Abstract
Neuroblastoma, a pediatric tumor of the sympathetic nervous system, is predominantly driven by copy number aberrations, which predict survival outcome in global neuroblastoma cohorts and in low-risk cases. For high-risk patients there is still a need for better prognostic biomarkers. Via an international collaboration, we collected copy number profiles of 556 high-risk neuroblastomas generated on different array platforms. This manuscript describes the composition of the dataset, the methods used to process the data, including segmentation and aberration calling, and data validation. t-SNE analysis shows that samples cluster according to MYCN status, and shows a difference between array platforms. 97.3% of samples are characterized by the presence of segmental aberrations, in regions frequently affected in neuroblastoma. Focal aberrations affect genes known to be involved in neuroblastoma, such as ALK and LIN28B. To conclude, we compiled a unique large copy number dataset of high-risk neuroblastoma tumors, available via R2 and a Shiny web application. The availability of patient survival data allows to further investigate the prognostic value of copy number aberrations.
Highlights
Background & SummaryNeuroblastoma is a pediatric tumor of the sympathetic nervous system, affecting mainly children under the age of five years[1]
Risk stratification of neuroblastoma patients is based on clinical parameters, histopathological parameters and genetic parameters including MYCN amplification, 11q loss and the global copy number profile[4,5]
Exploration of the collected and processed data confirmed the presence of segmental and focal aberrations in regions frequently affected in neuroblastoma and that samples cluster according to MYCN status rather than platform and inter-laboratory differences
Summary
Neuroblastoma is a pediatric tumor of the sympathetic nervous system, affecting mainly children under the age of five years[1]. Within the Ultra-High-Risk (UHR) working group of the International Neuroblastoma Response Criteria (INRC) consortium[5], we collected DNA copy number profiles and clinical data of 556 high-risk neuroblastoma patients, resulting in a unique dataset. Exploration of the collected and processed data confirmed the presence of segmental and focal aberrations in regions frequently affected in neuroblastoma and that samples cluster according to MYCN status rather than platform and inter-laboratory differences. In this data descriptor, we describe in detail the composition of the data with respect to sample inclusion criteria and clinical characteristics and the methods used to process the data. We provide access to normalized probe-level data and segmented data as well as instructions to analyze and visualize the data using either the R2 platform[10], the statistical programming language R or a Shiny web application
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