Mutation Clearance after Transplantation for Myelodysplastic Syndrome

Abstract

Background: Allogeneic hematopoietic stem-cell transplantation is the only curative treatment for patients with myelodysplastic syndrome (MDS). The molecular predictors of disease progression after transplantation are unclear.

Methods: We sequenced bone marrow and skin samples from 90 adults with MDS who underwent allogeneic hematopoietic stem-cell transplantation after a myeloablative or reduced-intensity conditioning regimen. We detected mutations before transplantation using enhanced exome sequencing, and we evaluated mutation clearance by using error-corrected sequencing to genotype mutations in bone marrow samples obtained 30 days after transplantation. In this exploratory study, we evaluated the association of a mutation detected after transplantation with disease progression and survival.

Results: Sequencing identified at least one validated somatic mutation before transplantation in 86 of 90 patients (96%); 32 of these patients (37%) had at least one mutation with a maximum variant allele frequency of at least 0.5% (equivalent to 1 heterozygous mutant cell in 100 cells) 30 days after transplantation. Patients with disease progression had mutations with a higher maximum variant allele frequency at 30 days than those who did not (median maximum variant allele frequency, 0.9% vs. 0%; P<0.001). The presence of at least one mutation with a variant allele frequency of at least 0.5% at day 30 was associated with a higher risk of progression (53.1% vs. 13.0%; conditioning regimen-adjusted hazard ratio, 3.86; 95% confidence interval [CI], 1.96 to 7.62; P<0.001) and a lower 1-year rate of progression-free survival than the absence of such a mutation (31.3% vs. 59.3%; conditioning regimen-adjusted hazard ratio for progression or death, 2.22; 95% CI, 1.32 to 3.73; P=0.005). The rate of progression-free survival was lower among patients who had received a reduced-intensity conditioning regimen and had at least one persistent mutation with a variant allele frequency of at least 0.5% at day 30 than among patients with other combinations of conditioning regimen and mutation status (P≤0.001). Multivariate analysis confirmed that patients who had a mutation with a variant allele frequency of at least 0.5% detected at day 30 had a higher risk of progression (hazard ratio, 4.48; 95% CI, 2.21 to 9.08; P<0.001) and a lower 1-year rate of progression-free survival than those who did not (hazard ratio for progression or death, 2.39; 95% CI, 1.40 to 4.09; P=0.002).

Conclusions: The risk of disease progression was higher among patients with MDS in whom persistent disease-associated mutations were detected in the bone marrow 30 days after transplantation than among those in whom these mutations were not detected. (Funded by the Leukemia and Lymphoma Society and others.).

Figure 1.. Distribution of Mutations before Allogeneic Hematopoietic Stem-Cell Transplantation in Patients with and Patients without Disease Progression.

Shown is the distribution of mutations in genes and pathways of interest detected by means of enhanced exome sequencing at initial sampling and grouped according to patients with and without disease progression after transplantation. PTPs denotes protein tyro-sine phosphatases, Ser–Thr serine–threonine, and Tyr tyrosine.

Figure 2.. Decreases in Variant Allele Frequencies after Allogeneic Hematopoietic Stem-Cell Transplantation in Patients with and Patients without Disease Progression.

Shown is the maximum variant allele frequency (VAF) detected per patient as measured by means of error-corrected sequencing at initial sampling and at day 30 and day 100 after transplantation in patients with no disease progression (green, Panels A and B) and with disease progression (orange, Panels C and D). Plots are further divided according to pretransplantation conditioning regimen (reduced-intensity conditioning in Panels A and C and myeloablative conditioning in Panels B and D). Shading represents the range of observed values (first two quartiles shown). The inset plots show the interval in the VAF from 0% to 3%; the bold line represents the median value of the maximum VAF observed in each patient. The numbers of patients with samples sequenced at each time point are indicated.

Figure 3.. Association of Mutation Clearance with Outcomes.

The VAF on day 30 after transplantation was determined with the use of error-corrected sequencing interrogating single-nucleotide variant mutations identified by enhanced exome sequencing of samples before transplantation. Patients are grouped according to the presence of positive (+) or negative (−) results for at least one mutation VAF of at least 0.5% (red lines) or all VAFs less than 0.5% (blue lines) and according to whether the patient received a reduced-intensity conditioning regimen (RIC, solid lines) or myeloablative conditioning (MAC, dashed lines). The rates of disease progression (Panel A) and disease progression or death (Panel B) are shown.

Figure 4.. Association of Outcomes with Mutation Clearance Determined with the Use of a 40-Gene Panel.

Only the VAFs of 40 genes recurrently mutated in myeloid cancers were used to assess mutation clearance at day 30 after transplantation. VAFs were determined with the use of error-corrected sequencing interrogating single-nucleotide variants identified by enhanced exome sequences of samples before transplantation. Patients are grouped according to the presence of at least one VAF of at least 0.5% (red lines) or all VAFs less than 0.5% (blue lines) and according to whether they received a reduced-intensity conditioning regimen (RIC, solid lines) or myeloablative conditioning (MAC, dashed line). The rates of disease progression (Panel A) and disease progression or death (Panel B) are shown.