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:
- Via the web interface for an individual patient’s data.
- By uploading Excel or csv files via the web interface (bulk upload)
for data from multiple patients.
- 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.