Use of optical genome mapping (OGM) to identify atypical or cryptic <i>KMT2A</i> (11q23) rearrangements and genomic structural mechanisms in acute myeloid leukemia.

Abstract

e18537 Background: KMT2A translocation and rearrangements are recurring chromosome abnormalities in acute leukemia and define a clinically important subset of acute myeloid leukemia (AML) with implications for diagnosis, prognosis, and therapeutic planning. KMT2A fusions frequently arise through various chromosome translocations, but may result from complex, multi-break structural variants (SVs) alterations, which can be cryptic by conventional chromosome analysis and FISH testing. Optical genome mapping (OGM) enables genome-wide SV and copy number alterations (CNAs) detection and may clarify genomic mechanisms of the fusions not apparent by karyotype and FISH testing. Methods: We applied OGM to clinical cases with suspected cryptic/complex KMT2A rearrangements, and compared with karyotyping, FISH, and targeted RNA sequencing (Archer FusionPlex). OGM results were reviewed to define SV structures, genomic mechanisms, and involved genomic junction and segments. Results: Three AML cases with cryptic KMT2A fusion cases were collected and analyzed. Two cases with KMT2A :: MLLT10 fusion showed no numerical or structural abnormalities involving both chromosomes 10 and 11 by karyotyping analysis and a normal KMT2A break-apart FISH pattern. OGM revealed an insertion mechanism in both, consistent with a 3’ MLLT10 portion inserted into the KMT2A locus. In one case, an ~900 kb inserted segment included 3′ MLLT10 and downstream genes; in the other, an ~150 kb 3′ MLLT10 segment was inserted, and OGM additionally detected a duplication involving MLLT10 with an adjacent gene. One case with KMT2A::MLLT3 fusion was cryptic by karyotype; OGM resolved the mechanism as insertion of an ~600 kb segment including 5′ KMT2A into the MLLT3 locus. Notably, this case also demonstrated copy-neutral loss of heterozygosity of the short arm of the derivative chromosome 9 spanning the insertion, suggesting potential allelic enrichment of the abnormal segment. A larger cohort analysis is ongoing. Conclusions: OGM complements routine cytogenetics by detecting and clarifying atypical, cryptic and novel gene fusions, including insertion-based mechanisms that may not be detected by karyotype or FISH testing. Our experience in these three AML cases with KMT2A fusions support OGM as a complementary approach in AML and other leukemia workup, especially in settings where RNA-based fusion testing is not routinely performed. Ongoing study on additional cases will expand the cohort and explore associations between SV mechanism, clinical outcomes, and response to Menin inhibitor therapy.