New Molecular Technologies for Minimal Residual Disease Evaluation in B-Cell Lymphoid Malignancies

Dogliotti, Irene; Drandi, Daniela; Genuardi, Elisa; Ferrero, Simone

doi:10.3390/jcm7090288

Cited by 25 publications

(19 citation statements)

References 106 publications

(149 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is required by the latest International Myeloma Working Group response criteria [13], is increasingly incorporated into follow-up after stem cell transplant in patients with MM [30,31], and is recommended by the International Workshop on CLL for use in clinical trials aimed at maximizing the depth of remission in patients with CLL [4]. However, several different methods of varying sensitivity are used to measure MRD, not all of which have been standardized, making comparability of test results between laboratories difficult [19,20]. The vital role that MRD assays play in clinical decision-making necessitates not only assay standardization but also analytical validation, to enable a full understanding of the capability and limitations of each assay and to ensure that it is fit for the intended purpose of monitoring MRD.…”

Section: Discussionmentioning

confidence: 99%

Analytical evaluation of the clonoSEQ Assay for establishing measurable (minimal) residual disease in acute lymphoblastic leukemia, chronic lymphocytic leukemia, and multiple myeloma

Ching

Duncan

Newman-Eerkes

et al. 2020

Preprint

View full text Add to dashboard Cite

Abstract Background: The clonoSEQ® Assay (Adaptive Biotechnologies Corporation, Seattle, USA) identifies and tracks unique disease-associated immunoglobulin (Ig) sequences by next-generation sequencing of IgH, IgK, and IgL rearrangements and IgH-BCL1/2 translocations in malignant B cells. Here, we describe studies to validate the analytical performance of the assay using patient samples and cell lines.Methods: Sensitivity and specificity were established by defining the limit of detection (LoD), limit of quantitation (LoQ) and limit of blank (LoB) in genomic DNA (gDNA) from 66 patients with multiple myeloma (MM), acute lymphoblastic leukemia (ALL), or chronic lymphocytic leukemia (CLL), and three cell lines. Healthy donor gDNA was used as a diluent to contrive test samples with specific DNA masses and malignant-cell frequencies. Precision was validated using a range of samples contrived from patient gDNA, healthy donor gDNA, and 9 cell lines to generate numerous measurable residual disease (MRD) frequencies spanning clinically relevant thresholds. Linearity was determined using samples contrived from cell line gDNA spiked into healthy gDNA to generate 11 MRD frequencies for each DNA input, then confirmed using clinical samples. Quantitation accuracy was assessed by (1) comparing clonoSEQ and multiparametric flow cytometry (mpFC) measures of ALL and MM cell lines diluted in healthy mononuclear cells, and (2) analyzing precision study data for quantitation bias between MRD results from clonoSEQ measurements of diluted gDNA and those expected from mpFC of original, undiluted samples. Repeatability of nucleotide base calls was assessed via the assay’s ability to recover malignant clonotype sequences across several replicates, process features, and MRD levels.Results: LoD and LoQ were estimated at 1.903 cells and 2.390 malignant cells, respectively. LoB was zero in healthy donor gDNA. Precision ranged from 18% CV at higher DNA inputs to 68% CV near the LoD. Variance component analysis showed MRD results were robust, with expected laboratory process variations contributing ≤3% CV. Linearity and accuracy were demonstrated for each disease across orders of magnitude of clonal frequencies. Nucleotide sequence error rates were extremely low.Conclusions: These studies validate the analytical performance of the clonoSEQ Assay, and demonstrate its potential as a highly sensitive diagnostic tool for selected lymphoid malignancies.

show abstract

Section: Discussionmentioning

confidence: 99%

Analytical evaluation of the clonoSEQ Assay for establishing measurable (minimal) residual disease in acute lymphoblastic leukemia, chronic lymphocytic leukemia, and multiple myeloma

Ching

Duncan

Newman-Eerkes

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Another technique for detection of MRD in lymphoma is based on PCR for known chromosomal translocations like the t (11;14), t (14;18) or immunoglobulin heavy chain genes (IgH) [30,31]. Newer molecular technologies such as droplet digital PCR and next generation sequencing have also been described for monitoring MRD in B cells lymphoproliferative disease [32]. PCR technique, like the flow cytometry will not detect the CD34+ population within MRD since CD34+ cells have the same genetic composition as parent cells, at least by karyotype and CGH analyses ( Supplementary Figure 1).…”

Section: Discussionmentioning

confidence: 99%

Isolation and characterization of a CD34+ sub-clone in B-cell lymphoma

et al. 2020

View full text Add to dashboard Cite

Non-Hodgkin's lymphoma (NHL) is the most common hematological malignancy in the US. Many types remain incurable despite response to initial therapy and achievement of complete remission (CR). Advanced laboratory techniques like multicolor flow cytometry (FCM) and polymerase chain reaction (PCR) have demonstrated persistence of rare malignant cell population post therapy. However, the functional and biological characteristics of this population have not been elucidated. Established B-lymphoma cell lines (B-NHL) and patient-derived samples (PDS) were analyzed using 8-color FCM. CD34 + sub-population was enriched using in vitro exposure to 2-chlorodeoxyadenosine (2-CdA) and by CD34 magnetic beads. Genetic analysis of cell fractions was done by karyotyping and array comparative genomic hybridization (aCGH). Sensitivity to chemotherapy was assayed by short-term in vitro exposure to chemotherapy. Clonogenicity was determined by soft agar colony formation assay, and proliferation was determined using DNA staining with propidium iodide and FCM. FCM demonstrated the presence of a minute sub-clone of monotypic B-cells that express CD34 in B-NHL cell lines (3 of 3) and in PDS (8 of 8). This sub-population enriched up to 50 fold in vitro by exposure to 2-CdA and up to 80% purity by CD34 magnetic bead column isolation. Except for CD34 expression, this population expressed identical phenotype and genotype to parent cells, but was more proliferative, Hoechst 33342-positive, clonogenic, and resistant to chemotherapy compared with the CD34population. The isolated CD34 + monotypic B-cells may contribute to resistance of certain NHL to treatment and should be targeted by potential new drugs for NHL.

show abstract

“…For instance, in treatment-resistant or relapsed liquid tumors, this is represented by a so-called minimal residual disease (MRD) [ 75 , 76 ], which often results in false negative variant calls as the variants may exhibit VAFs below the cutoff used by a typical variant caller. In these situations, sequencing techniques that utilize barcoding followed by variant callers designed to detect low VAFs, such as DeepSNVMiner [ 16 ] and smCounter2 [ 17 , 18 ], are advised, and if possible, longitudinal samples should be taken to monitor disease dynamics [ 77 ].…”

Section: Biological Featuresmentioning

confidence: 99%

Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables

Bohannan

Mitrofanova

2019

Computational and Structural Biotechnology Journal

View full text Add to dashboard Cite

Deep sequencing genomic analysis is becoming increasingly common in clinical research and practice, enabling accurate identification of diagnostic, prognostic, and predictive determinants. Variant calling, distinguishing between true mutations and experimental errors, is a central task of genomic analysis and often requires sophisticated statistical, computational, and/or heuristic techniques. Although variant callers seek to overcome noise inherent in biological experiments, variant calling can be significantly affected by outside factors including those used to prepare, store, and analyze samples. The goal of this review is to discuss known experimental features, such as sample preparation, library preparation, and sequencing, alongside diverse biological and clinical variables, and evaluate their effect on variant caller selection and optimization.

show abstract

New Molecular Technologies for Minimal Residual Disease Evaluation in B-Cell Lymphoid Malignancies

Cited by 25 publications

References 106 publications

Analytical evaluation of the clonoSEQ Assay for establishing measurable (minimal) residual disease in acute lymphoblastic leukemia, chronic lymphocytic leukemia, and multiple myeloma

Analytical evaluation of the clonoSEQ Assay for establishing measurable (minimal) residual disease in acute lymphoblastic leukemia, chronic lymphocytic leukemia, and multiple myeloma

Isolation and characterization of a CD34+ sub-clone in B-cell lymphoma

Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables

Contact Info

Product

Resources

About