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Comparison of RNA‐ and DNA‐based methods for measurable residual disease analysis in NPM1 ‐mutated acute myeloid leukemia
Author(s) -
Pettersson Louise,
Johansson Alm Sofie,
Almstedt Alvar,
Chen Yilun,
Orrsjö Gustav,
ShahBarkhordar Giti,
Zhou Li,
Kotarsky Heike,
Vidovic Karina,
Asp Julia,
Lazarevic Vladimir,
Saal Lao H.,
Fogelstrand Linda,
Ehinger Mats
Publication year - 2021
Publication title -
international journal of laboratory hematology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.705
H-Index - 55
eISSN - 1751-553X
pISSN - 1751-5521
DOI - 10.1111/ijlh.13608
Subject(s) - npm1 , digital polymerase chain reaction , minimal residual disease , myeloid leukemia , leukemia , dna , real time polymerase chain reaction , biology , polymerase chain reaction , cancer research , bone marrow , genomic dna , microbiology and biotechnology , immunology , gene , genetics , karyotype , chromosome
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.