Clinical Validation and Implementation of a Measurable Residual Disease Assay for NPM1 in Acute Myeloid Leukemia by Error-Corrected Next-Generation Sequencing

Lauren L. Ritterhouse*, Megan Parilla, Chao Jie Zhen, Michelle N. Wurst, Rutika Puranik, Candace M. Henderson, Neda Z. Joudeh, Madeline J. Hartley, Rishikesh Haridas, Pankhuri Wanjari, Larissa V. Furtado, Sabah Kadri, Jeremy P. Segal

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Background: Nucleophosmin 1 (NPM1) is one of the most commonly mutated genes in acute myeloid leukemia, with mutations observed in approximately 30% of all adult cases. The persistence of NPM1 mutations following chemotherapy is associated with a greater risk of relapse as well as a lower rate of survival, making NPM1 measurable residual disease (MRD) an informative clinical target. Methods: Herein, we have developed a straightforward unique molecular identifier (UMI)-based amplicon next-generation sequencing method for the detection of NPM1-mutated MRD that addresses some of the limitations present in other assays. Results: The NPM1 assay allowed for accurate counting of individual mutant and wild-type molecules down to 0.01% variant allelic frequency. In silico contamination experiments highlighted the ability of this UMI methodology to maximize specificity through dramatic reductions in sequencing/demultiplexing bleed-through error. Conclusion: Performance and clinical utility of the NPM1 MRD assay are established via both validation experiments and analyses of live performance over 1.5 years of routine clinical service.

Original languageEnglish (US)
Pages (from-to)791-802
Number of pages12
JournalMolecular Diagnosis and Therapy
Volume23
Issue number6
DOIs
StatePublished - Dec 1 2019

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Pharmacology

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