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Supplementary Figure Legends for A1-A3

Table A1. Therapies received for samples submitted on this study; Table A2. Genes and Primer and Probe Sets for NB5 assay; Table A3. Clinical Evaluations and NB5 TLDA Assays Performed; Table A4. Contribution of Individual Gene to NB5 Signature and AUC.

Comparison of 1 year EFS in two groups defined by a range of ∆CT cut points (left column) and corresponding ROC analysis of the ability of ∆CT values above the cutpoint to predict 1 year EFS (right column), for assays based on different combinations of genes. NB5 assay (A, B), Phox2B/TH/DDC (C, D), Phox2B/TH (E, F), Phox2B/TH/Dcx (G, H), Th/Dcx (I, J). These analyses show that the NB5 assay is at least as or more predictive then the other gene combinations.

Change in BM and Blood NB5 �Ct for patients with progressive disease vs. non-progressive disease. Change in NB5 �Ct was assessed between pairs of time points where both NB5 �Ct and clinical disease assessments were performed. Observations are classified by whether there was clinical disease progression or not between the time points.

Correlation of morphologically-defined NB cells in BM and MIBG Curie score. Analysis of BM biopsies and MIBG scans were performed concurrently on 173 patients.

Purpose: We determined whether quantifying neuroblastoma-associated mRNAs (NB-mRNAs) in bone marrow and blood improves assessment of disease and prediction of disease progression in patients with relapsed/refractory neuroblastoma.Experimental Design: mRNA for CHGA, DCX, DDC, PHOX2B, and TH was quantified in bone marrow and blood from 101 patients concurrently with clinical disease evaluations. Correlation between NB-mRNA (delta cycle threshold, ΔCt, for the geometric mean of genes from the TaqMan Low Density Array NB5 assay) and morphologically defined tumor cell percentage in bone marrow, 123I-meta-iodobenzylguanidine (MIBG) Curie score, and CT/MRI-defined tumor longest diameter was determined. Time-dependent covariate Cox regression was used to analyze the relationship between ΔCt and progression-free survival (PFS).Results: NB-mRNA was detectable in 83% of bone marrow (185/223) and 63% (89/142) of blood specimens, and their ΔCt values were correlated (Spearman r = 0.67, P < 0.0001), although bone marrow Ct was 7.9 ± 0.5 Ct stronger than blood Ct. When bone marrow morphology, MIBG, or CT/MRI were positive, NB-mRNA was detected in 99% (99/100), 88% (100/113), and 81% (82/101) of bone marrow samples. When all three were negative, NB-mRNA was detected in 55% (11/20) of bone marrow samples. Bone marrow NB-mRNA correlated with bone marrow morphology or MIBG positivity (P < 0.0001 and P = 0.007). Bone marrow and blood ΔCt values correlated with PFS (P < 0.001; P = 0.001) even when bone marrow was morphologically negative (P = 0.001; P = 0.014). Multivariate analysis showed that bone marrow and blood ΔCt values were associated with PFS independently of clinical disease and MYCN gene status (P < 0.001; P = 0.055).Conclusions: This five-gene NB5 assay for NB-mRNA improves definition of disease status and correlates independently with PFS in relapsed/refractory neuroblastoma. Clin Cancer Res; 23(18); 5374–83. ©2017 AACR.