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

Published: 31-03-2020| Version 1 | DOI: 10.17632/st69pzcgvg.1
Fu Zhao,
Pinan Liu,
Jing Zhang


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.