Animals, Samples, and Assay Committee report

Standardization of every assay/protocol involved in the functional annotation of animal genomes is an essential prerequisite for sharing, integrating and global analysis of multiple datasets.  The overall objective of the Animals/Samples/Assays (ASA) Committee is to propose, develop and standardize animal/tissue collection protocols, storage practices, and processing protocols for the FAANG community.

Concerning animal/sample collections, 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 molecular 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). Committee's members are working to adapt these assays where necessary, taking into account the complexities of individual species and the different tissues available. Once drafted, protocols are shared through the Committee’s page of the FAANG wiki (http://www.ebi.ac.uk/seqdb/confluence/display/FAANG/) and finally published on the ASA Committee webpage as proposed standards to the FAANG community.

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.