Center for Medical Genetics, Ghent University, Ghent, Belgium.
Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.
Sci Data. 2018 Oct 30;5:180240. doi: 10.1038/sdata.2018.240.
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.
神经母细胞瘤是一种源于交感神经系统的小儿肿瘤，主要由拷贝数异常驱动，这些异常可预测全球神经母细胞瘤队列和低危病例的生存结果。对于高危患者，仍然需要更好的预后生物标志物。通过国际合作，我们收集了 556 例高危神经母细胞瘤的拷贝数谱，这些样本是在不同的阵列平台上生成的。本文描述了数据集的组成、用于处理数据的方法，包括分割和异常调用，以及数据验证。t-SNE 分析表明，样本根据 MYCN 状态聚类，并显示出阵列平台之间的差异。97.3%的样本具有神经母细胞瘤中常见的片段性异常。局灶性异常影响已知参与神经母细胞瘤的基因，如 ALK 和 LIN28B。总之，我们编译了一个独特的高危神经母细胞瘤肿瘤的大型拷贝数数据集，可通过 R2 和 Shiny 网络应用程序获得。患者生存数据的可用性允许进一步研究拷贝数异常的预后价值。
