Within the third reporting period of the project, EASI-Genomics resolved the fourth TNA call, which added 20 user projects to the 105 projects reported in RP2. In RP3, the infrastructure successfully provided access to 100 user projects. Of the 515 service requests we received across all calls, we were able to grant a total of 170 service requests. Collaboration between facilities on complex proposals added a level of sophistication that is hard to achieve by a single organization. The number of applications with a broad distribution across and beyond Europe and the proven high-impact publication output clearly demonstrate the need for a pan-European advanced genomics infrastructure.
Regarding wet-lab method developments, a complete NGS workflow was developed from urine collection to data analysis for urine cfDNA methylation and showed that a standardized preanalytical workflow is key for reliable NGS analysis from liquid biopsies. Recommendations for the use of HMW DNA extraction kits when working with long-fragments have been established. In the ISS methodology, direct RNA detection to look at CNVs and initial results for analyzing methylation levels with ISS were developed.
Regarding dry-lab method developments, integrating single-cell multi-omics data via various methods, including spatial analysis, is pivotal for comprehending cellular organization and intercellular signaling within native tissue contexts. The development of SSAM-lite, a user-friendly web application, democratizes spatial omics analysis and facilitates integration with non-spatial single-cell data. This accessible platform empowers researchers to explore and visualize spatial transcriptomics data through an intuitive interface. In addition, the creation of the EASI-Genomics Cloud marks step towards simplifying data analysis for individuals without extensive computational resources. Its web-based interface, terminal-based access, and notebook interfaces offer multiple avenues for data analysis, training, and collaboration.
