NanoString RNA gene expression analyses
tumor, DNA/RNA/miRNA
TUMOR, INFILTRATION
RNA was isolated from baseline fresh-frozen patients’ tumor biopsies that had sufficient tumor material based on the pathologists’ scoring (at least 30% tumor cells). If the tumor cell percentage was too low, a new biopsy was required. For on-treatment biopsies (week 3), RNA was isolated in case of the presence of tumor bed and/or immune infiltration, independent of the percentage viable tumor. RNA was isolated at the Molecular Diagnostics department of the NKI using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen; cat: 80224) according to the manufacturer’s protocol. RNA gene expression analysis of baseline (