Digital spatial profiling (GeoMxTM platform and the Human Whole Transcriptome Atlas probe set) of Homo sapiens: primary breast cancers
Digital spatial profiling was performed on 10 ER-heterogenous (10-60% ER+) and 10 highly ER+ (>190% ER+) primary breast cancers using the GeoMxTM platform and the Human Whole Transcriptome Atlas probe set. A tissue microarray was constructed with each case representing a region of interest (ROI); within each ROI we defined areas of interest (AOIs) including ER-negative (ER-neg), ER-low (ER-lo), ER-high (ER-hi) tumor regions, and stroma using quantitative immunofluorescent ER and cytokeratin staining. mRNA was collected separately from each AOI and sequenced. Data was analyzed on the GeoMx next generation sequencing platform