Clinical application of next-generation sequencing-based monitoring of minimal residual disease in childhood acute lymphoblastic leukemia

The emerging role of next-generation sequencing in minimal residual disease assessment in acute lymphoblastic leukemia: a systematic review of current literature

Background

Minimal residual disease (MRD) is a critical prognostic marker in acute lymphoblastic leukemia (ALL). The well studied and used MRD detection methods, multiparametric flow cytometry (MFC) and real-time quantitative polymerase chain reaction (qRT-PCR) for fusion genes and receptor gene rearrangements have significantly improved risk stratification, but have limitations in sensitivity and applicability. Next-generation sequencing (NGS) has emerged as a promising approach for MRD assessment, offering better sensitivity and the ability to track clonal evolution.

Objectives

This systematic review evaluates the clinical utility and prognostic value of NGS for MRD detection in ALL, comparing its performance with conventional methods and exploring its potential role in therapeutic guidance.

Methods

A comprehensive literature search was conducted across PubMed and Web of Science following PRISMA guidelines. Studies were included if they assessed MRD using NGS in ALL patients and provided data on sensitivity and prognostic value. Comparative analyses with MFC or qRT-PCR were considered. Data on end-of-induction MRD values, event-free survival (EFS), and overall survival (OS) were extracted.

Results

Thirteen studies met the inclusion criteria. NGS demonstrated superior sensitivity in detecting MRD-positive cases compared to MFC in patients classified as MRD-negative. Higher correlation was observed in MRD-positive cases than in MRD-negative cases. NGS-based MRD stratification correlated strongly with clinical outcomes, with patients achieving NGS-MRD negativity exhibiting superior EFS and OS rates. Additionally, NGS was highly predictive of relapse following hematopoietic stem cell transplantation and CAR-T cell therapy. The IGH rearrangements as the primary marker in NGS panels has demonstrated good prognostic value in B-ALL.

Conclusion

NGS represents a transformative tool for MRD monitoring in ALL, offering enhanced sensitivity and prognostic accuracy. Challenges such as high costs, complex bioinformatics analysis and the need for standardization remain. While its integration into clinical practice holds significant promise, further research is needed to establish standardized protocols, cost-effectiveness, and its optimal role in treatment decision-making. The combination of NGS with MFC may provide complementary advantages.

Presence of minimal residual disease determined by next-generation sequencing is not a reliable prognostic biomarker in children with acute lymphoblastic leukemia

The role of next-generation sequencing (NGS) for minimal residual disease (MRD) assessment in pediatric acute lymphoblastic leukemia (ALL) is still under consideration. Fifty pediatric patients were prospectively evaluated for specific clonal rearrangements of immunoglobulin and T-cell receptor genes using NGS analysis at diagnosis and on days 33 and 78 from therapy onset. The prognostic value or the NGS-MRD status was analyzed after a median follow-up of 4 years. All but one patient with negative NGS-MRD status on day 33 are in clinical remission. A total of 29 (58%) patients were NGS-MRD positive on day 33, of which 9 (18%) patients remained positive on day 78. However, only a small percentage of the patients with positive NGS-MRD status on day 33 and day 78 relapsed: 21% (6/29) and 33% (3/9), respectively. Positive NGS-MRD status is not a reliable prognostic biomarker in children with ALL and warrants careful consideration in disease stratification.

Methionine Synthase Reductase A66G Variant in Pediatric Acute Lymphoblastic Leukemia Patients

Background

Methionine synthase reductase, which is encoded by the methionine synthase reductase (MTRR) gene, plays a crucial role in the methylation reactions and the production of DNA and its epigenetic processes. There was a correlation between the MTRR (A66G) polymorphism and the likelihood of developing acute lymphoblastic leukemia (ALL). This study was carried out to investigate the correlation among pediatric ALL cases.

Methods

Within the participant population of this case-control study, there were 86 individuals who had been diagnosed with ALL, and there were also 150 healthy persons who acted as the control group. To determine the MTRR (A66G) polymorphism, DNA was first extracted and then observed through the use of real-time polymerase chain reaction.

Results

The results of the flow cytometry analysis showed that the prevalence of B-cell ALL (B-ALL) was much higher than that of T-cell ALL (T-ALL), which accounted for only 20 cases (23.3%). Upon comparing the hematological parameters of ALL subtypes in patients with T-ALL, it was discovered that there was a statistically significant higher mean total white blood count (P < 0.0005) and mean blast percentage (P = 0.050). Upon examination, it was discovered that both of these figures were much higher than the average. In accordance with the results of the molecular analysis, the occurrence of the MTRR homozygous GG genotype was found to be considerably lower in the patients' group (4.65%) than in the control group (20.67%). However, the MTRR homozygous AA and heterozygous AG were nearly similar in the two groups. The risk of acute lymphoblastic leukemia and MTRR genotypes, on the other hand, exhibited a correlation that was not statistically significant (P = 0.082).

