Cool stuff the Ensembl VEP can do: variant citations

If you are filtering a set of variants to look for those potentially involved in disease, your first stop will probably be databases of phenotype associations, like ClinVar. There is also a lot of valuable information on variant-disease associations in the literature, which may not yet have been extracted into curated databases. It can be hard to compile lists of citations for a large set of variants, but Ensembl VEP is here to help! 

We collect citations submitted with variants to databases like dbSNP, dbGAP and ClinVar, those curated in the GWAS Catalog as well as those resulting from data mining performed by our collaborators at Europe PMC and the University of California, Santa Cruz. Most of the citations are for human variants, but other species have some data too. The PubMed IDs for these citations are all available in the VEP cache – they are reported by default in our REST and web interfaces and are available in command line VEP using the –pubmed option. The web interface has a handy link to the publication in Europe PMC so you can find more details quickly.

If you are using VEP on the command line, there is another source of citations you can add to your results using the plugin system. The Genomenon Mastermind Cited Variants Reference holds variants for which clinical evidence has been cited in the medical literature and, importantly, mines variants by HGVS style names. The VEP Mastermind plugin tells you if a variant is in Mastermind, provides the number of citations available and the information you need to build a URL to get further information.

Together, these options can help you to easily extract valuable, in-depth information that others have published about your variants of interest and aid your understanding of the variants’ potential effect.