Custom NanoString Gene Expression Assay for Subtype Identification in Glioblastoma

Using non-negative matrix factorization to identify glioblastoma subtypes from NanoString gene expression data RNA was extracted from tissue cores using the Qiagen Allprep DNA/RNA FFPE kit per manufacturer's protocol. 300 ng of total RNA of each sample were analyzed by NanoString gene expression assay using a custom codeset of 70 probes representing 4 housekeeping genes and 30 classifier genes corresponding to the classical (CL), mesenchymal (MES), proneural (PN), and neural (NL) subtypes. Raw counts were background subtracted then normalized using the geometric mean of the samples analyzed using NanoString nSolver.

本研究采用非负矩阵分解（non-negative matrix factorization）从Nanostring基因表达数据中识别胶质母细胞瘤亚型。实验中，按照制造商操作手册的标准流程，使用Qiagen Allprep DNA/RNA FFPE试剂盒从组织芯样本中提取总RNA；每份样本取300 ng总RNA，采用Nanostring基因表达检测技术，搭配包含70个探针的自定义编码集完成分析——该探针集涵盖4个持家基因与30个分类基因，分别对应经典型（classical, CL）、间质型（mesenchymal, MES）、原神经型（proneural, PN）及神经型（neural, NL）四种胶质母细胞瘤亚型。原始计数数据先进行背景扣除，随后借助Nanostring nSolver软件，以所分析样本的几何均值为基准完成归一化处理。