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 25773 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

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

Service Upgrade Tuesday 3 April 07:00 08:00 UK local time

There will be some disruption to this service on Tuesday 3 April 07:00 08:00 UK local time due to upgrades. We apologise for any inconvenience this may cause.

DECIPHER v9.21 Released

We released version 9.21 of DECIPHER on the 7th of March, 2018. Improvements include:

  • Copy number variants are now displayed (and deposited) with a class (deletion, duplication, triplication, duplication/triplication, amplification) and genotype (hemizygous, heterozygous, homozygous). Mean ratio is now an optional field. This allows the context of the copy number variants in a patient to be recognised more easily.
  • A pathogenicity filter has been added to the LSDB track in the genome browser, allowing users to select the pathogenicity of variants they would like to visualise.
  • Matching patients with sequence variants can now be filtered by sex.
  • Phenotypes associated with sequence variants in your gene of interest are now shown in separate tables for pathogenic variants and for pathogenic/uncertain/unclassified variants. This allows users to select which cohort of variants in which they would like to visualise discriminatory phenotypes.

DECIPHER Pre-Release Announcement: Data Deposition Changes

In early March there will be some changes to the information required to deposit copy number variants and sequence variants to DECIPHER.

For copy number variants the changes will be:

  • Mean ratio will be optional.
  • Class will be mandatory (deletion, duplication, triplication, duplication/triplication, amplification).
  • Genotype will be mandatory (hemizygous, heterozygous, homozygous, mitochondrial homoplasmy, mitochondrial heteroplasmy).

For sequence variants the changes will be:

  • Genotype will be mandatory (hemizygous, heterozygous, homozygous, mitochondrial homoplasmy, mitochondrial heteroplasmy). This is currently an optional field.

These changes will also affect bulk upload and the templates available to download from the website will be changed accordingly.

If you have any queries or concerns about these changes, please let us know by emailing

DECIPHER v9.20 Released

We released version 9.20 of DECIPHER on the 24th of January, 2018. Improvements include:

  • All information regarding matching patients can now be filtered by attribute. This allows the most appropriate patient data to be displayed and considered more easily.

  • A list of phenotypes absent in matching patients in now displayed when viewing matching patients in a patient record.

  • Pertinent evidence and links to relevant evidence are now shown for each evidence line when recording ACMG pathogenicity evidence, assisting variant classification.

  • The protein viewer now displays DECIPHER sequence variants mapped onto proteins, alongside other relevant information, for proteins for which no pfam domain information is available.

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:

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 and via email from Funding for the project was provided by Wellcome."

Please see Citing DECIPHER for more information.