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Functional
Annotation of
ANimal
Genomes (FAANG) Project
— A coordinated international action to accelerate Genome to Phenome
|
INRAE, Institut Agro, Brittany region & ANR ANR-CE20-EFFICACE [€400,000] (2019-03-01~2025-12-31)
Objectives: 1) Extend the ENSEMBL catalog by gathering different LNC resources (NCBI, NONCODE, ALDB, Fr-AgENCODE, LNC predicted from additional 356 RNA-seq data) 2) Investigate LNC conservation between chicken and mammals 3) Extract a gold standard LNC set 4) Atlas of tissue expression of LNC & protein coding genes (PCG) 5) Assess the genetic basis of intra-tissue LNC expression and PCG-LNC co-expression (200+ animals) in metabolic tissues with a focus on liver which will be related to lipid phenotypes, using RNA-seq, ATAC-seq, HiC and methylation profiles.
Project directors:
Primary contact: Sandrine.lagarrigue@agrocampus-ouest.fr Linked projects: FR-AgENCODE, GENE-SWitCH
Contact: Sylvain Foissac (sylvain.foissac@inrae.fr)
INRAE, Institut Agro, Brittany region 10^nRnaSeq [€130,000] (2020-01-06~2023-12-31)
Objectives: 1) Workflow for identifying SNP variants and genotypes from RNAseq data 2) Workflow for identifying cis-eQTL by Allele Specific Expression from RNAseq data 3) Explore cis-eQTL and short variants in protein-coding genes (PCG) and LNC in different populations.
Project directors:
Primary contact: Christophe.klopp@inrae.fr & Sandrine.lagarrigue@agrocampus-ouest.fr Linked projects: FR-AgENCODE, GENE-SWitCH
Contact: Sylvain Foissac (sylvain.foissac@inrae.fr)
EU Horizon Grant 815668 [€6,033,458] (2019-09-01~2023-08-31)
Objectives: The BovReg consortium will provide a comprehensive map of functionally active genomic features in cattle and how their (epi)genetic variation in beef and dairy breeds translates into phenotypes. we will generate functional genome data based on FAANG core assays from representative bovine tissues and newly established cell lines covering different ontological stages and phenotypes applying novel bioinformatic pipelines. We will establish detailed knowledge on traits related to robustness, health and biological efficiency in cattle. Data, knowledge and protocols will be deposited in European biological archives, aiming to set up and maintain a knowledge hub and establish gold standards. Our biology-driven genomic prediction tools will integrate biological knowledge on regulatory genomic variation into genomic selection schemes for local and global cattle populations.
Project directors:
Additional Info: The consortium consist of 20 partners from nine European countries and represent both academia and industry.
Contact: Christa Kuehn (kuehn@fbn-dummerstorf.de)
EU Horizon Grant 817923 [€6,000,000] (2019-05-01~2023-04-30)
Objectives: AQUA-FAANG will functionally annotate the genomes of all six fish species, employing standardized experimental assays and analysis pipelines defined by the FAANG initiative. AQUA-FAANG datasets will be shared and coordinated with other FAANG initiatives via the FAANG data coordination centre, and made available through the Ensembl genome browser. Functional assays will be used to study intermediate phenotypes and prioritise causative genetic variants in trait-associated genomic regions to accelerate selection of disease-resistant stocks. Functionally-enriched marker panels will be developed to improve accuracy of genomic selection.
Project directors:
Additional Info: Sigbjørn Lien, head of CIGENE, will be the coordinator of the project, with support from Daniel Macqueen from University of Edinburgh. The consortium consist of 24 partners from nine European countries and represent both academia and industry. (https://tinyurl.com/y2nvrbfo)
Contact: Sigbjorn Lien (sigbjorn.lien@nmbu.no)
INRAE INRAE-SELGEN-2015b [€29,444] (2021-01-01~2021-12-31)
Objectives: 1) Improve the genome annotation of 4 livestock species by producing and analyzing RNA-seq data using 11 tissue samples from the FR-AgENCODE project (including the 3 original ones). 2) Investigate gene conservation between the 4 species. 3) Characterize the tissue specificity of protein-coding and non-coding genes.
Project directors:
Website: www.fragencode.org This project is an extension of the original FAANG pilot project FR-AgENCODE and runs with the remaining part of the original grant.
Contact: Sylvain Foissac (sylvain.foissac@inrae.fr)
BBSRC Grant 0000-0000 [£543,722] (2016-01-11~2020-10-31)
Objectives: (1) Ensure high quality and rich supporting metadata to describe the project's animals, specimens, cell cultures and experimental assays by developing tools for the community to enrich and validate against FAANG metadata standards. (2) Develop the FAANG data portal (http://data.faang.org/) to provide a focused functional data resource from which researchers can explore, identify and download validated, richly described, high quality and comparable datasets for their genome to phenome research. (3) Provide a responsive helpdesk to the community, and promote and provide training on best practices in data management for the farmed and companion animal community.
Project directors:
Contact: Paul Flicek (flicek@ebi.ac.uk)
COST Action Award 15112 [$497000] (2016-04-13~2020-04-12)
Objectives: To facilitate the aims of the FAANG project through coordination, development of agreed standards for experiments, data and metadata, training and dissemination of standards and results.
Project directors:
Contact: Alan Archibald (alan.archibald@roslin.ed.ac.uk)
INRAE INRAE-SELGEN-2015 [€299,700] (2015-01-01~2017-12-31)
Objectives: As one of the first pilot projects of the FAANG initiative, the goal of the FR-AgENCODE project is to improve the functional annotation of 4 animal species: cattle, pig, chicken and goat. It includes the production and the analysis of mRNA-seq, sRNA-seq, ATAC-seq and Hi-C data on CD4/CD8 sorted T cells and liver samples from 2 males and 2 females of each species (Bos taurus, Sus scrofa, Gallus gallus and Capra hircus).
Project directors:
Reference: Foissac et al, 2019. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biol 17, 108 (2019). https://doi.org/10.1186/s12915-019-0726-5 Project web site: http://www.fragencode.org
Contact: Sylvain Foissac (sylvain.foissac@inrae.fr)
France-Berkeley Fund Grant 2016-0070 [$12,000] (2016-03-01~2017-02-28)
Objectives: Jointly develop standardized sampling protocols for the core “omics” FAANG assays
Project directors:
Contact: Huaijun Zhou (Hzhou@ucdavis.edu)
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