Novel NUP98::ASH1L Gene Fusion in Acute Myeloid Leukemia Detected by Optical Genome Mapping

Cancers (Basel). 2023 May 27;15(11):2942. doi: 10.3390/cancers15112942.


Optical genome mapping (OGM) recently has demonstrated the potential to improve genetic diagnostics in acute myeloid leukemia (AML). In this study, OGM was utilized as a tool for the detection of genome-wide structural variants and disease monitoring. A previously unrecognized NUP98::ASH1L fusion was detected in an adult patient with secondary AML. OGM identified the fusion of NUP98 to Absent, Small, or Homeotic-Like Histone Lysine Methyltransferase (ASH1L) as result of a complex structural rearrangement between chromosomes 1 and 11. A pipeline for the measurement of rare structural variants (Rare Variant Pipeline, Bionano Genomics, San Diego, CA, USA) was used for detection. As NUP98 and other fusions are relevant for disease classification, this demonstrates the necessity for methods such as OGM for cytogenetic diagnostics in AML. Furthermore, other structural variants showed discordant variant allele frequencies at different time points over the course of the disease and treatment pressure, indicating clonal evolution. These results support OGM to be a valuable tool for primary diagnostics in AML as well as longitudinal testing for disease monitoring and deepening our understanding of genetically heterogenous diseases.

Keywords: clonal evolution; cytogenetics; disease monitoring: structural variants; karyotyping; rare variant pipeline.

Grants and funding

We thank FoRUM of the Faculty of Medicine at the Ruhr-University Bochum for funding MT (medical doctoral thesis program) and V.N.-E. (female scientific clinician program). The work is funded by a grant of the InnovationsFoRUM (No. IF-007-22) of the Ruhr-University Bochum.