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Teixeira, A.; Carreira, L.; Abalde-Cela, S.; Sampaio-Marques, B.; Areias, A.C.; Ludovico, P.; Diéguez, L. Techniques for Monitoring of MRD in AML. Encyclopedia. Available online: https://encyclopedia.pub/entry/42485 (accessed on 14 December 2025).
Teixeira A, Carreira L, Abalde-Cela S, Sampaio-Marques B, Areias AC, Ludovico P, et al. Techniques for Monitoring of MRD in AML. Encyclopedia. Available at: https://encyclopedia.pub/entry/42485. Accessed December 14, 2025.
Teixeira, Alexandra, Luís Carreira, Sara Abalde-Cela, Belém Sampaio-Marques, Anabela C. Areias, Paula Ludovico, Lorena Diéguez. "Techniques for Monitoring of MRD in AML" Encyclopedia, https://encyclopedia.pub/entry/42485 (accessed December 14, 2025).
Teixeira, A., Carreira, L., Abalde-Cela, S., Sampaio-Marques, B., Areias, A.C., Ludovico, P., & Diéguez, L. (2023, March 23). Techniques for Monitoring of MRD in AML. In Encyclopedia. https://encyclopedia.pub/entry/42485
Teixeira, Alexandra, et al. "Techniques for Monitoring of MRD in AML." Encyclopedia. Web. 23 March, 2023.
Techniques for Monitoring of MRD in AML
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This entry is adapted from the peer-reviewed paper 10.3390/cancers15051362

After diagnosis of acute myeloid leukemia (AML), patients undergo chemotherapy, achieving complete remission (CR) in the majority of cases. However, some residual leukemic cells (up to 1010 to 1012 cells) can remain undetectable, causing a high percentage of patients to relapse. This condition is conventionally referred to as minimal residual disease, although more recently this nomenclature has been replaced by measurable residual disease (MRD). The term “measurable” was proposed to indicate some contexts where Leukemic Stem Cell (LSC) levels are detectable by modern technologies that have a high sensitivity. MRD monitoring in AML is performed routinely in clinical practice since it is a strong indicator of relapse. Besides, MRD can also have implications in the planning and personalization of treatment, when assessed in conjunction with other well-established clinical, cytogenetic, and molecular data. Furthermore, it has been shown that when MRD detection is successfully performed at an early stage, it results in improved prognosis, disease management, and patient outcome. Some of the currently used techniques for MRD assessment in AML are multiparametric flow cytometry (MFC) and molecular-based techniques, such as reverse transcription polymerase chain reaction (RT-PCR) and next-generation sequencing (NGS), further described below.

acute myeloid leukemia (AML) measurable residual disease (MRD) microfluidics

1. Multiparametric Flow Cytometry (MFC)

MFC is one of the most common techniques used for the diagnosis, classification, and prognosis of AML disease. This technique identifies a signature of aberrant expression of antigens present on AML cells, through specific panels of fluorochrome-labeled monoclonal antibodies [1]. Recent advances, based on the development of multicolor panels (>8 colors), brought the levels of sensitivity of cytometric analysis closer to those obtained by molecular biology techniques [2][3]. Thus, MRD analysis based on MCF presents moderate sensitivity, with a LOD of 1:10−3 up to 1:10−4 (1 leukemic cell in 10,000 to 10,000 WBCs), which is dependent on the number of cells analyzed, the gating strategy, and the number of antibody markers used [4][5][6]. The main advantage of MCF over other techniques is the ability to characterize millions of cells in a short period of time, while distinguishing viable cells from debris and dead cells [7][8][9]. Furthermore, it has the advantage of being applicable to the vast majority of AML patients, unlike other techniques that focus on the genetic and/or molecular signature [6].
MRD condition can be monitored in AML patients by MFC, assessing the abnormal expression of immunophenotypic markers that provide the distinction of the leukemic cells, also called leukemia-associated immunophenotypes (LAIPs)  [10][11]. Conventionally, for the detection of LAIPs, several markers can be used, including CD34, CD117, CD45, CD33, CD13, CD56, CD7, HLA-DR (for MRD), among others [4]. Much work has been completed to improve this strategy and its application in MRD. In most of the cases, the improvements consist of the combination of several antibodies with different fluorophores (at least eight) to detect more than one LAIP at a time, improving the diagnostic performance [12][13].
Several other studies were conducted to understand the ability and efficiency of cytometric analysis to detect MRD. For example, a study with 451 BM samples from adult AML patients assessed the clinical utility of MRD detection, demonstrating that MFC is useful for outcome prediction and guidance of post-remission in AML [14].
The biggest drawback of this technique is the requirement of significant technical expertise and the intervention of an interpreting pathologist. The future use of artificial intelligence to reduce potential bias and/or human interpretive errors can bring accurate interpretations of the results. The low sensitivity and the high change of the aberrant immunophenotype during disease progression makes the assessment of MRD more difficult, leading to a high rate of false negatives and limiting the detection of the different aberrant markers.

