Phenotypic Data
DECIPHER supports detailed phenotype data capture (Fig. 4A) which enables the in-depth comparison of patient phenotypes, as well as the delineation of new syndromes. Much of the phenotype is represented using Human Phenotype Ontology (HPO) terms - a standardised, controlled vocabulary which supports deep phenotyping (Köhler et al ., 2019). This allows phenotypic information to be described unambiguously, and for phenotypic similarity between patients to be established computationally by comparing related terms in the ontology. This is essential for finding potential patient matches. The DECIPHER phenotype deposition interface provides a search tool, allowing HPO terms to be added to a patient record quickly and easily. DECIPHER also supports the recording of the absence of clinically relevant phenotypes, and of manifestations of HPO terms (clinical modifiers), such as severity, age of onset, and pace of progression. This information can be helpful to users trying to determine the accuracy of a patient match, especially when the number of patient phenotypes is small.
In collaboration with ophthalmologists, DECIPHER has developed forms for groups of HPO phenotypes for the eye community, to assist phenotyping in the clinic. These forms contain a predetermined list of HPO terms which can be marked absent or present, and include common retinal and non-retinal disease, and symptoms and signs (extraocular features, ocular features, and electrodiagnostic testing and imaging).
Family history: In the case of inherited disorders, it is important to capture family phenotype history. In DECIPHER, users can record whether or not relevant family members are affected with similar or related phenotypes. Presence of absence of HPO terms can also be indicated for each family member if known.
Quantitative data: In addition to HPO terms, DECIPHER supports quantitative phenotype data capture (Fig. 4B). Developmental milestones (age of social smile, sat independently, walked independently, first words) and anthropometric measurements (growth, visual function, fundus imaging) can be deposited. Aggregated observations from open-access patient records are shared openly (See Quantitative phenotypic data to confirm fit with diagnosis section and Fig. 6A). DECIPHER also provides an interface to record birth and pregnancy information, such as age of the mother/father at birth of the patient, consanguinity, maternal illness, and gestation (which is also used to adjust growth charts); this information is not currently shared openly, but is shared within a consortium.