Ensembl - adding value to animal genomes through high quality annotation

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

This project will deliver high quality up-to-date annotated genomes for key farmed and domesticated animals to enable research on these economically and socially important species.

Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in the animal sector of agriculture, contributing to medical research by providing animal models, improving animal health and welfare and informing understanding of natural and wild animal populations. High quality annotated genome sequences are key resources to enable such research.

The sequence of almost all genes (a reference genome sequence) has been determined for major farmed and domesticated animal species such as cattle, goats, sheep, pigs, chickens, ducks, turkeys, dogs and horses as well as for several important fish species, including cod, rainbow trout, salmon and tilapia. However, the strings of billions of bases (symbolised as four letters A, C, G, T) that constitute these genome sequences are not particularly useful or understandable on their own. Once a genome has been sequenced, it needs to be 'annotated' (i.e. explanatory notes need to be added to identify key features within the genome sequence) in order for research scientists to make sense of it.

Annotating reference genome sequences with features such as where the coding and regulatory parts of genes are located, and the bases which differ between individuals within a species (genetic variants) greatly enhances the value and utility of the genome sequence. Visualising the genome sequences complete with annotations in a freely accessible manner further improves the value of the information.
Ensembl provides a means for researchers to look at or 'browse' the annotated genome information. The databases and tools provided by Ensembl have been shown to be a powerful and effective means of annotating the complex genomes of animal species including humans, mice and more recently farmed and domesticated animals.

Enabled by advances in genome sequencing technologies and associated computational methods scientists around the world are generating more and better genome sequences. As the genome sequence of a single individual does not completely represent the genetic make-up of a species, scientists are also sequencing multiple individuals within a species. Individual research groups and international consortia are also generating sequence information that can be used in the annotation and analysis pipelines that we will run to identify both coding and regulatory sequences. We will use these data to annotate the genomes of farmed and domesticated animals, including aquaculture species. We will run comparative analyses to compare genomes both between species and between individuals within a species.

These richly annotated genome sequences, which are in effect maps of where the coding gene content and regulatory sequences are located, will be made freely available to the scientific community and others via the Ensembl Genome Browser mounted on the World Wide Web as well as via an Application Programming Interface for power users. We will also provide between and within species comparative views.

The annotated genomes that we will deliver are valuable not only to academic researchers, but also to scientists working in industry, including those in the animal breeding, animal health and pharmaceutical sectors. Keeping this information up-to-date, by characterising new genome sequences and integrating new data as it becomes available, is essential for reference genome sequences to remain current and useful.

Technical Summary

High quality annotated genomes are essential resources for life sciences research.

Draft reference genome sequences have been established for several farmed and domesticated animals: cattle, goat, pig, sheep; chicken, duck, turkey; dog, horse; rainbow trout, salmon, tilapia. Substantially improved genome assemblies have been established for goat, pig, cattle, sheep, water buffalo, chicken) using long read sequencing technologies. There are gaps in the annotation of these genomes in terms of transcript complexity, non-coding genes, pseudogenes and regulatory sequences. Moreover, the pseudo haploid genome sequence of one individual provides an incomplete view of a species' genome.
Scientists are generating more and better genome sequences for additional species and individuals within a species. Researchers, especially in the FAANG and FAASG consortia are generating functional data for annotation of coding, non-coding and regulatory sequences.

We will analyse and annotate farmed and domesticated animal genomes as they are released, exploiting the growing volumes of functional data (short and long read RNA-seq / transcript sequences; ChIP-seq; ATAC-Seq; CAGE; bisulfite sequence) to identify coding genes, non-coding genes and regulatory sequences. We will acquire data from re-sequencing projects to characterise genetic variation within species (SNPs, indel, structural variants) and display this variation in its genomics context. We will run comparative genomics analyses both between species and within species.

We will disseminate the resulting richly annotated genome sequences freely via the Ensembl Genome Browser and via an API for power users. These annotated genomes will provide an integrated view of functional sequences (coding, non-coding and regulatory) and sequence variation for a single or multiple individuals for key farmed and domesticated animals.

