Copy number variations and uniparental disomy predict poor survival in patients with idiopathic cytopenia of undetermined significance and are associated with macrocytosis

Background: Approximately half of patients with idiopathic cytopenia of undetermined significance (ICUS) have somatic mutations associated with increased risk of progression to MDS. The cause of cytopenia in the remaining ICUS patients is unknown. Aims: We hypothesize that uniparental disomy (UPD) and submicroscopic copy number variations (CNVs), i.e., gains and deletions (dels), are present in ICUS patients and may be associated with prognosis. Methods: Patients (n = 154) referred with ICUS in Denmark between 2008–2017 were included if cytopenia persisted for > 6 months, cytogenetics was normal and bone marrow (BM) morphology was not diagnostic. SNP‐A was performed on DNA from mononuclear cells or granulocytes using Illumina Infinium CytoSNP‐850K and analyzed with GenomeStudio v1.1 (Illumina). Only dels > 30 markers, gains > 90 markers and UPDs > 5 Mb were reported. Results: A total of 33 structural variations (17 dels, 9 UPDs, and 7 gains), excluding deletion of the Y chromosome, were detected in 27/154 patients (18%) in all chromosomes except chromosome 5, 10, 13, 14, 18, 21 and X. Median sizes were 187 Kb, 1.9 Mb and 82.4 Mb of dels, gains and UPDs, respectively. Mutations were present in 12/27 patients (44%) with CNV/UPD. Twenty‐six deletions or UPDs (del/UPD) were detected in 21/154 patients (14%) of whom 11/21 (52%) harbored mutations. A hemizygous subclonal deletion of DNMT3A was found in a 72 year old male with anemia and neutropenia with no somatic mutations. Subclonal UPD involving almost the entire q arm of chromosome 11 and, thus, the CBL gene was identified in a 84 year old male with mutations in CBL and TET2 . Three patients had structural variations involving the TET2 gene (subclonal deletion or UPD), and all three patients also had TET2 mutations. In a 25 year old bipenic male (hemoglobin 6 mM, platelet count 110 x 10^9/L) a 187 Kb hemizygous deletion of the KANK1 gene at chromosome 9p24.3 was detected as the only genetic abnormality. After a median follow‐up of 25 months (range, 2–114), median overall survival (OS) was 67 months (95% CI: 19‐not reached) in patients with del/UPD while it was not reached in the patients without ( p = 0.003), Figure 1 . The association with poor OS was also significant when including gains ( p = 0.02), however, the impact seemed to be driven by del/UPD, and here only results with del/UPD are presented. In multivariate analysis, del/UPD (HR = 2.7, 95% CI: 1.22–5.9, p = 0.014) and deep anemia (hgb < 6.2) (HR = 2.2, 95% CI: 1.10–4.4, p = 0.025) were independent adverse prognostic factors for OS, whereas mutational status was not (HR = 1.1, 95% CI: 0.55–2.3, p = 0.74). Interestingly, an almost identical pattern was observed between macrocytosis (MCV > 100 fL) and del/UPD in Cox proportional hazard regression models indicating a linked impact on survival. Consequently, del/UPD and macrocytosis were not included in the same model due to multicollinearity. Patients with del/UPD had significantly higher MCV ( p = 0.005) and P‐ferritin ( p = 0.03). Importantly, macrocytosis was not associated with deep anemia ( p = 0.317). Summary/Conclusion: To our knowledge this is the first study investigating CNVs/UPDs in ICUS patients. In a subset of patients with otherwise no detectable genetic abnormalities, we identified structural variations involving genes recurrently affected in MDS. Importantly, our results suggest that SNP‐A can aid the prognostics of ICUS patients by identifying submicroscopic structural variations as risk markers for poor OS. A possible role of macrocytosis as a surrogate marker should be explored in a validation cohort and will be prepared for the EHA meeting. image