2. Molecular-Based Techniques

Molecular techniques are used to assess the presence of MRD by analyzing well-known AML mutations [4][5]. The most common markers used to monitor MRD are NPM1 insertion, CFB-MYH11, AML1-ETO, and PML-RARA (chimeric fusion genes) [15]. NPM1 is one of the most prevalent mutations in AML (present in 25–35% of patients) and is reported as a definitive leukemia-founder mutation that has already been validated as an optimal and reliable MRD marker [16][17]. Recent studies are focused on introducing/validating new markers for MRD monitoring. For example, many studies are now focused on the relevance of IDH mutations [4]. IDH1 and IDH2 mutations have been shown to be prevalent in AML (occurring in ~20% of cases), but there are still conflicting data, whether they represent pre-leukemic mutations or dominant clonal mutations, hence their value in monitoring MRD is not yet well established [2][16][18][19]. Moreover, NPM1 is frequently one of the references for the studies involving IDH mutations [20][21].
Furthermore, the prognostic significance of combined mutations, such as NPM1, FLT3, DNMT3A, and IDH is still unclear. However, recent studies state that some combinations may have an impact on the risk of relapse and overall survival of AML patients compared with other specific combinations [22][23][24]. Thus, in AML disease, and even in the MRD condition, it is crucial to use reliable and sensitive molecular techniques to detect these mutations, even when present in small amounts, in order to have a better understanding of their prognostic value.

2.1. Reverse Transcription Polymerase Chain Reaction (RT-PCR)

In AML, the development of RT-PCR has been crucial to detect residual elements conventionally characterized by molecularly cloned chromosome translocations [25][26]. The use of RT-PCR enables the detection of the fusion genes RUNX1-RUNX1T1 and CBFB-MYH11 [27] as well as PML-RARA [28][29] and mutated-NPM1 [30][31], important for the sensitive detection and quantification of MRD in AML [2][32]. In fact, in the case of CBF fusion transcripts (RUNX1-RUNX1T1 and CBFB-MYH11), some studies in peripheral blood (PB) or bone marrow (BM) have demonstrated the prognostic value of detection and quantification of MRD at specific time points allowing the identification of patients with a high risk of relapse [27][33]. In addition, several studies have investigated the clinical implications of monitoring NPM1 and its association with relapse and survival rates [34][35]. In the study performed by Ivey et al., using BM and PB of the AML patients, the presence of NPM1-mutated transcripts after the second chemotherapy cycle was associated with a significantly higher relapse risk and poorer survival rates, independent of other known prognostic factors [34].
Given the high specificity and sensitivity for LSCs, the decreased risk of contamination and better evaluation of RNA quality, the technique of RT-PCR has been widely implemented for routine patient care [5]. However, the detection of MRD based on RT-PCR or PCR is currently limited to around 50% of patients, since not all patients carry the fusion transcript RUNX1-RUNX1T1 (characteristic of t[8;21]), CBFB-MYH11 [inv 16] or t[16;16]), or NPM1 mutations [36]. The optimized RT-PCR assays presents a limit of detection (LOD) of 10−4 to 10−6, and is therefore more sensitive or equal than other technologies used, such as MFC (range 1:10−3 up to 1:10−4 ) [2][37][38][39].
As is the case with any other technique, there are some limitations of RT-PCR-based MRD tests, namely their dependence on specific mutations, requiring individual standard reference curves based on serial dilutions of targets, intensive labour, expertise, cost, time-consuming, and computationally demanding work [3][40].