To maximise use of this resource we will provide demonstrations, on-line and face-to-face training.

Planned Impact

Who will benefit?
We expect that the beneficiaries will include: academic and industry researchers, animal breeding companies, owners or farmed and domesticated animals, suppliers of 'omics tools and wider society.

How will they benefit?
The Ensembl farmed and domesticated animal resources facilitates research on domesticated animals that has important socio-economic impacts, including underpinning improvements in the livestock sector, contributions to medical research, animal health and welfare, the evolution of domestication and the understanding of natural animal populations. Thus, the benefits to wider society are expected to be the result of research enabled by the Ensembl resources.

1. academic and industry researchers
High quality annotated animal genomes enable a wide range of research, including genetics studies of the target species, understanding gene networks that drive developmental biology and the development of improved animal models using precision genome editing.

2. animal breeding companies
Genomic prediction and selection has delivered significant improvements in the accuracy of selective animal breeding. Geneticists and breeders in the world's leading animal breeding and aquaculture breeding companies, of which some of the largest are UK companies will have access to improved annotation of functional sequences and sequence variation that will allow them to develop more sophisticated models for genomic prediction.

3. owners of farmed and domesticated animals
Owners of farmed animals will benefit indirectly through the supply of superior breeding stock and greater confidence in the genetic merit and performance of the resulting production animals. Owners of domestic and companion animals will also benefit indirectly through the use of genetic tests for inherited conditions developed through research enabled by the Ensembl resources.

4. suppliers of 'omics tools
Suppliers 'omics tools such as expression arrays, exon and other sequence capture products and SNP chips will also benefit from access to annotated genomes sequences that be used to design species specific products.

5. infrastructure and capacity building
The proposed project will contribute directly to capacity building by providing training including demonstrations, online tutorials and workshops in the use of the genome portal. This programme trains PhD students, Post Docs and research scientists to develop their skills in genome annotation, genome browsing and importantly how to interpret and understand their own data. Finally, the Ensembl - farmed and domesticated animals resource contributes to infrastructure to support the life sciences and is recognised as an ELIXIR resource in this context.

Organisations

Publications

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Yates AD (2020) Ensembl 2020. in Nucleic acids research

 
Description Since the start of the current round of funding in summer 2019, there have been 2 releases of Ensembl annotation from Ensembl Release 98 in September 2019 to the current Ensembl release 99 in January 2020. The key deliverables and milestones with respect to the farmed and companion animal species of interest are:

Pig
September 2019, Release 98 - a further 11 pig genome assemblies were annotated and released http://www.ensembl.org/Sus_scrofa/Info/Strains?db=core
These breed-specific annotations represent a significant resource for non-reference pig genomics. To better facilitate comparison between the reference and breed annotations, the reference gene set was also updated, utilising the latest gene finding code

Atlantic salmon
January 2020, Release 99 - the first annotated reference genome of the Atlantic salmon was released http://www.ensembl.org/Salmo_salar/Info/Index?db=core
Annotation tracks from Salmobase and RefSeq were also loaded to help researchers reconstruct a clearer picture of the complex evolution of the salmon gene set

Carp
January 2020, Release 99 - three strains of common carp (german mirror, hebao red and huanghe) were released:
http://www.ensembl.org/Cyprinus_carpio_german_mirror/Info/Index
http://www.ensembl.org/Cyprinus_carpio_hebao_red/Info/Index
http://www.ensembl.org/Cyprinus_carpio_huanghe/Info/Annotation

Dog
September 2019, Release 98 - an updated and patched genebuild was released for the CamFam3.1 assembly: http://www.ensembl.org/Canis_familiaris/Info/Index
This updated gene set used the updated gene finding software and a wide range of transcriptomic data to significantly improve the existing annotation, particularly in terms of building more complete gene models
January 2020, Release 99 - a further 2 dog genome assemblies, Basenji and Great Dane, were annotated and released: https://www.ensembl.org/Canis_familiaris/Info/Strains

Horse
September 2019, Release 98 - an updated and patched genebuild was released for the EquCab3.0 assembly: https://www.ensembl.org/Equus_caballus/Info/Annotation
This updated gene set used the updated gene finding software and a wide range of transcriptomic data to significantly improve the existing annotation, particularly in terms of building more complete gene models

Cat
September 2019, Release 98 - an updated and patched genebuild was released for the Felis_catus_9.0 assembly: https://www.ensembl.org/Felis_catus/Info/Annotation
This updated gene set used the updated gene finding software and a wide range of transcriptomic data to significantly improve the existing annotation, particularly in terms of building more complete gene models

Rabbit
September 2019, Release 98 - an updated and patched genebuild was released for the OryCun2.0 assembly: https://www.ensembl.org/Oryctolagus_cuniculus/Info/Index
This updated gene set used the updated gene finding software and a wide range of transcriptomic data to significantly improve the existing annotation, particularly in terms of building more complete gene models

Tilapia
September 2019, Release 98 - a new genebuild was released for the O_niloticus_UMD_NMBU assembly:
http://www.ensembl.org/Oreochromis_niloticus/Info/Annotation
This updated assembly and gene set used the updated gene finding software and a wide range of transcriptomic data to significantly improve the existing annotation, particularly in terms of building more complete gene models
Exploitation Route The ongoing development of the richly annotated reference genomes of farmed and domestic animals is essential to research on these species and on applications that exploit genomic information.
Sectors Agriculture, Food and Drink

URL https://www.ensembl.org
 
Description AQUA-FAANG 
Organisation AquaGen
Country Norway 
Sector Private 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation Aquicultura Balear SA
Country Spain 
Sector Private 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation French National Institute of Agricultural Research
Department INRA Versailles
Country France 
Sector Academic/University 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation French Poultry and Aquaculture Breeders Association
Country France 
Sector Charity/Non Profit 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation Hellenic Centre for Marine Research (HCMR)
Country Greece 
Sector Private 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation Norwegian University of Life Sciences (NMBU)
Country Norway 
Sector Academic/University 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation Panittica Italia Societa Agricola SRL
Country Italy 
Sector Private 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation Polish Academy of Sciences
Country Poland 
Sector Public 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation Stolt-Nielsen
Department Stolt Sea Farm S.A.
Country Spain 
Sector Private 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation University of Aberdeen
Country United Kingdom 
Sector Academic/University 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation University of Barcelona
Country Spain 
Sector Academic/University 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation University of Birmingham
Country United Kingdom 
Sector Academic/University 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation University of Edinburgh
Department The Roslin Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation University of Padova
Country Italy 
Sector Academic/University 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation University of Santiago de Compostela
Country Spain 
Sector Academic/University 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation University of Wageningen
Country Netherlands 
Sector Academic/University 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation Valle Ca' Zuliani (S.R.L.)
Country Italy 
Sector Private 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description AQUA-FAANG 
Organisation Xelect Ltd
Country United Kingdom 
Sector Private 
PI Contribution Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation.
Collaborator Contribution The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results.
Impact The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation Aarhus University
Country Denmark 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation Centre for Genomic Regulation (CRG)
Country Spain 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation Diagenode
Country Belgium 
Sector Private 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation ETH Zurich
Country Switzerland 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation Edinethics
Country United Kingdom 
Sector Private 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation European Federation of Animal Science
Country Italy 
Sector Public 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation Faculdade de Medicina de MarĂ­lia
Country Brazil 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation French National Institute of Agricultural Research
Department INRA Versailles
Country France 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation Leibniz Association
Department Leibniz Institute for Farm Animal Biology
Country Germany 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation Martin Luther University of Halle-Wittenberg
Country Germany 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation Natural Resources Institute Finland
Country Finland 
Sector Public 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation University of Alberta
Country Canada 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation University of Edinburgh
Department The Roslin Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation University of Liege
Country Belgium 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation University of Limoges
Country France 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation University of Wageningen
Country Netherlands 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle 
Organisation Utrecht University
Country Netherlands 
Sector Academic/University 
PI Contribution Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis.
Collaborator Contribution The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination.
Impact This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative.
Start Year 2017
 
