Evaluation and Reproducibility Study using NanoString GeoMx Immune Pathway Panels

The NanoString GeoMx DSP (digital spatial profiling) platform enables spatial profiling using formalin-fixed, paraffin-embedded (FFPE) tumor biopsy samples with a read out using either the nCounter or next generation sequencing. Q2 Solutions evaluated healthy tonsil sections and a well characterized breast carcinoma biopsy in a study examining variability across days, patient biopsies and sample stability.


FFPE tissue biopsy sections were hybridized to RNA probes or antibodies conjugated with UV photocleavable oligonucleotide tags to a targeted panel of genes or proteins within the Immune Pathways RNA panel or Immune Cell Profiling Core panel. The slide is then scanned by the DSP and the pathologist will then select Regions of Interest (ROIs). In this study, PanCK (epithelium), CD45 (immune cells), and Syto13 (DNA) were used as morphology markers. The ROIs can then be segmented into discrete biological compartments or areas of illumination (AOI) for precise profiling. Once the ROIs were selected, the oligos were cleaved, deposited into a plate, pooled and processed using the nCounter workflow for quantification.


Two healthy donor tonsil biopsies and three breast cancer biopsies were analyzed across two independent runs: collecting 6 AOIs per slide. Variance between samples tested on different days was < 30% both within and across tissue samples. Unsupervised clustering of the tonsil biopsies stratified germinal center AOIs from mantle zone AOIs. Similar analysis of the breast cancer biopsies stratified intra-tumoral regions from infiltrating boarder immune microenvironments and in situ from invasive carcinoma regions and normal peri-ductal vs. invasive carcinoma immune microenvironments.


The NanoString GeoMx DSP platform provides a robust method for investigating spatial relationships within an FFPE tissue section. Low variability across sections and runs provides the opportunity to clearly stratify cell populations, tissue areas and cellular states.


Watch this poster presentation to learn more.