Phenopacket

A Phenopacket is an anonymized phenotypic description of an individual or biosample with potential genes of interest and/or diagnoses. It can be used for multiple use cases. For instance, it can be used to describe the phenotypic findings observed in an individual with a disease that is being studied or for an individual in whom the diagnosis is being sought. The phenopacket can contain information about genetic findings that are causative of the disease, or alternatively it can contain a reference to a VCF file if exome sequencing is being performed as a part of the differential diagnostic process. A Phenopacket can also be used to describe the constitutional phenotypic findings of an individual with cancer (a Biosample should be used to describe the phenotypic abnormalities directly associated with an extirpated or biopsied tumor).

Definition of the Phenopacket element
Field Type Status Definition
id string required Arbitrary identifier
subject Individual recommended The proband
phenotypic_features PhenotypicFeature (list) recommended Phenotypic features observed in the proband
biosamples Biosample optional Samples (e.g., biopsies), if any
genes Gene optional Gene deemed to be relevant to the case (application specific)
variants Variant (list) optional Variants identified in the proband
diseases Disease (list) optional Disease(s) diagnosed in the proband
hts_files HtsFile (list) optional High-throughput sequencing files (e.g. VCF)
meta_data MetaData required Information about ontologies and references used in the phenopacket

id

The id is an identifier specific for this phenopacket. The syntax of the identifier is application specific.

subject

This is typically the individual human (or another organism) that the Phenopacket is describing. In many cases, the individual will be a patient or proband of the study. See Individual for further information.

phenotypic_features

This is a list of phenotypic findings observed in the subject. See PhenotypicFeature for further information.

biosamples

This field describes samples that have been derived from the patient who is the object of the Phenopacket. or a collection of biosamples in isolation. See Biosample for further information.

genes

This is a field for gene identifiers and can be used for listing either candidate genes or causative genes. The resources using these fields should define what this represents in their context. This could be used in order to obfuscate the specific causative/candidate variant to maintain patient privacy. See Gene for further information.

variants

This is a field for genetic variants and can be used for listing either candidate variants or diagnosed causative variants. The resources using these fields should define what this represents in their context. See Variant for further information.

diseases

This is a field for disease identifiers and can be used for listing either diagnosed or suspected conditions. The resources using these fields should define what this represents in their context. See Disease for further information.

hts_files

This element contains a list of pointers to the relevant HTS file(s) for the patient. Each element describes what type of file is meant (e.g., BAM file), which genome assembly was used for mapping, as well as a map of samples and individuals represented in that file. It also contains a URI element which refers to a file on a given file system or a resource on the web.

See HtsFile for further information.

meta_data

This element contains structured definitions of the resources and ontologies used within the phenopacket. It is expected that every valid Phenopacket contains a metaData element. See MetaData for further information.