Description Development of tools to detect chromosomal translocations in pigs 
Organisation Cytocell Ltd
Country United Kingdom 
Sector Private 
PI Contribution I provided my detailed knowledge of the Swine Genome Sequencing Consortium's project that produced the draft pig reference genome sequence (Sscrofa10.2) as described by Groenen et al. 2012. Pig genomes provide insight into porcine demography and evolution. Nature 491: 393-398 and the pig physical mapping project as described by Humphray et al. 2007. A high utility integrated map of the pig genome. Genome Biology 8:R139. My research team had also established the bacterial artificial chromosome (BAC) library resource described by Anderson et al. 2000. A large fragment porcine genomic library resource in a BAC vector. Mammalian Genome 11, 811-814. BAC clones from this library were used as probes for fluorescent in situ hybridisation (FISH) experiments in this collaborative project. My knowledge of the pig physical mapping and pig genome sequencing projects was critical in interpreting the anomalous and unexpected results from the initial FISH experiments.
Collaborator Contribution This collaboration was initiated and led by Prof Darren Griffin and colleagues at the University of Kent. In addition to leading the collaboration the Kent team delivered the expertise in cytogenetics analysis. JSR Genetics provided animal materials and phenotypes. Cytocell Ltd provided technical expertise and the Chromoprobe Multiprobe System. The work was funded by an Innovate UK Knowledge Transfer Partnership to Prof Darren Griffin and Cytocell Ltd.
Impact The project has demonstrated that FISH-based translocation screening is a powerful and reliable approach to screening for chromosomal translocation that can have adverse effects on fertility. The device described by O'Connor et al. (see below) is now a commercial product marketed by Cytocell Ltd. The project results have been useful if anchoring the new improved pig reference genome sequence to chromosomes and confirming the order and orientation for each chromosomal sequence. The results of the study have been published by O'Connor et al. Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly. Animal Genetics (in press). The research undertaken by Rebecca O'Connor is a major component of her PhD research studies.
Start Year 2014
 
Description Development of tools to detect chromosomal translocations in pigs 
Organisation JSR Genetics
Country United Kingdom 
Sector Private 
PI Contribution I provided my detailed knowledge of the Swine Genome Sequencing Consortium's project that produced the draft pig reference genome sequence (Sscrofa10.2) as described by Groenen et al. 2012. Pig genomes provide insight into porcine demography and evolution. Nature 491: 393-398 and the pig physical mapping project as described by Humphray et al. 2007. A high utility integrated map of the pig genome. Genome Biology 8:R139. My research team had also established the bacterial artificial chromosome (BAC) library resource described by Anderson et al. 2000. A large fragment porcine genomic library resource in a BAC vector. Mammalian Genome 11, 811-814. BAC clones from this library were used as probes for fluorescent in situ hybridisation (FISH) experiments in this collaborative project. My knowledge of the pig physical mapping and pig genome sequencing projects was critical in interpreting the anomalous and unexpected results from the initial FISH experiments.
Collaborator Contribution This collaboration was initiated and led by Prof Darren Griffin and colleagues at the University of Kent. In addition to leading the collaboration the Kent team delivered the expertise in cytogenetics analysis. JSR Genetics provided animal materials and phenotypes. Cytocell Ltd provided technical expertise and the Chromoprobe Multiprobe System. The work was funded by an Innovate UK Knowledge Transfer Partnership to Prof Darren Griffin and Cytocell Ltd.
Impact The project has demonstrated that FISH-based translocation screening is a powerful and reliable approach to screening for chromosomal translocation that can have adverse effects on fertility. The device described by O'Connor et al. (see below) is now a commercial product marketed by Cytocell Ltd. The project results have been useful if anchoring the new improved pig reference genome sequence to chromosomes and confirming the order and orientation for each chromosomal sequence. The results of the study have been published by O'Connor et al. Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly. Animal Genetics (in press). The research undertaken by Rebecca O'Connor is a major component of her PhD research studies.
Start Year 2014
 
Description Development of tools to detect chromosomal translocations in pigs 
Organisation University of Kent
Department Medway School of Pharmacy
Country United Kingdom 
Sector Hospitals 
PI Contribution I provided my detailed knowledge of the Swine Genome Sequencing Consortium's project that produced the draft pig reference genome sequence (Sscrofa10.2) as described by Groenen et al. 2012. Pig genomes provide insight into porcine demography and evolution. Nature 491: 393-398 and the pig physical mapping project as described by Humphray et al. 2007. A high utility integrated map of the pig genome. Genome Biology 8:R139. My research team had also established the bacterial artificial chromosome (BAC) library resource described by Anderson et al. 2000. A large fragment porcine genomic library resource in a BAC vector. Mammalian Genome 11, 811-814. BAC clones from this library were used as probes for fluorescent in situ hybridisation (FISH) experiments in this collaborative project. My knowledge of the pig physical mapping and pig genome sequencing projects was critical in interpreting the anomalous and unexpected results from the initial FISH experiments.
Collaborator Contribution This collaboration was initiated and led by Prof Darren Griffin and colleagues at the University of Kent. In addition to leading the collaboration the Kent team delivered the expertise in cytogenetics analysis. JSR Genetics provided animal materials and phenotypes. Cytocell Ltd provided technical expertise and the Chromoprobe Multiprobe System. The work was funded by an Innovate UK Knowledge Transfer Partnership to Prof Darren Griffin and Cytocell Ltd.
Impact The project has demonstrated that FISH-based translocation screening is a powerful and reliable approach to screening for chromosomal translocation that can have adverse effects on fertility. The device described by O'Connor et al. (see below) is now a commercial product marketed by Cytocell Ltd. The project results have been useful if anchoring the new improved pig reference genome sequence to chromosomes and confirming the order and orientation for each chromosomal sequence. The results of the study have been published by O'Connor et al. Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly. Animal Genetics (in press). The research undertaken by Rebecca O'Connor is a major component of her PhD research studies.
Start Year 2014
 
Description Ensembl - farmed and companion animals 2014 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution This partnership continues a 10 year collaborative effort to annotate the reference genome sequences of the major farmed animal species. The Roslin Institute partner contributes reference genome sequences for some of these farmed animal species through its leadership and participation in international farm animal genome sequencing projects / consortia. The Roslin Institute partner also provides ancillary sequence data which are used for annotation, such as extensive RNA-seq data from multiple sheep tissues. Finally, the Roslin Institute partner also provides key links to the farm animal genetics and genomics research community and the user communities in academia and industry.
Collaborator Contribution The Ensembl team at EMBL-EBI provide the expertise semi-automated genome sequence annotation, including gene builds, comparative genome analyses, functional annotation and evaluation of sequence variants. The EMBL-EBI also provide the compute infrastructure for the annotation processing and for access to the annotated genomes via the Ensembl Genome Browser. Finally, the EMBL-EBI team lead the training activities.
Impact The primary output from this collaboration are annotated reference genome sequences for farmed and companion animal species, including chickens, duck, turkey, pig, sheep, cattle, dog and horse.
 
Description Functional Annotation of Animal Genomes (FAANG) 
Organisation AgResearch
Department Invermay Agricultural Centre
Country New Zealand 
Sector Private 
PI Contribution I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young).
Collaborator Contribution The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term.
Impact 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site.
Start Year 2012
 
Description Functional Annotation of Animal Genomes (FAANG) 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young).
Collaborator Contribution The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term.
Impact 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site.
Start Year 2012
 
Description Functional Annotation of Animal Genomes (FAANG) 
Organisation French National Institute of Agricultural Research
Country France 
Sector Academic/University 
PI Contribution I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young).
Collaborator Contribution The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term.
Impact 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site.
Start Year 2012
 
Description Functional Annotation of Animal Genomes (FAANG) 
Organisation Iowa State University
Country United States 
Sector Academic/University 
PI Contribution I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young).
Collaborator Contribution The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term.
Impact 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site.
Start Year 2012
 
Description Functional Annotation of Animal Genomes (FAANG) 
Organisation Swedish University of Agricultural Sciences
Country Sweden 
Sector Academic/University 
PI Contribution I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young).
Collaborator Contribution The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term.
Impact 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site.
Start Year 2012
 
Description Functional Annotation of Animal Genomes (FAANG) 
Organisation U.S. Department of Agriculture USDA
Department Avian Disease and Oncology Laboratory (ADOL)
Country United States 
Sector Public 
PI Contribution I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young).
Collaborator Contribution The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term.
Impact 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site.
Start Year 2012
 
Description Functional Annotation of Animal Genomes (FAANG) 
Organisation U.S. Department of Agriculture USDA
Department National Animal Disease Center
Country United States 
Sector Public 
PI Contribution I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young).
Collaborator Contribution The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term.
Impact 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site.
Start Year 2012
 
Description Functional Annotation of Animal Genomes (FAANG) 
Organisation University of Adelaide
Department School of Animal and Veterinary Sciences
Country Australia 
Sector Academic/University 
PI Contribution I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young).
Collaborator Contribution The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term.
Impact 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site.
Start Year 2012
 
Description Functional Annotation of Animal Genomes (FAANG) 
Organisation University of California, Davis
Country United States 
Sector Academic/University 
PI Contribution I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young).
Collaborator Contribution The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term.
Impact 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site.
Start Year 2012
 
Description Functional Annotation of Animal Genomes (FAANG) 
Organisation University of Wageningen
Country Netherlands 
Sector Academic/University 
PI Contribution I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young).
Collaborator Contribution The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term.
Impact 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site.
Start Year 2012
 
Description Functional Annotation of Animal Genomes (FAANG) 
Organisation Uppsala University
Department Department of Medical Biochemistry and Microbiology
Country Sweden 
Sector Academic/University 
PI Contribution I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young).
Collaborator Contribution The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term.
Impact 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site.
Start Year 2012
 
Description International Swine Genome Sequencing Consortium 
Organisation Aarhus University Hospital
Country Denmark 
Sector Hospitals 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Aberystwyth University
Country United Kingdom 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Beijing Genomics Institute
Country China 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Catalan Institution for Research and Advanced Studies (ICREA)
Department ICREA Centre for Research in Agricultural Genomics (CRAG)
Country Spain 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Durham University
Country United Kingdom 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Earlham Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Eversole Associates
Country United States 
Sector Private 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation French National Institute of Agricultural Research
Department GABI: Animal Genetics and Integrative Biology unit
Country France 
Sector Private 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation French National Institute of Agricultural Research
Department Physiology of Reproduction and Behavior
Country France 
Sector Private 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation French National Institute of Agricultural Research
Country France 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Genetic Information Research Institute
Country United States 
Sector Charity/Non Profit 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Glasgow Caledonian University
Country United Kingdom 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Huazhong Agricultural University
Country China 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Iowa State University
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Jeju National University
Country Korea, Republic of 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Kansas State University
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Konkuk University
Country Korea, Republic of 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Konkuk University
Country Korea, Republic of 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Korea Research Institute of Bioscience and Biotechnology (KRIBB)
Country Korea, Republic of 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation National Health and Medical Research Council
Country Australia 
Sector Public 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation National Institute of Agrobiological Science, Japan
Country Japan 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation National Institute of Animal Science, Korea
Country Korea, Republic of 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation National Institute of Animal Science, Korea
Country Korea, Republic of 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Parco Tecnologico Padano
Country Italy 
Sector Private 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Penn State University
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Science for Life Laboratory
Country Sweden 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Seoul National University
Country Korea, Republic of 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation U.S. Department of Agriculture USDA
Department Beltsville Agricultural Research Center
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation U.S. Department of Agriculture USDA
Department U.S. Meat Animal Research Center
Country United States 
Sector Public 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation U.S. Department of Agriculture USDA
Country United States 
Sector Public 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University College London
Department Division of Infection and Immunity
Country United Kingdom 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of California, Berkeley
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of California, Davis
Department UC Davis Genome Cente
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of Copenhagen
Department Department of Basic Animal and Veterinary Sciences (IBHV)
Country Denmark 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of Illinois
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of Illinois at Urbana-Champaign
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of Illinois at Urbana-Champaign
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of Illinois at Urbana-Champaign
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of Illinois at Urbana-Champaign
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of Illinois at Urbana-Champaign
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of Kent
Country United Kingdom 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of Leipzig
Country Germany 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of Minnesota
Country United States 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation University of Wageningen
Country Netherlands 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Uppsala University
Country Sweden 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description International Swine Genome Sequencing Consortium 
Organisation Uppsala University
Country Sweden 
Sector Academic/University 
PI Contribution The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation.
Collaborator Contribution The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398)
Impact The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners.
 
Description The Ovine FAANG Project 
Organisation AgResearch
Department Invermay Agricultural Centre
Country New Zealand 
Sector Private 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The Ovine FAANG Project 
Organisation Baylor College of Medicine
Country United States 
Sector Hospitals 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The Ovine FAANG Project 
Organisation Commonwealth Scientific and Industrial Research Organisation
Country Australia 
Sector Public 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The Ovine FAANG Project 
Organisation U.S. Department of Agriculture USDA
Department U.S. Meat Animal Research Center
Country United States 
Sector Public 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The Ovine FAANG Project 
Organisation University of Idaho
Country United States 
Sector Academic/University 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The Ovine FAANG Project 
Organisation Utah State University
Country United States 
Sector Academic/University 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The Ovine FAANG Project 
Organisation Washington State University
Department Washington State University Spokane
Country United States 
Sector Academic/University 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) 
Organisation Diagenode
Country Belgium 
Sector Private 
PI Contribution The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis
Collaborator Contribution The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement.
Impact Successful application for European Commission H2020 funding. Multidisciplinary
Start Year 2017
 
Description The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis
Collaborator Contribution The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement.
Impact Successful application for European Commission H2020 funding. Multidisciplinary
Start Year 2017
 
Description The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) 
Organisation French National Institute of Agricultural Research
Department INRA Toulouse
Country France 
Sector Public 
PI Contribution The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis
Collaborator Contribution The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement.
Impact Successful application for European Commission H2020 funding. Multidisciplinary
Start Year 2017
 
Description The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) 
Organisation French National Institute of Agricultural Research
Country France 
Sector Academic/University 
PI Contribution The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis
Collaborator Contribution The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement.
Impact Successful application for European Commission H2020 funding. Multidisciplinary
Start Year 2017
 
Description The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) 
Organisation Hendrix Genetics
Country Netherlands 
Sector Private 
PI Contribution The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis
Collaborator Contribution The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement.
Impact Successful application for European Commission H2020 funding. Multidisciplinary
Start Year 2017
 
Description The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) 
Organisation University of Wageningen
Country Netherlands 
Sector Academic/University 
PI Contribution The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis
Collaborator Contribution The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement.
Impact Successful application for European Commission H2020 funding. Multidisciplinary
Start Year 2017
 
Description The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) 
Organisation Uppsala University
Country Sweden 
Sector Academic/University 
PI Contribution The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis
Collaborator Contribution The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement.
Impact Successful application for European Commission H2020 funding. Multidisciplinary
Start Year 2017