NPM1 Minimal Residual Disease Detection at Any Time by Clinical Next Generation Sequencing Predicts Poor Survival in Acute Myeloid Leukemia

Abstract

Abstract Introduction/Objective Acute Myeloid Leukemia (AML) is a deadly disease that accounts for 80% of adult leukemia cases and carries a 5-year survival rate of only 31.7%. Historically, prognosis hinged heavily on cytogenetic stratification, but more recently minimal residual disease (MRD) has emerged as a crucial prognostic marker. Flow cytometry, PCR, and NGS can all be employed for MRD detection, but each carries its own limitations. Though technically challenging, NGS has the advantage being able to simultaneously assay multiple mutations, thus providing for broader applicability. NPM1 is the most prevalently mutated gene in AML (25-35%). In this study, one of the largest of its kind, we investigate the feasibility and impact of NPM1 MRD detection by clinical NGS. Methods/Case Report IRB approval was obtained. We reviewed the medical record and clinical laboratory data sets from AML patients treated at Moffitt Cancer Center who had NPM1 status assessed by clinical NGS, Testing was performed at LabPMM (San Diego, CA). DNA was extracted, and NPM1 exon 12 was amplified. PCR products were sequenced on an Illumina MiSeq. The clinically reportable assay sensitivity was 5 x 10-5 though lower levels were detected on review of raw data. Kaplan-Meier analysis was conducted for overall survival assessment. Since patients often had multiple tests, we divide patients into those with NPM1+ at any time and NPM1 always negative. Results (if a Case Study enter NA) There was a total of 140 patients. Overall, 346 tests were conducted, with an average of 2.5 tests/patient. There were 85 patients (60%) who underwent serial testing. MRD+ patients (n=80) had a mean age of 66 years, while MRD- patients (n=60) had a mean age of 58 years. MRD+ patients exhibited a mean overall survival of 29.3 months versus 43.6 months for MRD- patients (p=0.005.) Conclusion Through our study encompassing a large patient cohort of 140 patients and nearly 350 testing data points, we confirm the feasibility and clinical utility of NPM1 MRD evaluation by NGS. The significantly poorer survival in patients who were MRD+ at any time during their disease provides a scientific rationale for serial NGS testing to enable risk stratification of NPM1+ AML patients.