetic variants that were otherwise missed by traditional workflows.”

In the 200 patients analyzed, OGM identified more than 640 clinically reportable genetic variants, compared with 444 detected by standard-of-care testing (karyotype, fluorescence in situ hybridization [FISH], and panel-based next-generation sequencing [NGS] combined). By providing a single, genome-wide view, OGM captured genetic changes across the full spectrum of size and complexity, overcoming limitations in resolution and scope in conventional tests.

“The finding that nearly 20% of cases within our cohort had a clinically significant abnormality missed by standard testing was striking, and as a tertiary care center that supports acute leukemia referrals provincially, this yield likely reflects the unique patient population we serve,” notes Dr. Spence.

Even without replacing the current standard-of-care tests, the use of OGM alongside these tests showed substantial clinical value as OGM results changed diagnoses and risk stratification in a meaningful proportion of cases, thereby improving therapy selection and refining expected outcome. The authors note that, although OGM’s longer turnaround time prevents it from fully replacing karyotyping at their institution, its high diagnostic yield justifies its routine use as a complementary tool for acute leukemia.

“This advanced clinical diagnostic technology offers the opportunity to meaningfully impact the individuals we serve, shedding light on genetic abnormalities that we previously could not visualize due to its incredibly refined resolution for detection of copy number and structural abnormalities. It is poised to guide treatment decisions and refine our understanding of expected outcomes. By sharing our experience and highlighting the additional diagnostic yield that OGM can provide, we hope to reduce barriers to implementation and support broader adoption of this powerful tool in clinical practice,” concludes Dr. Spence.