Periodic Reporting for period 1 - EuroFAANG (A European infrastructure for farmed animal genotype to phenotype research)
Período documentado: 2023-01-01 hasta 2023-12-31
The EuroFAANG Research Infrastructure builds on the goal of the global Functional Annotation of Animal Genomes initiative (FAANG) and six H2020 EuroFAANG projects. FAANG and EuroFAANG are global collaborations, comprising research communities that operate mainly on a geographical basis and interact through an open data policy. By bridging the gap between cell, tissue and whole animal scale knowledge, the FAANG and EuroFAANG initiatives aim to provide genomic information to sustainably improve farmed animal production in the face of challenges to the agri-food sector including a growing human population, changing climates and increased public concern about the welfare of production animals.
The main goal of the EuroFAANG RI project, funded through the INFRA-DEV funding stream is to streamline how the farmed animal research community best uses interdisciplinary capabilities for G2P research and provides access to all of the relevant facilities, expertise and knowledge to European stakeholders. In doing so the EuroFAANG research infrastructure will underpin G2P research in farmed animals in Europe, advancing excellent science and frontier research based on user-defined priorities.
To achieve this goal the EuroFAANG research infrastructure has the following four main objectives:
1. Creation of a common data structure and data access for G2P research in farmed animals (WP3).
2. Development, curation and biobanking of in vitro cellular models, for farmed animal species, as an accessible resource for G2P research (WP4).
3. Sharing and expanding capabilities in new breeding, phenotyping, and genomic technologies as a route to application of FAANG data for understanding the G2P link in farmed animals (WP5&6).
4. Connecting with existing projects and infrastructures to consolidate G2P research in farmed animals across Europe (WP7&8).
The EuroFAANG research infrastructure is currently in the concept development phase in the life cycle of a research infrastructure.
The main goal of the EuroFAANG RI project, funded through the INFRA-DEV funding stream is to streamline how the farmed animal research community best uses interdisciplinary capabilities for G2P research and provides access to all of the relevant facilities, expertise and knowledge to European stakeholders. In doing so the EuroFAANG research infrastructure will underpin G2P research in farmed animals in Europe, advancing excellent science and frontier research based on user-defined priorities.
To achieve this goal the EuroFAANG research infrastructure has the following four main objectives:
1. Creation of a common data structure and data access for G2P research in farmed animals (WP3).
2. Development, curation and biobanking of in vitro cellular models, for farmed animal species, as an accessible resource for G2P research (WP4).
3. Sharing and expanding capabilities in new breeding, phenotyping, and genomic technologies as a route to application of FAANG data for understanding the G2P link in farmed animals (WP5&6).
4. Connecting with existing projects and infrastructures to consolidate G2P research in farmed animals across Europe (WP7&8).
The EuroFAANG research infrastructure is currently in the concept development phase in the life cycle of a research infrastructure.
During the first period work has focused on concept development for the EuroFAANG RI project via seven different work packages. The work performed and main achievements in each work package are as follows:
Work performed in work package one aimed to identify scientific partners and stakeholders with specialized expertise and facilities that are not currently included in the existing consortia. To do this we performed a comprehensive survey of scientific and technological developments in the field and other international and national initiatives in farmed animal science, and were able to identify seven key areas for consortium expansion.
Work package two is focused on providing transnational access to the EuroFAANG research infrastructure. In the first period we provided a document describing the access policy for the infrastructure and describing the different types of use, users and units of access. As a foundation we used established standardized processes for TNA that were developed within three established research infrastructures for farmed animal breeding in Europe (AquaExcel, PigWeb and SmartCow).
The Data Management Plan and Data policy and Access principles for the EuroFAANG research infrastructure were developed in the first period by work package three and build on the existing FAANG Data Coordination Centre (FAANG DCC). Importantly, in the first period through interactions with the data infrastructure Elixir we established the focus group on Domestic Animal Genomes and Phenomes Going forwards Elixir standards and data management services can replace or synergise with existing FAANG DCC efforts.
Work package four tackles the main barriers that preclude a more widespread and harmonised use of in vitro cellular models for farmed animal G2P research. In the first period we created a list of existing biorepositories of cellular systems to be connected via a common portal. We also established a working group on in vitro cellular systems and organised a summer school on innovative cellular models to build networks of researchers using organoids for farm animal science.
The aim of work package five is to develop a framework for sharing and expanding capabilities in genome editing in farmed animals in Europe. In the first period, to achieve this aim, we ran a stakeholder workshop to identify barriers and opportunities and generated a list of labs using genome editing for farmed animal research. We also established a European think-tank on genome editing which has over one hundred members and meets quarterly.
