Periodic Reporting for period 3 - EASI-Genomics (European Advanced infraStructure for Innovative Genomics)
Reporting period: 2022-02-01 to 2023-07-31
Over the past 20 years, few other scientific fields have witnessed an innovation spree comparable to that of genomics. The field of genomics is characterized by rapid technological and methodological developments, high cost of equipment, and a highly specialized level of expertise required in sample preparation as well as analysis of results. Due to these multiple constrains, researchers often lack access to cutting-edge sequencing technologies while genomics infrastructures concentrate the technological capacity and high level of expertise in this domain.
In the context of the generalization of genomics in healthcare and the imminent advent of personalized/precision medicine in Europe, the scientific community will tremendously benefit from leveraging the expertise and capacity of national genomics facilities. Access to the latest genomics technologies and analytical expertise will certainly accelerate scientific discoveries and improve the competitiveness of the research community.
The mission of EASI-Genomics is to provide easy and seamless access to cutting-edge DNA sequencing technologies to researchers from academia and industry covering the entire experimental cycle from study design to the interpretation of results. To achieve this goal, 11 state-of-the-art European genomics platforms regularly organise calls for proposals to offer transnational access to the research community and provide comprehensive support to access projects. Moreover, altogether the 16 partners of EASI-Genomics collaborate on research and networking activities to define new genomics standards, develop and integrate new laboratory and computational methodologies and develop a framework for ensuring ethical, legal, and societal highest standards. Eventually, EASI-Genomics is developing a powerful collaborative European infrastructure in genomics available to the research and industry community.
In conclusion, EASI-Genomics has been an excellent exhibition of the impact of advanced genomics technologies, of the diverse projects it has helped to realize, as well as on the positive influence EASI-Genomics had in boosting the careers of over 100 researchers. In addition, The exchange of best-practises with other genomic platforms led to the joint development and optimization of new genomics methods.
In the context of the generalization of genomics in healthcare and the imminent advent of personalized/precision medicine in Europe, the scientific community will tremendously benefit from leveraging the expertise and capacity of national genomics facilities. Access to the latest genomics technologies and analytical expertise will certainly accelerate scientific discoveries and improve the competitiveness of the research community.
The mission of EASI-Genomics is to provide easy and seamless access to cutting-edge DNA sequencing technologies to researchers from academia and industry covering the entire experimental cycle from study design to the interpretation of results. To achieve this goal, 11 state-of-the-art European genomics platforms regularly organise calls for proposals to offer transnational access to the research community and provide comprehensive support to access projects. Moreover, altogether the 16 partners of EASI-Genomics collaborate on research and networking activities to define new genomics standards, develop and integrate new laboratory and computational methodologies and develop a framework for ensuring ethical, legal, and societal highest standards. Eventually, EASI-Genomics is developing a powerful collaborative European infrastructure in genomics available to the research and industry community.
In conclusion, EASI-Genomics has been an excellent exhibition of the impact of advanced genomics technologies, of the diverse projects it has helped to realize, as well as on the positive influence EASI-Genomics had in boosting the careers of over 100 researchers. In addition, The exchange of best-practises with other genomic platforms led to the joint development and optimization of new genomics methods.
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.
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.
The EASI-Genomics consortium provided first-in-class access to state-of-the-art analysis for projects requiring genomics, starting from study design, over sequencing to bioinformatics analysis. It established and consolidated procedures for transnational access calls, covering calls' publication, proposals' reception, reviews, consolidation of reviews, notification, ethics checks, MoUs, and MTAs. EASI-Genomics advanced innovative science by contributing to European and International standardization efforts and developing novel technologies and protocols for Genomics workflows. Several manuscripts are in the pipeline and collaboration activities will continue after the end of the EASI-Genomics project.
The facilities partnering with EASI-Genomics have agreed to continue fostering knowledge exchange to annual meetings on a rotating basis and virtual tips & tricks jamborees. The most often requested sequencing methods in our consortium were and are single-cell and long-read. A half or more of the facilities began to offer these services in addition to the dynamic commercial implementations of biological nanopore (ONT), in situ capture (Visium by 10x), and in situ sequencing (Cartana Xenium by 10x) with a rising number also in the spatial sequencing domain. Therefore, it is foreseeable that the computational demands will become increasingly important, while the pricing of standard NGS technologies will continue to drop inversely.
The facilities partnering with EASI-Genomics have agreed to continue fostering knowledge exchange to annual meetings on a rotating basis and virtual tips & tricks jamborees. The most often requested sequencing methods in our consortium were and are single-cell and long-read. A half or more of the facilities began to offer these services in addition to the dynamic commercial implementations of biological nanopore (ONT), in situ capture (Visium by 10x), and in situ sequencing (Cartana Xenium by 10x) with a rising number also in the spatial sequencing domain. Therefore, it is foreseeable that the computational demands will become increasingly important, while the pricing of standard NGS technologies will continue to drop inversely.