Next Generation Sequence Minimal Residual Disease (NGS-MRD) Predicts Event Free Survival (EFS) Irrespective of Hematopoietic Cell Transplantation (HCT) Conditioning Regimen, Graft Αβ T and B-Cell Depletion or Patient Weight Category 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 analysis 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). We evaluated baseline blast samples from 74 patients for dominant BCR/TCR rearrangements and to follow MRD by NGS. Dominant clones were identified in 100% of B-ALL patients, 96.8% (61/63) in BCR and 3.2% in TCR gamma. For T-ALL patients, clones 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 NGS-MRD from peripheral blood (PB) trended similarly (n=27, P=0.17, Figure 2). 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 (Figure 3) or chronic graft-vs-host-disease (GVHD) in NGS-MRD- patients. 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 in positive and negative predictive power. Αβ-T and B-cell 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 similar 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 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 was converted to a percentile through population norms for age, gender, and defined thresholds published by the Centers for Disease Control and prevention (CDC). Lean patients (