Genome Interpretation | EMBL-EBI

Genome Interpretation

Genome Interpretation Team Leader



PhD in bioinformatics, University of Cambridge, 2014. At EMBL-EBI since 2008, Variation Annotation Team Leader since 2016, Genome Interpretation Team Leader since 2021.

Dr Fiona Cunningham is interested in problems where building large-scale systems for genomic data can lead to fundamental biological insights, particularly for understanding genomic variation. At EMBL-EBI she is responsible for genome interpretation and variation resources. Her team developed Ensembl's Variant Effect predictor (VEP), the software tool for annotating variation data.

Fiona is part of the senior management for Ensembl (, a genome information system, and led the creation of the variation and phenotype data in Ensembl. Fiona shares leadership of Ensembl’s genome interpretation strategy and has overall responsibility for the variation resources in Ensembl. In collaboration with the NHGRI, she is one of the PIs for the GWAS Catalog and formally, she led the Variant Annotation task team for the Global Alliance for Genomic Health project (GA4GH).

Fiona is committed to open data and standards, in particular to share data and facilitate the transfer of research knowledge into valuable resources. In collaboration with the NCBI in the USA, Fiona leads the Matched Annotation from NCBI and EMBL-EBI (MANE) initiative, which aims to release a genome-wide transcript set with only one well-supported transcript per protein-coding locus. All transcripts in the MANE set will perfectly align to GRCh38 and will represent 100% identity between RefSeq and Ensembl/GENCODE. She also worked on the development of reference sequences, called LRG (Locus Reference Genomic) sequences, a stable data standard for reporting clinical variants with support for legacy sequences as part of the Transforming Genomic Medicine Initiative (TGMI).

Prior to EMBL-EBI, Dr Cunningham worked at the Wellcome Sanger Institute, Cold Spring Harbor Laboratory, and at deCODE Genetics in Iceland.


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