Using Ensembl to Understand Variation Data

Date: Sunday, January 13, 2013
Time: 9:30 AM
Room: California
Laura Clarke , European Molecular Biology Laboratory, Cambridge, United Kingdom
Fiona Cunningham , EBI, Cambridge, United Kingdom
William McLaren , EBI, Cambridge, United Kingdom
Graham Ritchie , EBI, Cambridge, United Kingdom
Laurent Gil , EBI, Cambridge, United Kingdom
Anja Thormann , EBI, Cambridge, United Kingdom
Sarah Hunt , EBI, Cambridge, United Kingdom
Ensembl (http://www.ensembl.org) is a genome information system-- a central repository for biological data with a comprehensive web-based genome browser.

Ensembl provides comprehensive variation annotation: short sequence variants, allele and genotype frequencies, ancestral alleles, structural variants and human phenotype data. For all species, we calculate the effect of each variant allele on overlapping transcripts, and whether the variant falls within a regulatory feature, transcription factor binding motif, or a high information position within the motif.

Recognising the utility of this pipeline, we have created an independent ‘Variant Effect Predictor’ (McLaren et al, Bioinformatics 2010) as a tool for your own data. This accepts variation positions and allele changes from the user and outputs the predicted consequence of these variants. The output can contain the: transcript, CDS and amino acid position; codon and amino acid change; exon number; regulatory regions and identifiers of known variants at that position.

To support the many different use cases for this tool, we have written a plugin system for adding functionality so that the VEP may be extended by the user. In addition custom annotation or variation data can be simultaneously queried in a local tabix- indexed file. We are planning to release a version supporting structural variants.