Optical Genome Mapping Reveals Frequent Cryptic Structural Aberrations in Normal Karyotype Acute Myeloid Leukemia

Approximately half of newly diagnosed acute myeloid leukemia (AML) cases are cytogenetically normal (CN) when analyzed with conventional karyotyping. However, CN-AML exhibits a wide range of clinical heterogeneity, which may partly be explained by structural variants (SVs) that are not detected with current standard cytogenetic techniques. Here, 48 CN-AML cases were analyzed using optical genome mapping (OGM) for comprehensive SV assessment and to identify novel candidate gene alterations. Abnormalities were detected in 22 of 48 cases (46%). Large SVs, or those affecting leukemia-associated genes, were identified in 16 cases (33%), encompassing 18 abnormalities. Copy-neutral loss-of-heterozygosity regions were detected in seven cases (15%), and they were mutually exclusive with the presence of SVs in all but one case. SVs included eight deletions, six partial tandem duplications, two balanced translocations, and two complex rearrangements. The most frequently altered genes were KMT2A (5 cases) and RUNX1 (3 cases), followed by deletions of NF1 and the 13q14 (DLEU) region (2 cases each). Single alterations included NUP98::NSD1 and deletions of TET2, PRPF8, and FLT3. In addition, as a novel finding, we identified a balanced translocation t(3;20)(p13;q13.12) leading to a putative FOXP1::EYA2 fusion. Notably, the presence of OGM-detected abnormalities was associated with worse disease-specific survival (Mantel-Cox test, p = 0.007). Overall, this study demonstrates that a significant proportion of CN-AML cases harbor clinically relevant SVs, especially those associated with adverse prognosis, that escape detection by standard techniques. Our results support the use of OGM as a streamlined, genome-wide tool for both research and diagnostic applications in AML.