Greetings from a wet and cloudy Cambridge.
In this update:
- Version 10.3 released
- Important updates to study documents
Version 10.3 released
You can also view this on the web at: http://decipher.sanger.ac.uk/about/news
In this release, when your mouse hovers over a 3D protein view, information such as amino acid/position and ligand are now displayed in the top left corner. To access the 3D protein view, click on a green bar in the 3D Structures track. View the EP300 protein here: https://decipher.sanger.ac.uk/gene/EP300/overview/protein-info
DECIPHER now displays ClinGen Sequence Variant Interpretation Working Group (https://clinicalgenome.org/working-groups/sequence-variant-interpretation) recommendations for the loss of function PVS1 criterion, de novo criteria PS2/PM6 and in trans PM3 criterion. These recommendations can be accessed by clicking on the "Further information" icon next to the relevant criteria on the pathogenicity evidence tab. An interactive version of the PVS1 decision tree is also available: https://decipher.sanger.ac.uk/patient/262118/genotype/210873/pathogenicity
CADD (https://pubmed.ncbi.nlm.nih.gov/24487276) and spliceAI (https://pubmed.ncbi.nlm.nih.gov/30661751) scores are now displayed on the pathogenicity evidence tab when adding computational and predictive data evidence criteria. In addition, a reminder to add variant grouping is shown on the pathogenicity evidence tab when viewing allelic data. Variant grouping can be used to represent, for example, compound heterozygous variants or rare pathogenic haplotypes.
Exon and intron numbering is now displayed in the transcripts track in the genome browser. This allows users to easily determine the location of their patient's variant.
Also in this release, the date of variant deposition and the date of last pathogenicity call is now displayed to registered DECIPHER users for patients for which they have read/write or write permissions. This enables depositing centres to determine the length of time since deposition and pathogenicity assessment. Variant deposition for sequence variants using HGVS codes in GRCh38, is also now supported.
Important updates to study documents
Following a recent research ethics amendment, the DECIPHER patient information sheet, consent form and assent form have been updated. The new documents are available to download from the DECIPHER website: https://decipher.sanger.ac.uk/about/downloads/documents. If you are using these documents, please now use the updated versions.
The project proposal, data flowchart and ethical framework have also been updated.
Clinical genetics centres from around the world deposit data to DECIPHER. In view of this, the web domain will be updated over the coming months from https://decipher.sanger.ac.uk to https://deciphergenomics.org. This change is reflected in the updated documents. At present anyone visiting https://deciphergenomics.org will be re-directed to https://decipher.sanger.ac.uk to ensure that our users do not have any issues accessing the DECIPHER website.
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 in.
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager