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 25047 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 v9.19 Released

We released version 9.19 of DECIPHER on the 29th of November, 2017. Improvements include:

  • Exon boundaries are now shown in the protein browser allowing the position of patient variants in relation to exon structure to be easily identified. Positional information and exon number is provided by clicking on the relevant exon or exon border.
  • Minor Allele Frequency information for combined gnomAD exome and genome data is now available on the annotation tab.
  • A link to Genomics England PanelApp, a crowdsourcing tool from Genomics England which allows gene panels to be shared, downloaded, viewed and evaluated by the scientific community, is now available on the clinical tab.

DECIPHER v9.18 Released

We released version 9.18 of DECIPHER on the 4th of October, 2017. Improvements include:

  • Protein browser track settings are now available, allowing users to customise which information is visible on the protein browser. Pathogenicity filters for DECIPHER and ClinVar variants have also been added.
  • DECIPHER and ClinVar variants on the protein browser are now represented as hollow outlines, unless they are annotated as likely pathogenic/definitely pathogenic. This provides the user with an overview of the location of pathogenic variants in their gene of interest.
  • A ClinVar 3 and 4 star review status filter has been added to the genome and protein browsers.
  • The overlapping patient interface now includes a phenotype summary to assist in determining recurrent overlapping phenotypes.
  • Pathogenicity evidence is now shown on a patients summative assessment. The summative assessment tool supports multidisciplinary teams working to evaluate whether a variant(s) explains the clinical features seen in a patient.
  • Matchmaker Exchange search requests now include DDD research variants. The DDD research variants are variants of unknown significance in 4293 children with developmental disorders in the UK DDD study.
  • The diagnosed disorder code (OMIM phenotype MIM code) from openly shared patient summative assessments is now shared over Matchmaker Exchange.

DECIPHER v9.17 Released

We released version 9.17 of DECIPHER on the 9th of August, 2017. Improvements include:

  • Minor Allele Frequencies for sequence variants from gnomAD are now shown in the patient sequence variant table. This allows the frequency of the patient variant(s) in the population to easily be viewed.The link to the Minor Allele Frequency can be found in the Annotation column in the sequence variation table in the Genotype tab
  • Minor Allele Frequency information from gnomAD for variants that match the patient variant are now showed on an Annotation tab when viewing the patient record. Consequence prediction (VEP) information can also be viewed on the “Annotation” tab.
    Minor Allele frequency is shown with all subpopulations in gnomAD
  • A tolerated population variation calculator described by Whiffin et al., 2017 is now available in DECIPHER. The calculator allows the determination of whether a variant observed in the reference sample is too common to cause a given Mendelian disorder of interest. The calculator can be accessed from the new Annotation tab when viewing a patient record or by clicking on the exome/genome MAF in the sequence variant table.
    The allele frequency calculator for the LAMA2 variant
  • Missense constraint data can now be viewed on the genome and protein browsers. Missense constraint analysis is based on the ExAC dataset and evaluates how intolerant (“constrained”) a gene or gene region is to missense variants.
    There are four regions within CDK13 which have different missense constraint levels, here shown on a protein view in DECIPHER
  • Within the summative assessment tool, a new very strong level has been created for the evidence line clinical fit. The Summative assessment tool supports multidisciplinary teams working to evaluate whether a variant(s) explains the clinical features seen in a patient.

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.