Deposition and breadth of sharing
DECIPHER has been carefully designed to ensure that the depth and breadth of sharing is proportionate to the scientific/clinical needs and level of consent. For example, a user who does not belong to a DECIPHER project can only access the openly shared patient data, while data which is visible to registered users who are logged in reflects their project and consortium memberships.
Patient genotype and phenotype data can be deposited to DECIPHER in three ways:
  1. Via the web interface for an individual patient’s data.
  2. By uploading Excel or csv files via the web interface (bulk upload) for data from multiple patients.
  3. Using the deposition API to allow programmatic uploading of data and synchronisation of data across systems (e.g. synchronisation between a centre’s electronic health records and the patient records in that centre’s DECIPHER project).
DECIPHER users at the depositing centre determine the sharing level of each patient record and variant. Patient records, and individual variants within these records, can be kept private to the depositing centre. This allows DECIPHER’s tools to be used for assessing variant pathogenicity to inform the conversation with the patient before seeking consent for wider sharing. With explicit patient consent, patient records are shared openly, with the data available to anyone who visits the website. DECIPHER also supports consortium sharing. This allows sharing of patient records between a defined group of centres, where there is an expectation of collaboration for patient care, again before explicit patient consent for open sharing has been obtained. DECIPHER currently hosts six consortia, which share more than 63,000 patient records. Consortia include the United Kingdom National Health Service consortium, the Deciphering Developmental Disorders (DDD) consortium which shares research data from the DDD study (Wright et al ., 2014), and a data-sharing consortium covering New South Wales and Western Australia.
DECIPHER is a live interface and data deposited is available to view, interpret, and share in real time. Patient records can be added and edited iteratively as more information becomes available, e.g. additional phenotype terms, the inheritance status of a variant, or new functional data. Information can be added to a record by a clinician and clinical scientist working asynchronously and in different locations.