Scaling Spatial Genomics: A Deep Dive into Applications, Workflows and Analysis at the Wellcome Sanger Institute

Spatial genomics has become indispensable for resolving cellular heterogeneity and understanding tissue architecture within its native context. To meet the demands of large-scale collaborative projects, the Spatial Genomic Platform at the Wellcome Sanger Institute has established a comprehensive, high-throughput service portfolio utilizing spatial technologies.

This presentation details the standardized and scalable workflows designed to support a diverse range of spatial transcriptomic analyses applications. The core service spans the entire process, from sample receipt through final library generation, accommodating both fresh frozen (FF) and formalin-fixed, paraffin-embedded (FFPE) tissue samples. Critical workflow components are outlined, including tissue processing, meticulous quality control (H&E staining, molecular integrity checks), and robust sample tracking via the Spatial Tissue ANalysis (STAN) Laboratory Information Management System (LIMS) system.

The Platform leverages multiple technologies to address varying research questions: Visium (including CytAssist) is employed for whole transcriptome spatial discovery across both FF and FFPE tissues, while Xenium In Situ Hybridization is utilized for high-resolution, targeted analysis of gene panels (up to 5,000 genes) at subcellular resolution. Finally, the presentation touches on downstream data analysis. By establishing these efficient and standardized pipelines, the Sanger Institute enables rapid, reliable spatial data generation to accelerate biological discovery for global research initiatives.