Whole-Genome Sequencing Identifies Patient-Specific DNA Minimal Residual Disease Markers in Neuroblastoma Esther M. van Wezel, Danny Zwijnenburg, Lily.

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Whole-Genome Sequencing Identifies Patient-Specific DNA Minimal Residual Disease Markers in Neuroblastoma Esther M. van Wezel, Danny Zwijnenburg, Lily Zappeij-Kannegieter, Erik Bus, Max M. van Noesel, Jan J. Molenaar, Rogier Versteeg, Marta Fiocco, Huib N. Caron, C. Ellen van der Schoot, Jan Koster, Godelieve A.M. Tytgat The Journal of Molecular Diagnostics Volume 17, Issue 1, Pages 43-52 (January 2015) DOI: 10.1016/j.jmoldx.2014.09.005 Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Structural alterations for patients N600, N701, and N607. Circos plots show structural variants for patients N600 (A), N701 (B), and N607 (C). The inner ring represents the copy number variations (green, loss; red, gain), based on coverage of the tumor and lymphocyte genomes. The lines traversing the ring indicate interchromosomal and intrachromosomal rearrangements identified by discordant mate pairs from paired-end reads. The Journal of Molecular Diagnostics 2015 17, 43-52DOI: (10.1016/j.jmoldx.2014.09.005) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Comparison of breakpoint PCRs in primary tumor and BM metastases. The percentage relative to albumin for several targets in the primary tumor and in BM at diagnosis for patients N600 (A), N607 (B), N701 (C), N576 (D), N753 (E), N540 (F), and N691 (G). The y axis indicates the MRD level as determined by the different targets [percentages were calculated relative to albumin and taking PCR efficiency into account, according to the following formula: 2dCt × 100/PCR efficiency (of the target)]. The dashed line indicates that for these targets the slope of the standard curve was less than −3.9. BM, bone marrow; Del, deletion; Dup, tandem duplication; Inv, inversion; MRD, minimal residual disease. The Journal of Molecular Diagnostics 2015 17, 43-52DOI: (10.1016/j.jmoldx.2014.09.005) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 Target dynamics for several DNA breakpoints at diagnosis and during treatment. The dynamics of the different targets for patients N600 (A), N607 (B), N701 (C), N576 (D), N753 (E), N540 (F), N691 (G), and N718 (H). The x axis shows different time points. The y axis indicates the MRD level as determined by the different targets [percentages were calculated relative to albumin and taking PCR efficiency into account, according to the following formula: 2dCt × 100/PCR efficiency (of the target)]. MRD level determined by using a panel of RNA markers is indicated by a gray line. Colored lines represent differences in response. The dashed line indicates that for these targets the slope of the standard curve was less than −3.9. All markers for the different samples were tested in triplicate. BM, bone marrow; Del, deletion; Dup, tandem duplication; Dx, diagnosis; Inv, inversion; M, months, MRD, minimal residual disease. The Journal of Molecular Diagnostics 2015 17, 43-52DOI: (10.1016/j.jmoldx.2014.09.005) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 4 Logarithmic correlation between the PCR results of a panel of RNA markers and a single chromosomal rearrangement. Results of PCR-based quantification by a chromosomal rearrangement or a panel of RNA markers for eight patients (22 samples within quantitative range). The x axis indicates the MRD level determined by the median of a panel of RNA markers relative to the primary tumor. The y axis indicates the MRD level determined by a single chromosomal rearrangement with the highest abundance in the primary tumor. MRD, minimal residual disease. The Journal of Molecular Diagnostics 2015 17, 43-52DOI: (10.1016/j.jmoldx.2014.09.005) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions