Journal Article

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

Tracy, Jeffrey M., Newman-Eerkes, Tera, Sang, Charles, Kirsch, Ilan R., Howie, Bryan, Vignali, Marissa, Duncan, Megan E., Watson, Drew, Sherwood, Anna, McWhorter, Mollie M. E., Cimler, B. Melina, Venkatasubbarao, Srivatsa, Moorhead, Martin E., Akers, Nicholas K., Brown, Ryan P., Swatkowski, Pamela L., Mann, Tobias P., Robins, Harlan S., Ching, Travers, Steen, Michelle S., Emerson, Ryan O.

2020

Overview

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 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 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) measurements of ALL and MM cell lines diluted in healthy mononuclear cells, and (2) analyzing precision study data for bias between clonoSEQ MRD results in diluted gDNA and those expected from mpFC based on 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 (coefficient of variation) 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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Acute lymphoblastic leukemia / Acute lymphocytic leukemia / Analysis / Analytical validation / B cells / Biomedical and Life Sciences / Biomedicine / Biotechnology industries / Bone marrow / Bone Marrow - pathology / Cancer / Cancer Research / Cell and molecular biology / Chronic lymphocytic leukemia / Clinical medicine / Cyclin D1 - genetics / Deoxyribonucleic acid / DNA / Flow cytometry / Gene Rearrangement / Genomics / Health Promotion and Disease Prevention / Heavy chains / High-Throughput Nucleotide Sequencing - instrumentation / Humans / Immunoglobulin Heavy Chains - genetics / Immunoglobulin lambda-Chains - genetics / Immunoglobulins / Immunoglobulins - genetics / Laboratories / Leukemia / Leukemia, Lymphocytic, Chronic, B-Cell - blood / Leukemia, Lymphocytic, Chronic, B-Cell - diagnosis / Leukemia, Lymphocytic, Chronic, B-Cell - genetics / Leukemia, Lymphocytic, Chronic, B-Cell - therapy / Leukocytes (mononuclear) / Limit of Detection / Lymphatic leukemia / Lymphocytes B / Lymphomas / Measurable residual disease / Medicine/Public Health / Multiple myeloma / Multiple Myeloma - blood / Multiple Myeloma - diagnosis / Multiple Myeloma - genetics / Multiple Myeloma - therapy / Neoplasm, Residual / Next-generation sequencing / Nucleotide sequence / Oncology / Precursor Cell Lymphoblastic Leukemia-Lymphoma - blood / Precursor Cell Lymphoblastic Leukemia-Lymphoma - diagnosis / Precursor Cell Lymphoblastic Leukemia-Lymphoma - genetics / Precursor Cell Lymphoblastic Leukemia-Lymphoma - therapy / Proto-Oncogene Proteins c-bcl-2 - genetics / Quantitation / Reagent Kits, Diagnostic / Research Article / Surgical Oncology / Translocation / Translocation, Genetic / Tumor cell lines