The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL

Kotrová, Michaela; Mužíková, Kateřina; Mejstříková, Ester; Nováková, Michaela; Bakardjieva-Mihaylova, Violeta; Fišer, Karel; Stuchlý, Jan; Giraud, Mathieu; Salson, Mikaël; Pott, Christiane; Brüggemann, Monika; Füllgrabe, Marc; Starý, Jan; Trka, Jan; Froňková, Eva

doi:10.1182/blood-2015-07-655159

Cited by 91 publications

(89 citation statements)

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“…27 Briefly, depending on the IGH, TRG, and/or TRD rearrangements applied as MRD targets in the RQ-PCR analysis, we performed a targeted approach: the follow-up samples were amplified using the multiplex primer set(s) of the relevant immunoglobulin/TR locus only, and data analysis was focused on the specific junctional region sequence (ie, the 1 used for RQ-PCR analysis). The primers for TCRG were newly designed (supplemental Table 1), and individual primer combinations from multiplex PCR were tested for sensitivity using NGS for diluted diagnostic ALL samples from patients with respective V and Jgamma segment combinations, all reaching the sensitivity of 10…”

Section: Ngs-based Mrd Analysesmentioning

confidence: 99%

Standardized flow cytometry for highly sensitive MRD measurements in B-cell acute lymphoblastic leukemia

Theunissen

Mejstříková

Sędek

et al. 2017

Blood

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348

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Key Points• Standardized flow cytometry allows highly sensitive MRD measurements in virtually all BCP-ALL patients.• If sufficient cells are measured (.4 million), flow cytometric MRD analysis is at least as sensitive as current PCR-based MRD methods.A fully-standardized EuroFlow 8-color antibody panel and laboratory procedure was stepwise designed to measure minimal residual disease (MRD) in B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) patients with a sensitivity of £10 25, comparable to real-time quantitative polymerase chain reaction (RQ-PCR)-based MRD detection via antigen-receptor rearrangements. Leukocyte markers and the corresponding antibodies and fluorochromes were selected based on their contribution in separating BCP-ALL cells from normal/regenerating BCP cells in multidimensional principal component analyses. After 5 multicenter design-test-evaluate-redesign phases with a total of 319 BCP-ALL patients at diagnosis, two 8-color antibody tubes were selected, which allowed separation between normal and malignant BCP cells in 99% of studied patients. These 2 tubes were tested with a new erythrocyte bulk-lysis protocol allowing acquisition of high cell numbers in 377 bone marrow follow-up samples of 178 BCP-ALL patients.Comparison with RQ-PCR-based MRD data showed a clear positive relation between the percentage concordant cases and the number of cells acquired. For those samples with >4 million cells acquired, concordant results were obtained in 93% of samples. Most discordances were clarified upon high-throughput sequencing of antigen-receptor rearrangements and blind multicenter reanalysis of flow cytometric data, resulting in an unprecedented concordance of 98% (97% for samples with MRD < 0.01%). In conclusion, the fully standardized EuroFlow BCP-ALL MRD strategy is applicable in >98% of patients with sensitivities at least similar to RQ-PCR (£10 25 ), if sufficient cells (>4 3 10 6 , preferably more) are evaluated. (Blood. 2017;129(3):347-357)

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Section: Ngs-based Mrd Analysesmentioning

confidence: 99%

Standardized flow cytometry for highly sensitive MRD measurements in B-cell acute lymphoblastic leukemia

Theunissen

Mejstříková

Sędek

et al. 2017

Blood

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348

296

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“…Several other hospitals also regularly use the platform (London, Brussels, Kiel, Bergamo, Montpellier to cite a few). Other Vidjil users have estimated the immunological repertoire in mice and rats [29, 30] and have evaluated the clonal diversity for the monitoring of minimal residual disease to better stratify ALL patients [31]. …”

Section: Resultsmentioning

confidence: 99%

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing

et al. 2016

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BackgroundThe B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. Today, with new sequencing techniques, one can get billions of DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune response as well as pathologies such as leukemia.Methods and ResultsVidjil is an open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time. Vidjil is implemented in C++, Python and Javascript and licensed under the GPLv3 open-source license. Source code, binaries and a public web server are available at http://www.vidjil.org and at http://bioinfo.lille.inria.fr/vidjil. Using the Vidjil web application consists of four steps: 1. uploading a raw sequence file (typically a FASTQ); 2. running RepSeq analysis software; 3. visualizing the results; 4. annotating the results and saving them for future use. For the end-user, the Vidjil web application needs no specific installation and just requires a connection and a modern web browser. Vidjil is used by labs in hematology or immunology for research and clinical applications.

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“…However, this testing is not widely available across all institutions. NGS-based MRD assays are also being developed, and have demonstrated greater specificity for prediction of relapse than real time quantitative-PCR in some studies [80]. Still, these assays need to be standardized and tested in more rigorous studies before they become the standard of care in monitoring MRD.…”

Section: Mrd-directed Therapymentioning

confidence: 97%

Closing the gap: Novel therapies in treating acute lymphoblastic leukemia in adolescents and young adults

Friend

Schiller

2018

Blood Reviews

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The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL

Cited by 91 publications

References 10 publications

Standardized flow cytometry for highly sensitive MRD measurements in B-cell acute lymphoblastic leukemia

Standardized flow cytometry for highly sensitive MRD measurements in B-cell acute lymphoblastic leukemia

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing

Closing the gap: Novel therapies in treating acute lymphoblastic leukemia in adolescents and young adults

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