Manuscript | Spatial Exploration of Her2 Breast Cancer

We’ve put out a new manuscript on bioRxiv, where the expression landscape of HER2-positive breast cancer tumors is studied from a spatial perspective. This study contains several examples of how spatial data may be analyzed and what information beyond the obvious - like the spatial distribution of a certain gene - that can be mined from it. My hope is that anyone looking for ideas regarding how to analyze their own spatial data find this useful and relevant, irregardles of their interest in breast cancer. In the study we cluster spots by gene expression, but also take this one step further, using the clusters to find core signatures of immune and tumor cell populations within our samples. We also use stereoscope to map single cell data down onto our tissue sections, information which then is used to indentify potential TLS-sites as well as to study patterns of cell type co-localization. All the scripts and a neat app for visualization of the results can be found here.