by Sabrina Toro, on behalf of the ZFIN and Alliance teams
The Zebrafish Information Network (ZFIN; zfin.org) is one of the founding members of the Alliance of Genome Resources (Alliance; alliancegenome.org). The Alliance aims to provide a unified, comparative view of animal model and human data to facilitate foundational and translational biomedical research.
The ambitious effort to unify variant and allele information is currently underway, with the objective to compare human and animal model variants and alleles, their consequences, and the phenotypes they might induce.
Genomic coordinates and nucleotide change(s) of alleles/variations are becoming crucial information in order to make the variants/alleles and associated phenotype data relevant and accessible for display, prediction, cross-species comparison, and translational research application. Genome browsers (such as JBrowse) and tools to predict the effects of variants on transcripts and proteins (such as the Ensembl Variant Effect Predictor) require this genomic coordinate information. Precise genomic coordinate locations must include the genome build, chromosome and base number(s) in order to properly locate any variation. This detailed information is rarely reported in publications and therefore is often unavailable for alleles/variants recorded at ZFIN.
We need the zebrafish community’s help to obtain this missing information, and ultimately make the zebrafish alleles/variants information more relevant and valuable to the research and clinician community. If you have the build version, chromosome, genomic coordinates and nucleotide change of your mutant, or if you have any sequence data which would help us determine the location, please add this information to the genomic coordinates Excel file and submit to Sabrina@zfin.org. Feel free to contact us (firstname.lastname@example.org) for more information, or with questions or comments.