Greetings from a sunny East Anglia.
In this update:
- DECIPHER v11.16 Released
o ClinGen Clinical Actionability information on gene pages
o Protein browser
§ Cardiac VariantFX case cohort data
§ "Settings" menu renamed to "Tracks and filters"
§ DECIPHER and ClinVar variant consequence filters
§ DECIPHER variant patient filter
o Gene-disease associations
§ Display of Gene2Phenotype information on gene pages
§ GenCC badges in gene tables
o Additional title tags
- Move to EBI
DECIPHER v11.16 Released
You can also view this on the web at: https://www.deciphergenomics.org/about/news
ClinGen Clinical Actionability Report information is now displayed on gene clinical tabs for genes that, when significantly altered, confer a high risk of serious disease that could be prevented/ mitigated if the risk were known. Information for adult and paediatric subjects are available. In the following example a ClinGen Clinical Actionability report is available for Von Hippel Lindau Disease associated with variants in VHL: https://www.deciphergenomics.org/gene/VHL/overview/clinical-info
Cardiac VariantFX case cohort data is now displayed on the protein browser. This allows the visualisation of the distribution of case cohort data and allows users to browse the data. For each variant the allele number, count and frequency is displayed, with a link to a page which provides more in-depth cardiac case cohort information about the variant. The following example shows this feature for DSP: https://www.deciphergenomics.org/gene/DSP/overview/protein-genomic-info. In addition, the protein browser "Settings" menu has been renamed to "Tracks and filters" to increase findability. Consequence filters are now available for DECIPHER and ClinVar variants, allowing variants with only a defined predicted molecular consequence to be displayed. A DECIPHER variant patient filter is also available which allows only DECIPHER variants in, for example, "patients in my projects" or "patients not in my projects" to be displayed. These features can be viewed for ACTB here: https://www.deciphergenomics.org/gene/ACTB/overview/protein-genomic-info
The display of Gene2Phenotype gene/disease associations on gene pages has been updated, so that diseases associated with more than one panel are grouped, simplifying the display. This simplified view can be seen here for PTEN: https://www.deciphergenomics.org/gene/PTEN/overview/clinical-info. In addition, the strengths of gene/disease associations asserted by Gene2Phenotype and ClinGen in genes tables now match the colours used for those classifications by GenCC.
Finally, additional title tags are now available to allow users with multiple open tabs, to identify the relevant tab.
Move to EBI
In early 2023, DECIPHER's hosting and development will transition from the Wellcome Sanger Institute (where DECIPHER began and has been based for the last 18 years) to the European Bioinformatics Institute (EMBL-EBI), which runs Ensembl and its Variant Effect Predictor (VEP), Gene2Phenotype, UniProt and many other resources which are critical to DECIPHER's work. 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 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