Data for: Comparison of clinical, histopathological and genomic features between malignant peripheral nerve sheath tumors and cellular schwannomas of the eighth cranial nerve: a case series

Array comparative genomic hybridization (aCGH) data of two malignant peripheral nerve sheath tumors and two cellular schwannoma of the eighth cranial nerve were provided. Labeled genomic DNA was hybridized using an OncoScan FFPE Express 330K MIP platform (Affymetrix, Santa Clara, CA, US) according to the manufacturer's instructions. Arrays were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix) and analyzed using Command Console Software 3.1 (Affymetrix). Analysis of the OncoScan MIP data was carried out using Nexus Copy Number v.6.0 beta (BioDiscovery, CA, US). All samples had a median absolute pair-wise difference value of more than 0.6. Within each sample, probes that demonstrated a call rate of <90% and relative SD of >30% were excluded from further analysis. Probes were then clustered using the SNP-FASST2 algorithm. The median of the log2 ratio of each segment was calculated and used for copy number estimation. A segment was considered to have normal copy number, gain, loss, and loss of heterozygosity (LOH) if its log ratio value was zero, ≥2, ≤1, ≤0.5 respectively.

本数据集包含2例第八颅神经恶性外周神经鞘瘤及2例第八颅神经细胞性神经鞘瘤的阵列比较基因组杂交（array comparative genomic hybridization，aCGH）数据。标记后的基因组DNA依照生产商操作指南，采用OncoScan FFPE Express 330K MIP平台（美国加利福尼亚州圣克拉拉市Affymetrix公司）完成杂交反应。芯片扫描由GeneChip® Scanner 3000（货号：00-00212，Affymetrix公司）完成，数据分析则采用Command Console Software 3.1软件（Affymetrix公司）进行。OncoScan MIP数据的分析工作采用Nexus Copy Number v.6.0 beta版本软件（美国加利福尼亚州BioDiscovery公司）开展。所有样本的成对差异中位数绝对值均大于0.6。在每一份样本中，检出率低于90%且相对标准差大于30%的探针将被排除，不纳入后续分析。随后，剩余探针采用SNP-FASST2算法进行聚类。计算每个基因组片段的log₂比值中位数，以此作为拷贝数估算的依据。若某片段的log₂比值分别为0、≥2、≤1、≤0.5，则依次判定其为正常拷贝数、拷贝数增加、拷贝数缺失及杂合性缺失（loss of heterozygosity，LOH）。