Development and Application of a Novel Digital Array PCR for Acute Myeloid Leukemia (AML)

Minimal residual disease (MRD) refers to the presence of cancer cells that are present after therapy and not otherwise detectable by clinical findings, including standard clinical assays and radiographic imaging. Detection of MRD before it becomes clinically detectable provides an opportunity to intervene and optimize treatment, with the possibility of curing more patients. For the above reasons, detection of MRD through evaluation of blood-based biomarkers represents a promising area to improve clinical outcomes in patients with a variety of solid and liquid tumors. In liquid tumors such as acute lymphoblastic leukemia (ALL), MRD assessment is already part of routine clinical practice. MRD is strongly correlated with risk for relapse in ALL, and MRD assessment during and after induction therapy is one of the most informative prognostic markers available. For these reasons the National Comprehensive Cancer Network (NCCN) Guidelines Version 2.2020, indicate that MRD assessment is an "essential component of patient evaluation over the course of sequential therapy" for ALL, and there are >250 references to MRD in the pediatric and adult ALL NCCN Guidelines. In AML, MRD assessment is routinely used in academic medical centers. MRD is also strongly associated with risk of relapse in AML, and MRD status is a strong independent predictor of overall survival after completion of therapy. The AML NCCN Guidelines Version 3.2020, indicate the "undeniable need for monitoring," but further refinements are needed to make MRD monitoring in patients with AML more reliable. In this study we will apply a new highly multiplexed digital PCR technology, digital array PCR (daPCR), for evaluation of MRD in AML that will improve MRD assay reliability while reducing costs and time-to-results.

Currently, methods for MRD assessment in AML include flow cytometry for the detection of aberrant immunophenotypes as well as molecular PCR- and next generation sequencing (NGS)-based assays for detecting recurrent AML-associated genetic abnormalities. Both flow and molecular MRD assessment have much higher sensitivity than morphologic assessment alone, with flow cytometry having a lower limit of detection between 10-4 to 10-5 and molecular methods between 10-3 for NGS methods to 10-5 for PCR-based methods. Each of the current methods have major limitations that prevent broader adoption in AML. Standard NGS-based methods have insufficient sensitivity and high costs. Flow cytometry is a technically difficult method that is challenging to standardize, and a subset of AML cases do not have sufficient evaluable surface markers to allow detection. PCR-based methods can be very sensitive, but each assay currently targets a single recurrent genetic abnormality (e.g., PML/RARA fusion in acute promyelocytic leukemia), and many AML cases do not have genetic abnormalities that are targeted by current clinical assays. In contrast, the daPCR technology we propose to apply in this study provides a high throughput, multiplexed platform (24-96 variants) with unprecedented dynamic range (>108), high ease of use, low cost and rapid turnaround time. Because the daPCR can simultaneously probe for multiple variants, we estimate that our initial assay will have the potential to detect and quantify the abundance of at least one AML associated mutation in ~80% of AML samples. This technological advance would provide a real-world solution to enable frequent, deep monitoring of therapeutic response in patients with AML.