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 24909 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 v9.18 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.

DECIPHER v9.16 Released

We released version 9.16 of DECIPHER on the 26th of July, 2017. Improvements include:

  • Normalisation of patient sequence variants. The same variant can be represented in multiple ways by different systems. Patient variants on the DECIPHER website are now normalised to facilitate the comparison of patient variants with variants from other resources. Variants in DECIPHER are left aligned and parsimonious, as described in Tan et al. 2015.

  • DDD research variants, ClinVar variants and gnomAD variants shown in the genome and protein browsers are normalised using the same method as DECIPHER patient variants, allowing users to more easily identify matching variants.

DECIPHER v9.15 Released

We released version 9.15 of DECIPHER on the 31st of May, 2017. Improvements include:

  • gnomAD variant data replaces ExAC data in the genome and protein browsers. The Genome Aggregation Database (gnomAD), contains exome and genome sequencing data spanning 123,136 exomes and 15,496 genomes from unrelated individuals sequenced as part of various disease-specific and population genetic studies. In its first release, which contained exclusively exome data, it was known as the Exome Aggregation Consortium (ExAC).

  • gnomAD coverage data is now shown in the genome browser, allowing users to view sequencing coverage of both exomes and genomes.

  • The Summative Assessment tool, which supports multidisciplinary teams working to evaluate whether a variant(s) explains the clinical features seen in a patient, now has a free text box. This allows additional evidence for the genotype-phenotype relation to be recorded.

  • A legend for CNV colours has been added to the genome browser.

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.