Custom NanoString Gene Expression Assay for Subtype Identification in Glioblastoma. Custom NanoString Gene Expression Assay for Subtype Identification in Glioblastoma

Using non-negative matrix factorization to identify glioblastoma subtypes from NanoString gene expression data Overall design: 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.