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DECIPHER is used by the clinical community to share and compare phenotypic and genotypic data. The DECIPHER database contains data from 21728 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 1000 published articles since 2004. It's still free, and you are in control of what data to make public.
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DECIPHER v9.10 Released
We released version 9.10 of DECIPHER on the 10th of August, 2016. Improvements include:
- Bulk Upload via HGVS: you can now deposit sequence variants in bulk using a complete HGVS code instead of chromosomal position. There is a new Bulk Upload CSV/Excel template for you to use in this case.
- Prenatal patient records (patients initially referred to a clinicial geneticist before birth) can now also be deposited via Bulk Upload.
- Project pages now load much faster, particularly in cases where projects have thousands of patient records.
DECIPHER Data Centre essential maintenance and website downtime
Due to essential Data Centre maintenance, the DECIPHER website will be unavailable from 17:00 BST on Friday 26th August 2016 BST until 11:00 BST on Tuesday 30th August 2016.
If you require further information please contact email@example.com.
We apologise for any inconvenience caused.
DECIPHER v9.9 Released
We released version 9.9 of DECIPHER on the 29th of June, 2016. Improvements include:
- Developmental milestones and growth measurements of your patient are now shown on the gene tab when looking at a Sequence Variant:
- Splice acceptor/donor variants are now shown on proteins
- 3D protein structures now have a reset button so you can restore a protein-wide view if you have moved the protein out of view
We’ve also been working in the background to prepare as the clinical community transitions to GRCh38.
DECIPHER v9.8 Released
We released version 9.8 of DECIPHER on the 25th of May, 2016. In addition to the new features below, please note that starting on 23rd June, we will be activating our “two-year hold” policy: unshared patients can be stored in DECIPHER for up to two years while preliminary pathogenicity assessments are made and informed consent is obtained and recorded for sharing variants. Once patient data is shared (either in a consortium or by consenting patients and variants for open-access release), patients will continue to be available indefinitely. Emails have already been sent out to those with unshared patient data entered before May 2014, and logged-in depositors can check the status of any patient (including how long they have left to obtain informed consent, if relevant) by visiting the patient page.
- Gene pages and views (under the clinical tab) now include plots of quantitative data associated with patient genes, including:
- Birth Weight
- Occipital Frontal Circumference
- Social Smile
- Sat Unaided
- Walked Unaided
- First Words
- Sex Ratio
This helps us to see that patients with EP300 variants appear to be more likely to be smaller and lighter, and have much smaller OFC than either a normal distribution or the typical DECIPHER patient. The data does not show any clear difference in the time when EP300 children exhibit a social smile.
Growth and development charts are shown where sufficient data exists in DECIPHER (minimum five patients for any chart); physical measurements are shown as standard deviations from the median, adjusted for age and sex.
This data is taken only from patients with open-access DECIPHER variants in the gene in question. Most of this data will have been gathered through the Deciphering Developmental Disorders project.
- Consent button and status on patient pages: If you are a depositor, you will see a green ‘Consent’ button you can use to record informed consent for open-access sharing on patient records where consent has not yet been recorded.
- Ligands and other structures marked “hetero atoms” in the 3D protein structure view are now displayed using a “ball-and-stick” view, as displayed below.
- When viewing patient images, users may now opt for a black border surrounding the image (useful for retinal imaging).
DECIPHER v9.7 released
We released version 9.7 of DECIPHER on the 27th of April, 2016. Our headline feature in this release is a 3D protein view: a visualisation of a deposited sequence variant on an experimentally determined protein structure (where available) from the Protein Data Bank (PDB). Where there are experimental structures available for a region that contains one or more open-access sequence variants, these can be seen from our gene pages (e.g. MECP2 or TBL1XR1). Then, click on one of the green bars on the protein domain view (representing PDB structures and their coverage) and choose “view” to see the variants we have in the region covered by the structure in the 3D view.
We have also made many other under-the-hood changes to DECIPHER to allow us to roll out new features in future releases!
DECIPHER Video Tutorials
We are producing a series of video tutorials that showcase different aspects of the DECIPHER platform. Please subscribe to the DECIPHER YouTube channel to be kept updated on new tutorials as and when produced. We also welcome your suggestions for new tutorials.
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.