DROPLET DIGITAL PCR FOR ONCOGENIC KMT2AFUSION DETECTION

Acute myeloid leukemia (AML) is an aggressive blood cancer diagnosed in ∼120,000 individuals worldwide each year. During treatment for AML, detecting residual disease is essential for prognostication and treatment decision-making. Currently, methods for detecting residual AML are limited to identifying ∼1:100-1:1,000 leukemic cells (morphology, DNA sequencing) or difficult to implement (flow cytometry). AML arising after chemotherapy or radiation exposure is termed therapy-related AML (t-AML) and is exceptionally aggressive and treatment resistant. T-AML is often driven by oncogenic fusions resulting from prior treatments that introduce double-strand DNA breaks. The most common t-AML-associated translocations affect the histone-lysine N-methyltransferase 2A (KMT2A). There are at least 80 known KMT2Afusion partners, but about 80% of fusions involve just five partners — AF9, AF6, AF4, ELLand ENL. Here we present a novel droplet digital PCR (ddPCR) assay targeting the most common KMT2A-rearrangements to enable detection of rare AML cells harboring these fusions. This assay was benchmarked in cells lines and patient samples harboring oncogenic KMT2Afusions and demonstrated a limit of detection of approximately 1:1,000,000 cells. Future application of this assay could improve disease detection and treatment decision-making for t-AML patients with KMT2Afusions and detect pre-malignant oncogenic fusions in at-risk individuals after chemotherapy exposure.