Conclusions

The study's findings showed that among pediatric ALL patients, the MTRR A66G polymorphism was not linked to an increased risk of ALL.

Evaluation of next-generation sequencing for measurable residual disease monitoring in three major fusion transcript subtypes of B-precursor acute lymphoblastic leukaemia

The use of next-generation sequencing (NGS) for monitoring measurable residual disease (MRD) in acute lymphoblastic leukaemia (ALL) has been gaining traction. This study aimed to investigate the utility of NGS in MRD monitoring for the three major fusion transcript (FT) subtypes of B-precursor ALL (B-ALL). The MRD results for 104 bone marrow samples from 56 patients were analysed through NGS and real time quantitative reverse transcription PCR (RT-qPCR) for the three major FTs: BCR::ABL1, TCF3::PBX1, and ETV6::RUNX1. To validate the NGS approach, NGS-MRD was initially compared with allele-specific oligonucleotide-qPCR-MRD, and the coefficient of determination was good (R2=0.8158). A subsequent comparison of NGS-MRD with FT-MRD yielded a good coefficient of determination (R2=0.7690), but the coefficient varied by subtype. Specifically, the R2 was excellent for TCF3::PBX1 ALL (R2=0.9157), good for ETV6::RUNX1 ALL (R2=0.8606), and subpar for BCR::ABL1 ALL (R2=0.5763). The overall concordance between the two methods was 83.7%, and an excellent concordance rate of 95.8% was achieved for TCF3::PBX1 ALL. Major discordance, which was defined as a >1 log difference between discordant NGS-MRD and FT-MRD, occurred in 6.7% of the samples, with all but one sample being BCR::ABL1 ALL. Among the four non-transplanted patients with BCR::ABL1-MRD (+)/NGS-MRD (-), three did not relapse after long-term follow-up. Our finding indicates that NGS-MRD has a better prognostic impact than RT-qPCR-MRD in ETV6::RUNX1 and BCR::ABL1 ALL, whereas in TCF3::PBX1 ALL, both methods exhibit comparable efficacy.

Comparison of Measurable Residual Disease in Pediatric B-Lymphoblastic Leukemia Using Multiparametric Flow Cytometry and Next-Generation Sequencing

Measurable residual disease (MRD) testing, a standard procedure in B-lymphoblastic leukemia (B-ALL) diagnostics, is assessed using multiparametric flow cytometry (MFC) and next-generation sequencing (NGS) analysis of immunoglobulin gene rearrangements. We evaluated the concordance between eight-color, two-tube MFC-MRD the LymphoTrack NGS-MRD assays using 139 follow-up samples from 54 pediatric patients with B-ALL. We also assessed the effect of hemodilution in MFC-MRD assays. The MRD-concordance rate was 79.9% (N=111), with 25 (18.0%) and 3 (2.2%) samples testing positive only by NGS-MRD (MFC-NGS+MRD) and MFC-MRD (MFC+NGS-MRD), respectively. We found a significant correlation in MRD values from total nucleated cells between the two methods (r=0.736 [0.647-0.806], P<0.001). The median MRD value of MFC-NGS+MRD samples was estimated to be 0.0012% (0.0001%-0.0263%) using the NGS-MRD assays. Notably, 14.3% of MFC-NGS+MRD samples showed NGS-MRD values below the limit of detection in the MFC-MRD assays. The percentages of hematogones detected in MFC-MRD assays significantly differed between the discordant and concordant cases (P<0.001). MFC and NGS-MRD assays showed relatively high concordance and correlation in MRD assessment, whereas the NGS-MRD assay detected MRD more frequently than the MFC-MRD assay in pediatric B-ALL. Evaluating the hematogone percentages can aid in assessing the impact of sample hemodilution.

A spacer design strategy for CRISPR-Cas12f1 with single-nucleotide polymorphism mutation resolution capability and its application in the mutations diagnosis of pathogens

Infectious diseases remain a major global issue in public health. It is important to develop rapid, sensitive, and accurate diagnostic methods to detect pathogens and their mutations. Cas12f1 is an exceptionally compact RNA-guided nuclease and have the potential to fulfill the clinical needs. Based on the interaction between crRNA-SSDNA binary sequence and Cas12f1, here, we addressed the essential features that determine the recognition ability of CRISPR-Cas12f1 single-nucleotide polymorphism (SNP), such as the length of spacer region and the base pairing region that determines the trans-cleavage of ssDNA. A fine-tuning spacer design strategy is also proposed to enhance the SNP recognition capability of CRISPR-Cas12f1. The optimized spacer confers the Cas12f1 system a strong SNP identification capability for viral or bacterial drug-resistance mutations, with a specificity ratio ranging from 19.63 to 110.20 and an admirable sensitivity up to 100  copy/μL. Together, the spacer screening and CRISPR-Cas12f1 based SNP identification method, is sensitive and versatile, and will have a wide application prospect in pathogen DNA mutation diagnosis and other mutation profiling.