Optical Genome Mapping As Standard-of-Care in Acute Leukemia: Diagnostic and Clinical Impacts 10 Months Post-Implementation
Authors: McGinnis Eric , Stubbins Ryan J , Li Dan , Hamadeh Zeid , Spence Tara J 
Published: December 2024

Optical genome mapping (OGM) is a novel cytogenomic method which uses fluorescent labeling, imaging, and reference alignment of high molecular weight DNA for detection of structural and copy number variants at much higher resolution than is attainable using standard cytogenetic assays (karyotyping and FISH; CG). Our clinical laboratory in British Columbia, Canada's largest tertiary care hospital implemented OGM as front-line standard-of-care testing for all newly diagnosed acute leukemias in parallel with CG. We describe the performance and impact on diagnosis and risk stratification of clinical OGM in a prospective cohort of patients for whom OGM was performed in a 10-month period.

90 adults (mean age 55 years, 47% female) with acute leukemia had OGM performed at diagnosis, including 62 with acute myeloid leukemia (AML), 27 with lymphoblastic leukemia, including 22 B lineage (B-ALL) and 5 T lineage (T-ALL), and one mixed phenotype acute leukemia (T/myeloid). OGM was performed per manufacturer protocols on bone marrow aspirate or, when unavailable, blood using a Bionano Saphyr instrument and Rare Variant Analysis informatics (paired with De Novo or Guided Assembly for ALL). Detected variants were filtered using population thresholds and a custom 277-gene/region file and validated laboratory protocols for variant identification and classification in indication-specific contexts.

OGM provided adequate data for reporting for 88 individuals (98%) with a mean time to availability of results of 11.8 calendar days following sample procurement. Both instances of OGM failure resulted from inadequate bone marrow aspirate volume and insufficient circulating disease for processing. 201 reportable OGM variants were identified in 61 specimens (69%) compared to 132 identified by CG; specimens with reportable variants averaged 3.3 detected by OGM versus 2 by CG. Additional variants were observed at higher frequency in B-ALL and T-ALL (mean 3.4 and 3 additional variants per) than in AML (0.6 additional variants per), mostly accounted for by recurrent microdeletions. The great majority of specimens with no reportable OGM variants were AML with recurrent diagnostic mutations (44% NPM1, 15% CEBPA, 4% DDX41, 22% myelodysplasia-related). The assigned pathologic diagnosis was changed by OGM in 10 (11%) instances: 9 (15%) AML (3 MECOM rearrangements, 2 NUP98 rearrangements, 2 RUNX1 deletions, an unbalanced 7q rearrangement, and a confirmed constitutional exonic CHEK2 deletion) and 1 (5%) B-ALL with ZNF384 rearrangement. Additional variants predicting increased risk were identified in 12 (19%) individuals with AML (in addition to the above-described variants 5 KMT2A partial tandem duplications) and in 11 (50%) with B-ALL (11 with IKZF1 deletion, 1 with complex karyotype). OGM identified 8 recurrent rearrangements which CG failed to detect (owing either to their cryptic nature or to limitations inherent to techniques), including: MECOM::MYC, NUP98::NSD1, and ETV6::NTRK3 in AML; DDX3X::MLLT10, NOTCH1 deregulation, and HOXA::TCL1A in T-ALL; and IGH::CEBPB, IGH::TRA, FLT3::PAN3, TCF3::ZNF384, and TRA/D::MYB in B-ALL. 3 previously undescribed cryptic driver rearrangements were identified, including MECOM::IL12A-AS1/TRIM59-IFT80 resulting from inv(3)(q25.33q26.2) in AML, MECOM::AL589693.1 resulting from an unbalanced ins(6;3)(q25.3;q26.2q26.2) in oligoblastic AML, and MYB::HACE1 resulting from nested inversions on a der(6)inv(6)(q16.3q16.3)inv(6)(q16.3q23.3) in acute basophilic leukemia (the latter of which appears to phenocopy rare recurrent MYB rearrangements in infant basophilic leukemia).

This prospective cohort demonstrates the practicality and real-world clinical impacts of routine clinical genomic profiling of acute leukemia using OGM. Genome-wide high-resolution cytogenomic profiling enables timely and generally unbiased detection of somatic variants of critical value for appropriate diagnosis and risk stratification in the genomic era and circumvents limitations, such as low resolution and reliance on cell division in culture, inherent to current gold-standard CG. Data regarding the prognostic impact and actionability of recurrent variants now routinely detectable by OGM (e.g. FLT3::PAN3 rearrangements identified in 10% of B-ALL in this cohort) are urgently needed to maximally leverage this potentially transformative technology.