2.2. Next-Generation Sequencing (NGS)

Next-generation sequencing (NGS) refers to the deep, high-throughput, in-parallel DNA sequencing technologies that were developed in the decades after 1977, when the Sanger DNA sequencing method was developed. Unlike Sanger sequencing, NGS procedures provide a massive parallel and extremely high-throughput analysis (millions to billions of nucleotides) of multiple samples, bringing much faster results (due to multiplexing), and at a lower cost than individual testing [41]. Therefore, NGS is a tool that easily assesses genomic, transcriptomic, and epigenomic features [42]. More specifically, in the AML context, NGS has extreme relevance for diagnosis, due to the high clonal heterogeneity characteristic of this disease [43]. It provides information about the different AML mutations present in a patient, providing more information and allowing the design of personalized therapies, which will ultimately result in a better prognosis of remission and less cases of relapse [3]. It was already described that for patients in CR, the estimated percentage of the MRD measured by NGS was much greater than of aberrant blasts detected by MFC [44].
This technology has also revealed a set of mutations in rare mutant cells and gene sequences, as well as the discovery of genetic alterations that occur between diagnosis and relapse times [45]. In a study with a cohort of 482 patients, at least one mutation was detected in 430 patients (89.2%) showing the broad clinical application of targeted NGS [46]. Additionally, NGS showed a significant additive prognostic value compared to flow cytometry for the detection of MRD [46].
Recently, Alonso et al. tested a 19-gene AML-targeted NGS in a small cohort of 162 patients and showed that well-defined NGS panels are reliable in guiding clinical decisions by the current standards. Results had a 100% correlation with conventional molecular biology techniques, and all patients were successfully classified according to 2016 WHO classification systems (2016 WHO diagnostic categories, 2017 European LeukemiaNet, and Genomic classification) [47]. NGS was also explored in the context of allogeneic hematopoietic cell transplantation (alloHCT). For example, Thol et al. published a clinical study with a cohort of more than one hundred patients, demonstrating that MRD detection utilizing NGS before alloHCT is highly predictive of relapse and survival, and can therefore improve patient management [48]. It is worth noting that similar results were obtained from both BM and PB samples, demonstrating the usefulness of using less invasive body fluids [48]. Thus, through the molecular characterization of AML cells, NGS promotes a personalized and precise method for the assessment of MRD, since can reach a sensitivity of 10−4 to 10−5 [95, 132]. However, the widespread use of NGS has been limited due to its high cost, and the expertise required for the data analysis and interpretation [49][50]. Furthermore, other drawbacks of this technique are the non-standardization of the assay, the high variance of sensitivity across different platforms, and a long waiting time for the result analysis.
In summary, MRD has been shown to be an important and independent prognostic factor and predictor of relapse in AML, and also plays a crucial role in the design of personalized treatment strategies. However, when values of cells are lower than 10−5, it is generally more challenging to be detectable by the diagnostic procedures used in clinical settings. Thus, the development of novel techniques, such as microfluidics and surface-enhanced Raman scattering spectroscopy, has the potential to enable a more reliable and satisfactory detection of MRD and CR as well as the stratification of patients into different subtypes. Yet, the sensitivity of these techniques is still being optimized, and their implementation in clinical routine is pending. Despite the technological challenges, it remains crucial to develop new technologies for MRD detection and quantification that are more affordable, faster, and offer higher accuracy and sensitivity.

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