8. Reduced subclone diversity in clonal cytopenia of undetermined significance compared to myelodysplastic syndrome

Clonal cytopenias of undetermined significance (CCUS) is a precursor state to myelodysplastic syndrome (MDS), a blood cancer, and is distinguished solely on the absence of morphologic dysplasia, which has diagnostic variability. Determining differences in clonal architecture (total number and size of clones) may provide an objective assessment of disease status. We hypothesized that CCUS patients will have reduced molecular disease burden with fewer subclones compared to MDS patients suggesting that MDS is at higher risk of progressing to secondary acute myeloid leukemia (sAML). We performed whole genome sequencing with higher exome coverage (eWGS) on bone marrow (n=58) or peripheral blood (n=4) and paired normal DNA from baseline banked samples from patients with CCUS (n=13), MDS (n=29), and sAML (n=20) to define clonal architecture. While the median number of total validated somatic mutations per sample was not different between CCUS, MDS, and sAML, the median variant allele frequency of the dominant clone was lower in CCUS (21.3%) compared to MDS (39.2%, p<0.05) and sAML (45.2%, p<0.001). Additionally, the proportion of patients without subclones was higher for CCUS (5/13 [38.5%]) compared to MDS and sAML (4/29 [13.8%] and 0/20 [0%], respectively, p ≤ 0.0006), suggesting that CCUS samples have reduced subclonal diversity compared to MDS. The data suggest that leveraging clonal architecture and subclonal diversity in the evaluation of patients with low blood counts could provide an objective measure to characterize and monitor disease burden in CCUS and MDS, and potentially assess risk of sAML progression, rather than relying on dysplasia alone.