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.