Comparison of RNA- and DNA-based methods for measurable residual disease analysis in NPM1-mutated acute myeloid leukemia.

Publisher: Blackwell Scientific Publications Country of Publication: England NLM ID: 101300213 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1751-553X (Electronic) Linking ISSN: 17515521 NLM ISO Abbreviation: Int J Lab Hematol Subsets: MEDLINE

Original Publication: Oxford : Blackwell Scientific Publications, c2007-

Mutation* ; Real-Time Polymerase Chain Reaction* ; Reverse Transcriptase Polymerase Chain Reaction*; DNA, Neoplasm/*blood ; Leukemia, Myeloid, Acute/*blood ; Nuclear Proteins/*metabolism ; RNA, Neoplasm/*blood; Adult ; Aged ; DNA, Neoplasm/genetics ; Female ; Humans ; Leukemia, Myeloid, Acute/genetics ; Male ; Middle Aged ; Neoplasm, Residual/blood ; Nuclear Proteins/genetics ; Nucleophosmin ; RNA, Neoplasm/genetics

Introduction: Reverse transcriptase quantitative PCR (RT-qPCR) is considered the method of choice for measurable residual disease (MRD) assessment in NPM1-mutated acute myeloid leukemia (AML). MRD can also be determined with DNA-based methods offering certain advantages. We here compared the DNA-based methods quantitative PCR (qPCR), droplet digital PCR (ddPCR), and targeted deep sequencing (deep seq) with RT-qPCR.
Methods: Of 110 follow-up samples from 30 patients with NPM1-mutated AML were analyzed by qPCR, ddPCR, deep seq, and RT-qPCR. To select DNA MRD cutoffs for bone marrow, we performed receiver operating characteristic analyses for each DNA method using prognostically relevant RT-qPCR cutoffs.
Results: The DNA-based methods showed strong intermethod correlation, but were less sensitive than RT-qPCR. A bone marrow cutoff at 0.1% leukemic DNA for qPCR or 0.05% variant allele frequency for ddPCR and deep seq offered optimal sensitivity and specificity with respect to 3 log 10 reduction of NPM1 transcripts and/or 2% mutant NPM1/ABL. With these cutoffs, MRD results agreed in 95% (191/201) of the analyses. Although more sensitive, RT-qPCR failed to detect leukemic signals in 10% of samples with detectable leukemic DNA.
Conclusion: DNA-based MRD techniques may complement RT-qPCR for assessment of residual leukemia. DNA-based methods offer high positive and negative predictive values with respect to residual leukemic NPM1 transcripts at levels of importance for response to treatment. However, moving to DNA-based MRD methods will miss a proportion of patients with residual leukemic RNA, but on the other hand some MRD samples with detectable leukemic DNA can be devoid of measurable leukemic RNA.
(© 2021 The Authors. International Journal of Laboratory Hematology published by John Wiley & Sons Ltd.)

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ALFGBG-720681 the Swedish Government and the County Councils; Skåne University Hospital Research; Region Skåne UFo; Västra Götalandsregionen FoU; Swedish Cancer Society; Swedish Research Council; Lund University Medical Faculty; the Olle Engkvist Foundation; Wilhelm och Martina Lundgrens Vetenskapsfond; the Regional Scientific Council of Halland; the Sahlgrenska University Hospital

Keywords: NPM1; RT-qPCR; deep sequencing; digital PCR; measurable residual disease; qPCR

0 (DNA, Neoplasm)
0 (NPM1 protein, human)
0 (Nuclear Proteins)
0 (RNA, Neoplasm)
117896-08-9 (Nucleophosmin)

Date Created: 20210530 Date Completed: 20210817 Latest Revision: 20211204

20221213

10.1111/ijlh.13608

34053184