Next Generation Sequence Minimal Residual Disease (NGS-MRD) Predicts Outstanding Event Free Survival (EFS) Regardless of Hematopoietic Cell Transplantation (HCT) Preparative Approach or Graft Alpha/Beta Depletion in Children with Acute Lymphoblastic Leukemia (ALL)

MRD detected by flow cytometry (FC) or PCR has been associated with key outcomes after HCT for ALL. In a prospective multicenter trial (NCT02646839; Pediatric Blood and Marrow Transplant Consortium [PBMTC] ONC1401), we performed a planned sub-study of NGS-MRD to predict outcomes pre- and post-HCT for ALL patients (n=57, median follow-up 523 [range 58-1198] days post-HCT). In addition, we performed analyses of relevant clinical factors to assess their relationship to EFS. The larger trial studying the role of KIR favorable haploidentical vs. other transplantation approaches for children diagnosed with ALL, acute myeloid leukemia and myelodysplastic syndrome will be reported separately.

We evaluated baseline blast samples from 74 patients for dominant BCR/TCR rearrangements and to follow MRD by NGS. Dominant rearrangements were identified in 100% of B-ALL patients, 96.8% (61/63) in BCR and 3.2% in TCR gamma. For T-ALL patients, rearrangements were identified in 62.7% (7/11), with the remaining 37.3% being polyclonal. Patients proceeded to HCT only if they were in morphological remission.

Pre-HCT NGS-MRD from bone marrow (BM) was highly predictive of EFS (n=29 P=0.027, Figure 1) and although NGS-MRD from peripheral blood (PB) did not reach statistical significance due to decreased sample size (n=27, P=0.17, Figure 2), it trended similarly. In BM NGS-MRD negative patients, relapse was exceptionally low with all events due to transplant related mortality (TRM). There did not appear to be a benefit of acute graft-vs-host-disease (aGVHD) in NGS-MRD- patients (Figure 3) or chronic (c)GVHD, but sample size was a limitation.

Pre-HCT, 10% of the BM samples were MRD+ by FC, but 35% were MRD+ by NGS. Direct comparison of NGS-MRD in BM and PB with FC MRD pre- and post-HCT showed improvements positive and negative predictive power (data not shown).

Alpha/beta depleted haploidentical grafts had similar outcomes to other stem cell sources (Figure 4) with decreased incidence of GVHD [aGVHD > grade 2: n=1 (3.3%) and extensive cGVHD: n=1(3.3%)]. TBI (total body irradiation) based myeloablative conditioning (TBI/TT [Thiotepa]/CY [Cyclophosphamide], TBI/CY, or TBI/VP16; ± anti-thymocyte globulin [ATG]) and non-TBI reduced toxicity (Flu [Fludarabine]/Mel [Melphalan]/TT; ± ATG) had identical EFS (P= 0.31). TRM was very low 8.7%(n=5) in this population (n=57)) and rescue of relapse was high for the duration of follow up to date, resulting in similar OS for MRD- vs. MRD+ patients (P= 0.15), likely due to rescue with cell/immunotherapy.

We next examined the interaction of obesity, using body mass index (BMI) based on height/weight pre-HCT, in the context of NGS-MRD on EFS. The BMI score was converted to a percentile through population norms for age and gender and defined thresholds published by the Centers for Disease Control and prevention (CDC). Lean patients (< 85th percentile [%]) overall had better survival than the overweight (OW)/obese (85-94%/≥95%) (Figure 5: P=0.016). But among the lean patients, NGS-MRD still had an effect, with NGS-MRD+ patients had poorer EFS. Same was observed with the OW/obese group, where being NGS MRD+ adds further reduction in survival. Overweight/Obese patients who were pre-HCT MRD- had survival closer to the lean/MRD+ patients. We observed decreased EFS by weight category and NGS-MRD (Figure 6: P= 0.02).

In conclusion, NGS-MRD was highly predictive for EFS regardless of HCT preparative approach or graft Alpha/Beta Depletion. NGS improved predictive power for MRD positivity compared to FC. NGS was able identify rearrangements suitable for MRD tracking in all B-ALL and in most of T-ALL samples. In BM NGS-MRD negative patients, relapse was exceptionally low. There did not appear to be a benefit of aGVHD or cGVHD in NGS-MRD- patients. Alpha/beta depleted haploidentical grafts had similar outcomes to other stem cell sources with decreased incidence of severe GVHD. We observed decreased EFS by weight category and NGS-MRD. Lean patients had better survival, after HCT, than OW/Obese patients. But among the lean patients, NGS-MRD+ patients had poorer EFS.

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