Improving Detection of Variant MECOM Rearrangements Through Optical Genome Mapping and Repurposed Targeted RNA-Seq
Annual Clinical Genetics Meeting, March 2026
Paige Van Haute, Graduate Student in Diagnostic Genetics and Genomics, Graduate Program in Diagnostic Genetics and Genomics, The University of Texas MD Anderson Cancer Center-School of Health Professions, Houston TX 77030, Holly Welfley, PhD, Chi Young Ok, MD, Manjunath Nimmakayalu, PhD, ASCP(CG), Awdhesh Kalia, PhD, J. Bryan, MD, MPH, FCAP, L. Jeffrey Medeiros, MD, Gokce A. Toruner, MD, PhD, FACMG, Paige Van Haute
Introduction: MECOM rearrangement is an AML-defining genetic abnormality that carries adverse prognostic implications and which also can occur in other myeloid neoplasms. Accurate testing for MECOM rearrangement is a component of the diagnostic work-up of myeloid malignancies. The classic inv(3)(q21q26.2)/t(3;3)(q21;q26.2) is the best-characterized MECOM aberration and promotes leukemogenesis through enhancer hijacking, in which a distal GATA2 enhancer is repositioned near the EVI1 (MECOM) promoter, leading to MECOM overexpression. Beyond these canonical events, a wide spectrum of variant MECOM rearrangements involving numerous alternate partner loci have been identified. Many of these events are subtle, structurally complex, or cryptic and therefore escape detection by conventional karyotyping.
Following the implementation of optical genome mapping (OGM) at our institution in March of 2023, and the subsequent deployment of a 108-gene anchored multiplex PCR (AMP) targeted RNA-Seq panel in October of 2023, we observed an apparent increase in the detection of variant MECOM aberrations. Here we aim to: (1) determine whether variant MECOM rearrangements were historically underreported by routine cytogenetic analysis; and (2) correlate OGM-detected MECOM rearrangements with RNA-Seq findings, including the presence of chimeric fusion transcripts and MECOM overexpression.
Methods: In this retrospective study, 180 cases with MECOM rearrangements were identified in the clinical laboratories at MD Anderson Cancer Center between March 1, 2021 and February 28, 2025. All cases underwent FISH and karyotyping; 54 had OGM results, and 29 of those had both OGM and targeted RNA-Seq results. Cases were stratified into pre-OGM (March 2021–February 2023) and post-OGM (March 2023–February 2025) cohorts. Detection rates of variant rearrangements were compared using the chi-square test. OGM findings were correlated with RNA-Seq fusion calls. Additionally, RNA expression levels from the 29 MECOM-rearranged cases were compared with 202 non–MECOM-rearranged cases that were analyzed concurrently, using the Mann-Whitney-U test.
Results: In the pre-OGM cohort (n=96), 60.4% of MECOM rearrangements were classic and 39.6% were variants. In the post-OGM cohort (n=84), 31% were classic and 69% were variants demonstrating a significant increase in variant detection following OGM implementation (p < 0.05).
Variant spectrum analysis showed that the most common rearrangements/genes (if known; otherwise denoted by “?”) in the post-OGM period were:
t(3;12)(q26.2;p13)/ETV6 (n=7), t(3;8)(q26.2;q24.2)/MYC (n=5), t(3;21)(q26.2;q22)/RUNX1 (n=5), t(3;6)(q26.2;q25)/? (n=4), t(2;3)(p21;q26.2)/THADA (n=3), t(3;7)(q26.2;q21.2)/CDK6 (n=3), t(3;6)(q26.2;q23.3)/ARID1B (n=2), fus(3;3)(q25.33;q26.2)/MBNL1 (n=2), inv(3)(q26.2q26.2)/? (n=2), and t(3;21)(q26.2;q11.2)/NRIP1 (n=2).
In the pre-OGM cohort, the most frequent variants were: t(3;21)(q26.2;q22)/RUNX1 (n=10), inv(3)(p23q26.2)/? (n=5), t(2;3)(p23;q26.2)/? (n=3), t(3;12)(q26.2;p13)/ETV6 (n=3), t(3;8)(q26.2;q24.2)/MYC (n=4). Overall, OGM revealed broader structural diversity and identified partner loci not reliably detected by conventional cytogenetic methods.
Of the 29 cases with both OGM and RNA-Seq data, 7 (25%) had detectable chimeric fusion transcripts: RUNX1::MECOM (n=2), NRIP1::MECOM (n=2), ETV6::MECOM (n=1), MBNL1::MECOM (n=1) and RPN1::MECOM (n=1). Despite the low fusion-call frequency, MECOM expression was consistently and elevated, with approximately 20-fold higher expression compared with 202 non-MECOM rearranged cases (p < 0.001).
Conclusion: OGM enhances detection of variant and cryptic MECOM rearrangements and reveals a more diverse structural spectrum than previously recognized by conventional cytogenetics. RNA-Seq detects fusion transcripts in only a subset of cases, but MECOM overexpression is consistently demonstrable, supporting the enhancer-hijacking mechanism. Although AMP chemistry is designed primarily for clinical fusion detection, its underlying expression data can be repurposed to identify overexpression events. These findings underscore the complementary diagnostic power of combining OGM with targeted RNA-Seq and support integrated multi-platform genomic workflows for comprehensive characterization of MECOM-rearranged myeloid neoplasms.
