Greetings from sunny, chilly, autumnal East Anglia.
In this update:
* Wellcome funding and move to EBI
* DECIPHER v11.8 Released
o New sequence variant and protein pages
o Clinvar annotation tab
o Deposition of mosaicism by tissue, for mosaic UPD variants
* Optional DECIPHER ClinVar submission
Wellcome funding and move to EBI
We are pleased to announce that DECIPHER has been awarded a new Wellcome grant to continue
its work through to 2025.
Key goals include better support for variants in the non-coding genome, helping users find
relevant functional evidence, and building models to link genes and disorders with
phenotypes. The grant will allow us to keep DECIPHER up to date with best practice and
emerging opportunities in clinical interpretation as the landscape evolves.
The grant also provides for a transition of DECIPHER's hosting and development from
the Wellcome Sanger Institute (where DECIPHER began and has been based for the last 17
years) to the European Bioinformatics Institute (EMBL-EBI; https://www.ebi.ac.uk
runs Ensembl and its Variant Effect Predictor (VEP), Gene2Phenotype and many other
resources which are critical to DECIPHER's work. It is intended that the team will
move in April 2022. Co-PI Helen Firth will remain the clinical lead; Matt Hurles will step
back as co-PI but will remain involved as a collaborator and Fiona Cunningham, who leads
EBI's Genome Interpretation Team, will join as co-PI. Both institutes are committed to
a smooth transition and the migration will not involve any changes to the address (URL),
the appearance, or the functionality of DECIPHER.
The Deciphering Developmental Disorders (DDD) project (https://www.ddduk.org
), which has
recruited nearly 14,000 families in the UK and Ireland, will still deliver results through
DECIPHER, while the research work will remain at Sanger. We expect to provide further
information on the arrangements to DECIPHER depositors closer to the time of the move.
DECIPHER v11.8 Released
You can also view this on the web at: https://www.deciphergenomics.org/about/news
It is now possible to search for information about single sequence and protein variants.
DNA sequence variant search supports searching by GRCh38 location, by SPDI, HGVSg or
Ensembl stable IDs, in addition to HGVSc plus HGNC gene symbol or Refseq transcript.
Protein variant search supports searching by HGVSp (single letter or trigraph) plus HGNC
gene symbol of Refseq transcript. Searching for sequence variants now takes you to a
dedicated sequence variant page, which displays information relevant to that variant. The
following page provides information on a missense variant in SPOP:
Searching for protein variants takes you to a dedicated protein variant page, which
displays information relevant to that protein change. The following page provides
information on a Arginine to Tryptophan change in PACS1:
A new Clinvar annotation tab is available on patient variant, sequence variant and protein
variant pages. This tab contains information about ClinVar assertions. In this example,
the variant has 0, 1 and 2 star ClinVar assertions:
It is now possible for depositors to record mosaicism by tissue, for mosaic UPD variants.
Optional DECIPHER ClinVar submission
DECIPHER now supports the deposition of variant data to ClinVar
) to enable the greater sharing and aggregation of
variant data globally. Submission is optional and the coordinator(s) of a DECIPHER project
must approve ClinVar deposition before DECIPHER will deposit data to ClinVar on their
DECIPHER will only deposit variant data from openly shared patient records, for which
explicit patient consent for open sharing has been recorded in DECIPHER. Only openly
shared data will be included in the submission. DECIPHER will deposit variant information
and high level phenotype information, in addition to a link to the relevant DECIPHER
If you are interested in DECIPHER submitting the openly consented data in your project to
ClinVar, please speak with the coordinator(s) of the project at your centre and/or contact
us at email@example.com<mailto:firstname.lastname@example.org>
We look forward to your feedback and suggestions for improvement. Please use the
"Feedback" button which is available on every page and fill in the simple form
to get in touch with us. Your details will be filled in automatically if you are logged
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager