It’s free and you don’t need to log in
DECIPHER is used by the clinical community to share and compare phenotypic and genotypic data. The DECIPHER database contains data from 17623 patients who have given consent for broad data-sharing; DECIPHER also supports more limited sharing via consortia. Have a look at the numbers.
Anyone can browse publicly-available patient data on DECIPHER and request to be put in contact with the responsible clinician. Why? Because sharing benefits everyone.
Be part of the sharing community
Projects affiliated to DECIPHER can deposit and share patients, variants, and phenotypes to invite collaboration and facilitate diagnosis. Once deposited, you can use DECIPHER to identify and prioritise potential matches, and you can request notifications as soon as new matches arrive.
As well as influencing individual patient outcomes, use of DECIPHER has contributed to over 700 published articles since 2004. It's still free, and you are in control of what data to make public.
Already a member?
Log in to access your patient data
DECIPHER v9.1 Released
Version 9.1 of DECIPHER was released on Wednesday 19th August and introduces the following new features and enhancements:
- All new patients are associated with a point of contact. By default this will be the person creating the patient record. However, patient consent can only be recorded if the responsible contact is a clinician; it is the clinician who must establish that informed consent has been given. For existing patients who do not have a contact point assigned yet, the project coordinator has now been assigned.
- Genoverse can now be made fullscreen on most browsers.
- Selecting a region tells you the chromosome, start and end position of the region you’ve selected.
- You can now highlight features and regions, making it easier to compare features in multiple tracks.
- When viewing a sequence variant, the transcript the variant belongs to will always be at the top of the transcripts track and will be shaded.
- Feature and tracks menu are now opaque and icons have been standardised.
- Making contact requests are now easier if your own patients are in DECIPHER. When making contact requests, you can now add automatically-generated summaries of your own overlapping patients to the message.
- Patient copy-number variant to copy-number variant overlap can be filtered by the HGNC name of a common gene.
- Intergenic sequence variants can now be deposited. A transcript is not required but the gene the variant interacts with is required.
DECIPHER v9.0 Released
Version 9.0 is a major update to DECIPHER and was released on the 8th of July, 2015. Apart from many improvements to the overall look-and-feel of the website, we have introduced the following salient features in this release.
- New look main landing page: We have made changes to the front page to make it easier to find items including login, database statistics, help documents etc.
- Internal Matchmaker: Save time and find new matching records in DECIPHER! Get notified when a new variant matching one in your patient is seen in DECIPHER. Activate by clicking the bell icon next to your publicly shared variants in your consented patients to follow the variant. A notification will be generated automatically when a new variant functionally similar to yours is made available in DECIPHER. Access your notifications by logging back into DECIPHER periodically.
- External Matchmaker: DECIPHER is part of the Matchmaker Exchange project (MME). The MME provides a robust and systematic approach to rare disease gene discovery, through the creation of a federated network connecting databases of genotype and rare phenotypes.Using a common Application Programming Interface (API) connected databases (currently PhenomeCentral and GeneMatcher) will be queried for patient records that share similarity with your anonymous consented patients and the results will be displayed below. Find the “Matchmaker” tab on your patient page between “Karyotype” and “Citations”.
- Introducing “My Dashboard”: Dashboard is a page that is specific to you and includes a collection of items pertinent to your use of DECIPHER. We have included mechanisms to create or access your patients, or manage variants you are following (for automatic notifications when other matching variants are deposited in DECIPHER). You need to be logged in to view the dashboard.
- New Browser Tracks
- Sequence Conservation Track: Showing protein sequence conservation across species for orthologous genes.
- ExAC: Variants identified by the Exome Aggregation Consortium with genotype and allele counts.
- Updated Features
- Directionality of Genes.
- CNV Filters for pathogenicity: Choose to see all, pathogenic, uncertain or benign CNVs using track filters.
- CNV Filters for size: Choose to exclude overlapping DECIPHER CNVs based on size using track filters.
- CNV Shading: CNVs are now shaded according to pathogenicity.
- Population Data represented in dbSNP track (where available)
- Improvements to track-specific help.
- New Browser Tracks
- Functional Similarity Scores: Overlapping variants now have a functional similarity score associated with them. This is an estimate of the likelihood that the overall effects of two variants are similar and can be used to prioritise variants by relevance. This score is arrived at by comparing the type of effect the variants are believed to have (e.g. gain, loss, VEP consequence), and, for CNVs, how many genes the variants affect. You can find functional similarity scores under the “Overlapping Patients” section when viewing a patient variant.
- Dosage-sensitivity scores and sampling probabilities: We now automatically calculate dosage sensitivity (DS) scores for all CNVs deposited to DECIPHER. DS scores provide an estimate of the likely pathogenicity of the variant based on log-odds scores of predicted haploinsufficient genes within a copy-number variant. Higher scores indicate that the CNV is likely to be pathogenic while low or negative scores could be indicative of non-pathogenicity.
- Empowering Project Coordinators: Project Coordinators in DECIPHER will now need to login and approve any membership requests. They will also be able to keep track of the users with access to their projects and be able to revoke access for users who are no longer required to have access to the project.
For more news about DECIPHER, click here.
DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. Firth, H.V. et al (2009). Am.J.Hum.Genet 84, 524-533 (DOI: dx.doi.org/10/1016/j.ajhg.2009.03.010)
Authors who use data from the project must acknowledge DECIPHER using the following wording: "This study makes use of data generated by the DECIPHER community. A full list of centres who contributed to the generation of the data is available from http://decipher.sanger.ac.uk and via email from firstname.lastname@example.org. Funding for the project was provided by the Wellcome Trust."
Please see Citing DECIPHER for more information.