Periodic Reporting for period 2 - EASI-Genomics (European Advanced infraStructure for Innovative Genomics) Reporting period: 2020-08-01 to 2022-01-31 Summary of the context and overall objectives of the project 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. Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far During the first reporting period, EASI-Genomics launched two transnational access calls and one extraordinary call in response to the COVID-19 pandemic. EASI-Genomics launched a third ordinary transnational access call within the second reporting period. Within the third call, EASI-Genomics received 143 applications and awarded access to 33 research projects for a total budget of 1,18 million Euros. EASI-Genomics received 302 applications and awarded access to 105 research projects for a total budget of 4.98 million Euros through the three calls. The facilities are currently analysing ninety-nine projects, and 25 projects are completed. In parallel, EASI-Genomics developed and set up a comprehensive legal and ethical framework of access to genomics services for these calls. Networking activities have focused on the regulatory processes for acquiring the biological material used for interlaboratory comparison and defining genomics standards for cancer mutations. EASI-Genomics set up a procedure for technology watch and analysed the answers of more than 220 users to a questionnaire on the needs and interests of the research community. EASI-Genomics also developed several new laboratory methods and computational frameworks for data analysis. Finally, a full training programme was defined for EASI-Genomics to skill researchers in basic and specialized knowledge on genomics to empower users in their approach to producing and handling genomics data. Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) The EASI-Genomics consortium provides 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. During the two first reporting periods, EASI-Genomics launched three ordinary TNA calls, plus an extraordinary Covid-related one in May 2020, to contribute to the collective societal effort to fight the pandemic. Altogether, these calls granted access to 105 researchers from all across Europe and beyond. 24% of the selected projects have already been finalized, 66% are at or beyond the sequencing stage, and 10% have experienced an issue or been interrupted. The seven projects awarded in the extraordinary call for research projects related to Covid-19 will be key in deciphering the genetic predisposition behind severe forms of COVID-19 among a relatively young population with no or few pre-conditions and co-morbidities. The first TNA call and, in particular, the COVID call have already resulted in several high-impact publications. We expect an increasing number of publications in the third reporting period. EASI-Genomics has also developed new cutting-edge technologies. Furthermore, harmonization and benchmarking activities for developing cancer genomics standards are currently ongoing, as well as active efforts in technology watch, research community education, wide dissemination of the TNA calls, and stakeholder engagement geared towards the evolution of EASI-Genomics into a European Research Infrastructure. High-capacity fast short read sequencing Genomics Services Integrative Data Analysis Real-time high-throughput long read sequencing
