Additional file 1 of Sensitive liquid biopsy monitoring correlates with outcome in the prospective international GPOH-DCOG high-risk neuroblastoma RT-qPCR validation study
Creators: name: van Zogchel, Lieke M. J.
name: Decarolis, Boris
name: van Wezel, Esther M.
name: Zappeij‐Kannegieter, Lily
name: Gelineau, Nina U.
name: Schumacher‐Kuckelkorn, Roswitha
name: Simon, Thorsten
name: Berthold, Frank
name: van Noesel, Max M.
name: Fiocco, Marta
name: van der Schoot, C. Ellen
name: Hero, Barbara
name: Stutterheim, Janine
name: Tytgat, Godelieve A. M.
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology
subject: Cancer
subject: Science Policy
subject: Hematology

description: Supplementary Material 1: Supplemental Figure 1. Schematic overview of Dutch (DCOG NBL2009 trial) and German (GPOH NB2004-HR) trials. Dutch patients received 2 upfront courses of MIBG therapy, if clinically achievable. German patients were randomized to standard induction therapy, or two additional courses of N8 upfront. N5 = vindesine, cisplatin, etoposide; N6= vincristine, dacarbacine, ifosfamide, doxorubicin; N8 = topotecan, cyclophosphamide and etoposide; HD chemo = melphalan, carboplatin, etoposide, followed by autologous stem cell transplantation; RTx= radiotherapy, IT= immune therapy. Blue arrows indicate time points of sample acquisition. Supplemental Figure 2. Sample consort diagram. We investigated whether previous negative immunocytology results influenced sample acquisition. Of the 88 missing bone marrow samples after 2 cycles of therapy, 23 (26%) samples were from patients with a previous sample negative for immunocytology, while of the 257 sampled patients after 2 cycles of therapy, only 30 patients did have a negative previous sample or were not sampled before (12%). Of the 216 patients with missing samples at the end of induction, 102 patients (47%) had a previously negative sample for immunocytology, similarly to the 129 patient that were sampled at the end of induction (61 patients with a previously negative sample; 47%). Supplemental Figure 3 (A) Number of samples grouped by infiltration by RT-qPCR at diagnosis, after 2 cycles of therapy (2 CT) and at the end of induction therapy. (B) Number of samples grouped by infiltration based on GD2-immunocytology at diagnosis, after 2 cycles of therapy (2 CT) and at the end of induction therapy. Supplemental Figure 4. Kaplan-Meier event-free and overall survival curves (EFS on the left and OS on the right, respectively) of the cohort with patients stage M and age &gt;18 months, according to the level of mRNA infiltration by RT-qPCR detected in bone marrow at diagnosis (A, B), after 2 cycles of therapy (C, D), after induction therapy (E, F) and according to the level of GD2- immunocytology (IC) detected in bone marrow at diagnosis (G,H), after 2 cycles of therapy (I,J) and after induction therapy (K,L). 5-year survival rates are given in order according to the legend. The number of children at risk with time for each group is provided in the Data Supplement. Supplemental Figure 5. Landmark Kaplan-Meier overall surival (OS) analysis, starting 2 years after sample collection for A. diagnosis, stratified for relapse or progressive disease in the first 2 years after sample collection; B. level of bone marrow infiltration by RT-qPCR at diagnosis; C. diagnosis, stratified for RT-qPCR group and relapse/progressive disease; D. after 2 cycles of therapy, stratified for relapse or progressive disease in the first 2 years after sample collection; E. level of bone marrow infiltration by RT-qPCR after 2 cycles of therapy; F. after 2 cycles of therapy, stratified for RT-qPCR group and relapse/progressive disease. 5-year survival rates are given in order according to the legend.The number of children at risk with time for each group is provided in the Data Supplement. Supplemental Figure 6. Kaplan-Meier event-free and overall survival curves (EFS on the left and OS on the right, respectively) according to the level of GD2- immunocytology (IC) detected in bone marrow at diagnosis (A, B). Kaplan-Meier curves for patients with GD-2 IC negative bone marrow at diagnosis, stratified for RT-qPCR results (C, D) and patients with GD2- immunocytology positive bone marrow at the end of induction, stratified for RT-qPCR results (E, F). 5-year survival rates are given in order according to the legend. The number of children at risk with time for each group is provided in the Data Supplement. Supplemental Figure 7. Kaplan-Meier event-free and overall survival curves (EFS on the left and OS on the right, respectively) according to individual marker positivity in bone marrow samples at diagnosis. If a marker had a Ct value&lt;40 but ΔCt of the sample was within 3 Ct of the ΔCt of the normal control BM samples, it was regarded as negative for analysis, but is depicted here as‘below threshold’. 5-year survival rates are given in order according to the legend. The number of children at risk with time for each group is provided in the Data Supplement. Supplemental Figure 8. Kaplan-Meier event-free and overall curves (EFS on the left and OS on the right, respectively) according to individual marker positivity in bone marrow samples after 2 cycles of therapy. If a marker had a Ct value&lt;40 but ΔCt of the sample was within 3 Ct of the ΔCt of the normal control BM samples, it was regarded as negative for analysis, but is depicted here as ‘below threshold’. 5-year survival rates are given in order according to the legend. The number of children at risk with time for each group is provided in the Data Supplement. Supplemental Figure 9. Kaplan-Meier event-free and overall curves (EFS on the left and OS on the right, respectively) according to individual marker positivity in bone marrow samples at the end of induction therapy. If a marker had a Ct value&lt;40 but ΔCt of the sample was within 3 Ct of the ΔCt of the normal control BM samples, it was regarded as negative for analysis, but is depicted here as ‘below threshold’. 5-year survival rates are given in order according to the legend. The number of children at risk with time for each group is provided in the Data Supplement.