Minimal Residual Disease Detection by Droplet Digital PCR in Multiple Myeloma, Mantle Cell Lymphoma, and Follicular Lymphoma Daniela Drandi, Lenka Kubiczkova-Besse,

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Minimal Residual Disease Detection by Droplet Digital PCR in Multiple Myeloma, Mantle Cell Lymphoma, and Follicular Lymphoma Daniela Drandi, Lenka Kubiczkova-Besse, Simone Ferrero, Nadia Dani, Roberto Passera, Barbara Mantoan, Manuela Gambella, Luigia Monitillo, Elona Saraci, Paola Ghione, Elisa Genuardi, Daniela Barbero, Paola Omedè, Davide Barberio, Roman Hajek, Umberto Vitolo, Antonio Palumbo, Sergio Cortelazzo, Mario Boccadoro, Giorgio Inghirami, Marco Ladetto The Journal of Molecular Diagnostics Volume 17, Issue 6, Pages 652-660 (November 2015) DOI: 10.1016/j.jmoldx.2015.05.007 Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Comparison of serial DNA dilutions assessed by both qPCR and ddPCR. Linear 10-fold dilution standard curve with the Cq value for qPCR (A–C) and copy numbers for ddPCR (D–F) were plotted against the corresponding starting quantity of gDNA. A and D: Plasmid standard curves from an IGH rearrangement derived from a MM patient; 500 ng (R2 = 0.9934) versus 100 ng (R2 = 0.9951) by qPCR (A) and 500 ng (R2 = 0.9978) versus 100 ng (R2 = 0.9986) by ddPCR (D). B and E: gDNA standard curves from a MCL patient-specific IGH rearrangement; 500 ng (R2 = 0.9948) versus 100 ng (R2 = 0.9796) by qPCR (B) and 500 ng (R2 = 0.9979) versus 100 ng (R2 = 0.9640) by ddPCR (E). C and F: gDNA from Bcl-2/IGH MBR+ cell line (DOHH-2); 500 ng (R2 = 0.9966) versus 100 ng (R2 = 0.9016) by qPCR (C) and 500 ng (R2 = 0.9980) versus 100 ng (R2 = 0.9937) by ddPCR (F). R2 (coefficient of determination), represents how well the experimental data fit the regression line. Each dilution point represents the mean value of quantifiable replicates for different template amount (500 ng and 100 ng). ddPCR, droplet digital PCR; gDNA, genomic DNA; MBR, major breakpoint region; MCL, mantle cell lymphoma; MM, multiple myeloma; qPCR, quantitative real-time PCR. The Journal of Molecular Diagnostics 2015 17, 652-660DOI: (10.1016/j.jmoldx.2015.05.007) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Sensitivity and accuracy of qPCR and ddPCR on serial DNA dilution. A–C: qPCR data. D–F: ddPCR data of 500 ng DNA standard curves. Each dot represents a mean value of eight replicates, with SD shown as whiskers. Table below each graph shows the amount of negative replicates at each dilution point. ddPCR, droplet digital PCR; MBR, major breakpoint region; MCL, mantle cell lymphoma; MM, multiple myeloma; qPCR, quantitative real-time PCR. The Journal of Molecular Diagnostics 2015 17, 652-660DOI: (10.1016/j.jmoldx.2015.05.007) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 Correlation between qPCR and ddPCR in patient samples. Pearson correlation between target quantification in MM, MCL, and FL by both methods shows a significant concordance (r = 0.94, P < 0.0001). Forty-eight samples were undetectable by both methods (−/−). One hundred forty-two samples were scored positive by both methods, 141 of which were fully concordantly positive and 1 quantitative discordance (green). Major and minor qualitative discordances are labeled in red and yellow, respectively. PNQ samples are included between lines. Thirteen cases scored PNQ by both methods. ddPCR, droplet digital PCR; dPNQ, PNQ determined by ddPCR; FL, follicular lymphoma; MCL, mantle cell lymphoma; MM, multiple myeloma; PNQ, positive nonquantifiable; qPNQ, PNQ determined by qPCR; qPCR, quantitative real-time PCR. The Journal of Molecular Diagnostics 2015 17, 652-660DOI: (10.1016/j.jmoldx.2015.05.007) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 4 Example of MRD detection discordances in patient's follow-up samples. Comparison of MRD level at different tps, taken on the basis of availability of DNA, evaluated by qPCR (solid lines) and ddPCR (dashed lines), for three MM (A, D, and F) and three MCL (B, C, and E) patients. A–C: Three patients with fully concordant follow-up samples. D: A patient with three minor qualitative discordances (tp 3, 5, and 8). E: One case with a major qualitative discordance (tp 2) and a minor qualitative discordance (tp 4). F: A follow-up sample PNQ by qPCR but quantifiable by ddPCR at tp 5. The amount of target copies was log10 transformed. ddPCR, droplet digital PCR; MCL, mantle cell lymphoma; MM, multiple myeloma; MRD, minimal residual disease; PNQ, positive nonquantifiable; qPCR, quantitative real-time PCR; tp, time point. The Journal of Molecular Diagnostics 2015 17, 652-660DOI: (10.1016/j.jmoldx.2015.05.007) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions