Towards Common Standardized Procedures for the Functional Annotation of Animal Genomes (FAANG)

A central goal of ASA is to foster collaborations, avoid redundancies and enhance synergies in terms of animal/sample collection for each of the related molecular assays. Currently, a large set of tissues is shared by several pilot projects. Breed, age, environment and physiological state at sampling vary, which increases heterogeneity but also the potential for comparisons across tissues and cell types. To organize FAANG collections and deal with this complexity, ASA collaborates with the ‘Metadata & Data Sharing’ Committee for defining the minimum requirements, suitable ontologies, reference databases and example metadata for the FAANG collections. Protocols for assays are being developed based on standards defined by the ENCODE projects and the International Human Epigenome Consortium (IHEC) as references. A set of core assays, which primarily employ technologies (whole genome re-sequencing, RNA sequencing, chromatin accessibility and histone marks) that work across all targeted species  are the starting point; additional assays are being developed by individual research groups based on specific needs and research interests (Box 1 in Andersson et al. 2015; PMID: 25854118). The Committee is working to adapt these assays where necessary, taking into account the complexities of individual species and the different tissues available. These protocols will then be refined through the Committee’s page of the FAANG wiki (http://www.ebi.ac.uk/seqdb/confluence/display/FAANG/) and become standards. The expected outcome of these activities is to standardize the best practice tools and resources for facing the genotype-to-phenotype challenge in domesticated animals.