Structural Variant Analysis of Complex Karyotype Myelodysplastic Neoplasia Through Optical Genome Mapping

Myelodysplastic neoplasia with complex karyotype (CK-MDS) poses significant clinical challenges and is associated with poor survival. Detection of structural variants (SVs) is crucial for diagnosis, prognostication, and treatment decision-making in MDS. However, the current standard-of-care (SOC) cytogenetic testing, relying on karyotyping, often yields ambiguous results in cases with CK. Here, SV detection by novel optical genome mapping (OGM) technique was explored in 15 CK-MDS cases, which collectively harbored 85 chromosomes with abnormalities reported by SOC. Additionally, OGM was utilized in the discovery of novel SVs. Altogether, OGM detected corresponding > 5 Mbp alterations for 73 out of 85 SOC reported abnormalities, resulting in an 86% concordance rate. OGM provided further specification of these abnormalities, revealing that 64% of the altered chromosomes were affected by multiple SVs or chromoanagenesis. Prominently, only 5% of missing chromosomes reported by SOC were true monosomies. In addition, OGM detected alterations in chromosomes not reported as abnormal by karyotyping in 93% of cases and provided clinically relevant gene-level information, such as SVs in TP53, MECOM, NUP98, IKZF1, and ETV6. Analysis of novel SVs revealed two previously unreported gene-fusions (SCFD1::ZNF592 and VPS8::LRBA), both confirmed by transcriptome sequencing. Furthermore, the repositioning of CCDC26 (8q24.21) was identified as a potential cause of inappropriate gene activation in two cases, affecting MECOM and SOX7, respectively. This study shows that OGM can significantly enhance the diagnostic analysis of SVs in CK-MDS and highlights the utility of OGM identifying novel SVs in complex cancer genomes.