Minimal Residual Disease by Next-Generation Sequencing: Pros and Cons

2016 ◽  
Vol 36 ◽  
pp. e425-e430 ◽  
Author(s):  
Herve Avet-Loiseau
Keyword(s):  
Next Generation Sequencing ◽  
Minimal Residual Disease ◽  
Residual Disease ◽  
Next Generation ◽  
Pros And Cons ◽  
Generation Sequencing ◽  
Minimal Residual

scholarly journals Assessment of Minimal Residual Disease by Next Generation Sequencing in Peripheral Blood as a Complementary Tool for Personalized Transplant Monitoring in Myeloid Neoplasms

2020 ◽  
Vol 9 (12) ◽  
pp. 3818
Author(s):  
Paula Aguirre-Ruiz ◽  
Beñat Ariceta ◽  
María Cruz Viguria ◽  
María Teresa Zudaire ◽  
Zuriñe Blasco-Iturri ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Minimal Residual Disease ◽  
Peripheral Blood ◽  
Residual Disease ◽  
Mixed Chimerism ◽  
Clinical Relapse ◽  
Next Generation ◽  
Myeloid Neoplasms ◽  
Generation Sequencing ◽  
Minimal Residual

Patients with myeloid neoplasms who relapsed after allogenic hematopoietic stem cell transplant (HSCT) have poor prognosis. Monitoring of chimerism and specific molecular markers as a surrogate measure of relapse is not always helpful; therefore, improved systems to detect early relapse are needed. We hypothesized that the use of next generation sequencing (NGS) could be a suitable approach for personalized follow-up post-HSCT. To validate our hypothesis, we analyzed by NGS, a retrospective set of peripheral blood (PB) DNA samples previously evaluated by high-sensitive quantitative PCR analysis using insertion/deletion polymorphisms (indel-qPCR) chimerism engraftment. Post-HCST allelic burdens assessed by NGS and chimerism status showed a similar time-course pattern. At time of clinical relapse in 8/12 patients, we detected positive NGS-based minimal residual disease (NGS-MRD). Importantly, in 6/8 patients, we were able to detect NGS-MRD at time points collected prior to clinical relapse. We also confirmed the disappearance of post-HCST allelic burden in non-relapsed patients, indicating true clinical specificity. This study highlights the clinical utility of NGS-based post-HCST monitoring in myeloid neoplasia as a complementary specific analysis to high-sensitive engraftment testing. Overall, NGS-MRD testing in PB is widely applicable for the evaluation of patients following HSCT and highly valuable to personalized early treatment intervention when mixed chimerism is detected.

scholarly journals Detection of Fusion Genes to Determine Minimal Residual Disease in Leukemia Using Next-Generation Sequencing

2020 ◽  
Vol 66 (8) ◽  
pp. 1084-1092 ◽  
Author(s):  
Eddy N de Boer ◽  
Lennart F Johansson ◽  
Kim de Lange ◽  
Anneke G Bosga-Brouwer ◽  
Eva van den Berg ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Minimal Residual Disease ◽  
Residual Disease ◽  
Leukemic Cells ◽  
Fusion Genes ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Genetic Aberrations ◽  
Generation Sequencing ◽  
Minimal Residual

Abstract Background Measuring minimal residual disease (MRD), the persistence of leukemic cells after treatment, is important for monitoring leukemia recurrence. The current methods for monitoring MRD are flow cytometry, to assess aberrant immune phenotypes, and digital droplet PCR (ddPCR), to target genetic aberrations such as single-nucleotide variants and gene fusions. We present the performance of an RNA-based next-generation sequencing (NGS) method for MRD gene fusion detection compared with ddPCR. This method may have advantages, including the capacity to analyze different genetic aberrations and patients in 1 experiment. In particular, detection at the RNA level may be highly sensitive if the genetic aberration is highly expressed. Methods We designed a probe-based NGS panel targeting the breakpoints of 11 fusion genes previously identified in clinical patients and 2 fusion genes present in cell lines. Blocking probes were added to prevent nonspecific enrichment. Each patient RNA sample was diluted in background RNA, depleted for rRNA and globin mRNA, converted to cDNA, and prepared for sequencing. Unique sequence reads, identified by unique molecular identifiers, were aligned directly to reference transcripts. The same patient and cell-line samples were also analyzed with ddPCR for direct comparison. Results Our NGS method reached a maximum sensitivity of 1 aberrant cell in 10 000 cells and was mostly within a factor of 10 compared with ddPCR. Conclusions Our detection limit was below the threshold of 1:1000 recommended by European Leukemia Net. Further optimizations are easy to implement and are expected to boost the sensitivity of our method to diagnostically obtained ddPCR thresholds.

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