For work package six, in which activities are focused in the first and second period, we built web page content for interaction with key stakeholders and identified key contacts in EU projects focused on emerging species.
Work package seven is focused on building links with other EU research projects and infrastructures. The Elixir focus group developed with WP3 on Domestic Animal Genomes and Phenomes provides a visible a new scientific community for animal science in ELIXIR. In the first period several interviews with ESFRI landmark infrastructures were performed and the potential for collaboration with INFRAFRONTIER and the proposed INFRA-DEV farmed animal phenotyping infrastructure Pheno-Live were explored.
Work package 8 focuses on achieving the steps needed to ensure the longevity of the EuroFAANG research infrastructure. We have in the first period developed a communication plan, contacted ESFRI representatives and national contact points and explored funding options for the next stage of the research infrastructure.
Work performed in work package one aimed to identify scientific partners and stakeholders with specialized expertise and facilities that are not currently included in the existing consortia. To do this we performed a comprehensive survey of scientific and technological developments in the field and other international and national initiatives in farmed animal science, and were able to identify seven key areas for consortium expansion.
Work package two is focused on providing transnational access to the EuroFAANG research infrastructure. In the first period we provided a document describing the access policy for the infrastructure and describing the different types of use, users and units of access. As a foundation we used established standardized processes for TNA that were developed within three established research infrastructures for farmed animal breeding in Europe (AquaExcel, PigWeb and SmartCow).
The Data Management Plan and Data policy and Access principles for the EuroFAANG research infrastructure were developed in the first period by work package three and build on the existing FAANG Data Coordination Centre (FAANG DCC). Importantly, in the first period through interactions with the data infrastructure Elixir we established the focus group on Domestic Animal Genomes and Phenomes Going forwards Elixir standards and data management services can replace or synergise with existing FAANG DCC efforts.
Work package four tackles the main barriers that preclude a more widespread and harmonised use of in vitro cellular models for farmed animal G2P research. In the first period we created a list of existing biorepositories of cellular systems to be connected via a common portal. We also established a working group on in vitro cellular systems and organised a summer school on innovative cellular models to build networks of researchers using organoids for farm animal science.
The aim of work package five is to develop a framework for sharing and expanding capabilities in genome editing in farmed animals in Europe. In the first period, to achieve this aim, we ran a stakeholder workshop to identify barriers and opportunities and generated a list of labs using genome editing for farmed animal research. We also established a European think-tank on genome editing which has over one hundred members and meets quarterly.
For work package six, in which activities are focused in the first and second period, we built web page content for interaction with key stakeholders and identified key contacts in EU projects focused on emerging species.
Work package seven is focused on building links with other EU research projects and infrastructures. The Elixir focus group developed with WP3 on Domestic Animal Genomes and Phenomes provides a visible a new scientific community for animal science in ELIXIR. In the first period several interviews with ESFRI landmark infrastructures were performed and the potential for collaboration with INFRAFRONTIER and the proposed INFRA-DEV farmed animal phenotyping infrastructure Pheno-Live were explored.
Work package 8 focuses on achieving the steps needed to ensure the longevity of the EuroFAANG research infrastructure. We have in the first period developed a communication plan, contacted ESFRI representatives and national contact points and explored funding options for the next stage of the research infrastructure.
The EuroFAANG RI project includes several components exploring research innovations beyond the state of the art.
In the first period for deliverable 1.3 we performed a comprehensive survey of scientific and technological developments in the field of animal agriculture. This survey identified several innovations beyond the state of the art including, focused artificial intelligence technology and digital twins, the used of robotics for automated culture of in vitro systems and high-through-put CRISPR screens, and big data analytics for the measurement of millions of data points. In addition, in the first period, for D5.1 we are exploring advances in genome editing beyond state of the art, for example, using robotics to test hundreds of thousands of causal variants in cell lines with genome wide CRISPR screens. At present this technology is applied predominantly for human research, including to identify vaccine targets and for gene therapies but there is considerable potential for application in advancing G2P research in farmed animals.
In the first period for deliverable 1.3 we performed a comprehensive survey of scientific and technological developments in the field of animal agriculture. This survey identified several innovations beyond the state of the art including, focused artificial intelligence technology and digital twins, the used of robotics for automated culture of in vitro systems and high-through-put CRISPR screens, and big data analytics for the measurement of millions of data points. In addition, in the first period, for D5.1 we are exploring advances in genome editing beyond state of the art, for example, using robotics to test hundreds of thousands of causal variants in cell lines with genome wide CRISPR screens. At present this technology is applied predominantly for human research, including to identify vaccine targets and for gene therapies but there is considerable potential for application in advancing G2P research in farmed animals.