Ultrasensitive Genomic Minimal Residual Disease Detection in Peripheral Blood after Allogeneic HSCT for MDS Is Associated with Increased Relapse Risk and Inferior Survival

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Introduction Genomic minimal residual disease (MRD) detected in complete remission using droplet digital PCR (ddPCR) is associated with inferior survival in AML patients when measured after induction chemotherapy and before and after allogeneic HSCT. However, the utility of high sensitivity genomic MRD detection in the context of allogeneic HSCT for patients with myelodysplastic syndrome (MDS) is unclear. Here we present data evaluating the association of genomic MRD with survival in HSCT recipients with MDS. Methods Peripheral blood mononuclear cells (PBMC) from 72 MDS patients sampled prior to HSCT were enriched for CD34+ cells and CD3+ cells using MACS columns. Genomic DNA extracted from CD34+ fractions underwent targeted next generation sequencing of 49 genes recurrently mutated in MDS. Variants were confirmed in the CD34+ fraction and germline polymorphisms excluded in the CD3+ fraction using Sanger resequencing. To date, mutations identified in 43 cases have been quantified with ddPCR in unfractionated PBMC genomic DNA prior to conditioning and at day 30 post-transplant with a sensitivity as low as 0.002%. Results A median of 2 mutations per case (range 1-4) was identified with NGS and subsequently measured with ddPCR. Prior to HSCT, 70% of cases had mutations with a variant allele frequency (VAF) ≥10% and had inferior OS compared to those with Conclusion Ultrasensitive genomic MRD detection in PBMC of MDS patients 30 days after HSCT is feasible and is associated with increased relapse risk and inferior DFS and OS. The gene mutations of most MRDpos patients were detected at

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