Mapping the clinical genome

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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 22210 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.

Explore DECIPHER’s genome browser Delve into the Human Phenotype Ontology Search all open-access DECIPHER data

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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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Latest news

DECIPHER v9.12 Released

We released version 9.12 of DECIPHER on the 7th of December, 2016. Improvements include:

  • Loss Intolerance probability (pLI) scores from ExAC are now shown. You can choose to colour genes by their pLI scores in the genome browser. The pLI score is also shown on the gene tab and on the clinical overview tab.
    pli

  • The 2D protein view has been improved. DECIPHER sequence variants are now displayed above the protein domains, whilst the Pfam annotations are shown below the protein domains.

    pfam_dyrk1a

  • Sequence variants in the genome and protein browsers are now visually more distinct. Loss of function variants are shown in red and protein altering variants in yellow.
  • Users can now use Matchmaker exchangeto find patient matches in MyGene2in addition to PhenomeCentraland GeneMatcher.
  • The Pathogenicity evidence tab for sequence variants now allows users to record that pathogenicity evidence has been assessed and that none of the ACMG criteria are met. If pathogenicity evidence has been assessed for a variant, a link to the evidence is now shown in the genotype table below the pathogenicity contribution status.

DECIPHER v9.11 Released

We released version 9.11 of DECIPHER on the 2nd of November, 2016. Improvements include:

  • Patient sequence variant pathogenicity evidence can now be recorded based on the pathogenicity evidence given under ACMG standards and guidelines when adding or editing a sequence variant.
    pathogenicity evidence tab
  • Composite face images created from individuals with de novo mutations in twelve developmental genes can now be viewed with other quantitative data on the gene tab when looking at a sequence variant. These images highlight facial dysmorphologies specific to certain gene.

    composite-face

    Composite face of 19 patients with pathogenic sequence variants in KMT2A

  • The phenotyping interface has been remodelled to allow patient phenotype information to be added more easily.
    phenotyping interface
  • Classes of variants have been changed to a five-tier terminology system in line with ACMG recommendations; definitely pathogenic (>99%), likely pathogenic (>90%), uncertain significance (10-90%), likely benign (<10%) and benign (<1%). The possibly pathogenic class (>80%) has been removed.
  • Filters have been added to the transcript track allowing you to filter on non-coding/coding genes and filter on DD and Morbid genes.
  • Phenotypes have been added to overlapping syndromes page
  • Bulk upload template has changed: header row, allowed values for mother/father status, allowed values for pathogenicity.

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.

    HGVS Bulk Upload

    NB: If you have a complete HGVS code, you could already deposit sequence variants individually this way.

  • 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 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: Four of the nine growth and developmental charts for EP300
  • 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.

For more news about DECIPHER, click here.


Citing DECIPHER

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 decipher@sanger.ac.uk. Funding for the project was provided by the Wellcome Trust."

Please see Citing DECIPHER for more information.

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