Community
EASI-Genomics project aims to build a community of practice which leverages advanced sequencing technologies

First, we want to bring all partner sequencing facilities up to the same high standard.

Then,  provide a means for the community to assess and measure their quality and improve their sequencing based on this benchmarking.

We will also make resources available to sequencing facilities outside of the EASI-Genomics partnership to participate in our inter-laboratory comparisons with the purpose that Europe will be well prepared to deploy NGS-based analysis for personalized medicine.

The procedures for 2nd generation sequencing are complex, subjected to continuous changes in products that suppliers offer and changes in instruments and their capabilities. The methods, algorithms and procedures used for data analysis are to a large extent developed in academic laboratories, with limited documentation and their application and use of parameters is often based on arbitrary choices. The community has established very few standards. For DNA analysis there is no wet-lab standard, while for data analysis the Genome in a Bottle is available from the NIST (US National Institute of Standards). For wet- and dry-lab for somatic mutation analysis, members of this consortium coordinated a benchmark. Due to this situation the community largely operates with little control and no means to measure themselves against a standard. Proficiency testing of NGS for clinical diagnostics is possible through the EMQN run by the Manchester Centre for Genomic Medicine or the College of American Pathologists, which focus on DNA clinical diagnostics. Genome-wide DNA, RNA and DNA methylation tests so far are not included. However, several of the EASI-Genomics partners are ISO17025 accredited for DNA, RNA and DNA methylation analysis and maintain this accreditation by the organization of inter-laboratory comparisons with other EASI-Genomics partner laboratories. Two EASI-Genomics partners are accredited ISO15189 to deliver clinical NGS diagnostics. The objectives of this activity are designed to change the current situation and broaden the accreditation into the sphere of genome centres and sequencing units, by harmonizing wet-lab procedures, harmonizing dry-lab procedures, and establishing inter-laboratory comparisons and benchmarks for DNA, RNA, and epigenetic analyses.



EASI-Genomics concept is based on a user-centred integrated infrastructure that provides access to service, new methods and standards, interlaboratory comparisons, and a framework for Data Management and ELSI in genomics, contributing to the strengthening of the large genomics community.

Following user needs: user forum

Developments and techniques are quickly changing and updated in NGS facilities. With the start of the project, online queries for internal and external users of an extended list of ten European Genomics Facilities - excluding partners in the EASI-Genomics consortium - will be coordinated and released to systematically collect and scout trends in genomic technologies at semiannual intervals. This will include question categories such as, frequent user requests, automation or miniaturization, bottlenecks, limitations, protocol troubleshooting, and technology forecast. Based on the acquired evaluated data EASI-Genomics members will organize symposia in archived web streaming mode inviting key users, genomics centres (staff) and identified experts in the targeted fields. Data statistics and documented outputs of queries will be made publicly available online, and discussed in technology-oriented symposia. After constant validation, new technology watch and implementation tasks for the most requested methods will be announced.

EASI-Genomics will habilitate an open survey through this project website, where users will be allowed to post new requests regarding needed solutions or technologies at any time. The requests will be monitored and reported together with the data of the periodic online queries.

EASI-Genomics will also identify a set of individuals from the Stakeholder Platform representing the user community, and will constitute a focus group on user needs, which may bring new requests, contribute to the analysis and interpretation of survey data, or advice on the design of the queries and surveys.

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EASI-Genomics will reach out to the different stakeholders to transfer knowledge and consult with them about their future needs and interests.

It will also develop and organise workshops and seminars to train the new generation of users.

Central to these activities will be the creation of a Stakeholder Platform, as a meeting point where users, providers, suppliers, and also funders and policy makers may exchange information about challenges and opportunities.

Stakeholder Platform

We will create a platform including relevant contacts in industry, funding agencies, professional societies, policy makers, related infrastructures, etc. Once the Stakeholder Platform is established, EASI-Genomics will organize one big stakeholder event and several other focused groups (in some cases, linked to specific tasks regarding Access, Ethics and Data Management, Technology Watch and Implementation). EASI-Genomics has obtained written proof of support by our associated partners (see About).

The stakeholder meeting will be organized in the second year of the project to disseminate the EASI-Genomics concepts, evaluate specific stakeholder requirements, and discuss the concept of Expert Centres. The experiences from this meeting will be consolidated into recommendations that will contribute to the Expert Centre.

Due to close cooperation of the EASI-Genomics partners with other European and International initiatives (like BBMRI-ERIC, ELIXIR, GA4GH or EOSC-Hub), we will coordinate the activities, resources and services of EASI-Genomics with those of relevant networks. To make the outcome of EASI-Genomics sustainable, a high level of international integration and transfer of knowledge to larger-scale initiatives is needed.

Expert Centres concept

Access to high quality biological samples and data becomes increasingly difficult for industrial research and development outside of research partnerships with academic institutions.  The reason for this is that there is a strong aversion by the public towards the commercial exploitation of human biological material that has been obtained using public money, even if fees are levied only on a cost-recovery basis. A solution to this problem is, to generate data from samples in a pre-competitive, not-for-profit setting, eventually transferring these data into the public domain (e.g. the EOSC), following the FAIR principles. This does, however, not preclude exploitation in industrial research & development, or priority in academic research during a grace period before transferring these data to a public resource. In such a setting, that constitutes the rationale for ECs, industry can cooperate with academic partners, finance sample acquisition and analysis, and still benefit from priority access to the data, without ‘privatizing’ the results. This concept has been originally developed within BBMRI-ERIC and will be adapted to support cooperation between academia, industry and EASI-Genomics.

EASI-Genomics considers training as one of the most effective activities to reach out to the research community from academia and industry, and other users such as clinicians. It will enable them to leverage the newly developed technologies, and thereby increase the quality and impact of the projects selected for Transnational Access.


Training in EASI-Genomics will be organized around three axes to cover all community needs 



Our training activities will be tightly coordinated with those of our partner pan-European infrastructures, mainly ELIXIR, BBMRI and CORBEL. Moreover, we will build on our involvement on RRI and Open Science projects.

Format

We will organize three types of training activities: 1) collection of online courses, short tutorials and webinars; 2) two large workshops, as satellite events to relevant international conferences; and 3) advanced hands-on workshops and summer-schools provided locally at the participating infrastructure sites.

Content

Training will be organized around three main areas: 1) advanced technologies offered by the participating infrastructures; 2) new methods and standards developed by EASI-Genomics joint research and harmonization activities; and 3) transversal aspects addressing the highest RRI and Open Science standards (in the areas of ethics, research integrity, data management, open access, sex and gender aspect in research, public engagement).

Audience

The main target audience for the open training to the community will be potential future users, i.e. researchers in any area of life science, of both academy and industry. Open training activities will be complemented by ad hoc training to Access user teams when necessary. However, some training activities will be targeted to advanced users and/or to Research Infrastructure and facility operators.


Events

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