Minimal Residual Disease Detection in Adults with Acute Lymphoblastic Leukemia By Next Generation Sequencing: Impact on Clinical Outcomes

Introduction:

Measuring minimal residual disease (MRD) is an essential component of directing treatment and predicting outcomes in patients with acute lymphoblastic leukemia (ALL). Current methods used to detect MRD in patients with ALL include multiparameter flow cytometry (Flow), allele-specific and mutation-specific quantitative polymerase chain reaction, and more recently next-generation sequencing (NGS)-based methods. While flow cytometry remains standard of care for ALL MRD evaluation in most institutions, quantification of MRD with higher sensitivity assays could potentially improve early detection of clinical relapse resulting in better survival outcomes. The clonoSEQ NGS-based platform (Adaptive Biotechnologies, Seattle WA) tracks tumor specific V(D)J rearrangements in lymphoid malignancies and can detect MRD at less than 10-6 (0.0001%) level. Here we describe a real-world practice-based comparison of the impact of MRD testing by clonoSEQ and Flow on clinical outcomes in ALL.

Methods:

We retrospectively evaluated 45 adult patients with confirmed ALL admitted to the Norris Cancer Center (University of Southern California) between November 2017 and June 2020. In all patients, the presence/absence [(+)/(-)] of MRD was evaluated on bone marrow aspirates by both the clonoSEQ assay (clonoSEQ MRD) and by a flow cytometry-based COG ALL MRD assay (Flow). Descriptive statistics were used to characterize the cohort. The Fisher's exact test was used to describe groups with categorical outcomes. A p-value of < 0.05 was considered statistically significant.

Results:

Forty-five patients included in our study were aged 20 to 67 (median age 38), with 67% (30/45) males, 82% diagnosed with B-ALL (13% Ph-positive, 36% Ph-like, 51% Ph- negative),13% with T-ALL, and 5% with mixed-phenotype leukemia. Three patients were excluded from the analysis due to insufficient sampling. Among 38% (16/42) of patients with original Flow(-)/clonoSEQ(+) MRD, 31% (5/16) eventually became Flow(+) and later clinically relapsed, and 19% (3/16) received blinatumomab as a bridge to allogeneic hematopoietic cell transplantation (allo-HCT) and 2 remain in clinical remission (CR), 1 died from other medical complications.

11/14 Ph-like patients were analyzed post-induction. Post-induction clonoSEQ MRD status was used to direct these Ph-like B-ALL patients to allo-HCT (if positive, 8/11 patients) or to continue chemotherapy (if negative, 3/11 patients). Among 8/11 patients who underwent allo-HCT, 3/8 relapsed, while 5/8 remain in CR. All 3/11 patients who continued chemotherapy without allo-HCT, based on the clonoSEQ(-) MRD, remain in CR.

Comparative post-induction clonoSEQ/Flow MRD data was available for 12 patients. Among these, 25% (3/12) were Flow(+)/clonoSEQ(+), 25% (3/12) were Flow(-)/clonoSEQ(+), and 50% (6/12) were Flow(-)/clonoSEQ(-), with the 12-month disease-free survival (DFS) rates of 33%, 100%, and 50%, respectively.

Conclusions:

Adult ALL is commonly associated with high relapse rates, often requiring therapy intensification with other agents or allo-HCT. We observed a trend towards a lower relapse rate and better outcomes with early treatment with blinatumomab and/or allo-HCT. Patients with post-induction clonoSEQ(-) MRD, who continued chemotherapy without allo-HCT or immunotherapy maintained molecular CR for > 1 year after diagnosis. Our data supports the clinical benefit of early molecular MRD evaluation with clonoSEQ to guide subsequent additional treatment (to reduce/eliminate MRD) or defer allo-HCT in MRD(-) patients. It is also important to note that a substantial subset of our unique adult population had high risk disease, whereas previous studies have focused on pediatric populations. Due to the small number of patients included, this analysis was mainly descriptive, and a larger patient cohort would be needed to better evaluate the clinical impact of MRD testing in adult ALL.