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 23789 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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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 v9.14 Released

We released version 9.14 of DECIPHER on the 5th of April, 2017. Improvements include:

  • Additional family members can be created for patients and phenotypes recorded.
  • Manifestations for absent phenotypes can now be recorded, such as the patients age at clinical observation.

  • A pathogenicity filter has been added to the ClinVar track in the genome browser, allowing users to choose to see only pathogenic variants.
  • The amino acid position is now displayed in the pop-up when clicking on an amino acid in the transcript or human sequence in the conservation track.
  • For security reasons, users using Internet Explorer 8 or older can no longer access the DECIPHER website. Users using Internet Explorer versions 9 and 10 can access the site but will be unable to log in. These changes will not affect users accessing our website using Firefox, Chrome, or Internet Explorer 11.

Curating the Clinical Genome meeting 2017

The 2017 Curating the Clinical Genome meeting, co-hosted by ClinGen and DECIPHER, will take place in Washington, DC June 28-30, 2017.

Early bird registration deadline is March 31, 2017.

DECIPHER v9.13 Released

We released version 9.13 of DECIPHER on the 22nd of February, 2017. Improvements include:

  • A Summative Assessment tool to support multidisciplinary teams working to evaluate whether a variant(s) explains the clinical features seen in a patient. This tool uses a framework to evaluate the Clinical fit and then enables the user to select the OMIM gene-disease pair that best fits the patient and to select possible options to summarize the fit (for example, genetic diagnosis confirmed).

  • ClinVar variants are now shown on the protein browser.

  • A pathogenicity filter has been added to the DECIPHER sequence variant track.

  • The display of ClinVar and dbSNP variants in the genome browser has been improved, allowing the user to more easily identify if multiple variants are located in the same position when zoomed in.

  • The pathogenicity of DECIPHER sequence variants is now shown in the popups on the genome and protein browsers, when a user clicks on the variant.
  • The patient phenotype interface displays icons representative of high-level phenotype terms.

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 MyGene2 in 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.

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.