Family

Phenotype, sample and pedigree data required for a genomic diagnosis. This element is equivalent to the Genomics England InterpretationRequestRD.

In many cases, genetic diagnostics of Mendelian and other disease is performed on a family basis in order to check for cosegregation of candidate variants with a disease. Usually, one family member is designated as the proband, for instance, a child affected by a genetic disease might be the proband in a family. Genomic diagnostics might involve genome sequencing of the child and his or her parents. In this case, the Family element would include a Phenopacket for the child (proband element). If the parents themselves display phenotypic findings relevant to the analysis, then Phenopackets are included for them (using the relatives element). If the parents do not display any relevant phenotypic findings, then it is not necessary to include Phenopacket elements for them. Instead, their status as unaffected can be recorded with the Pedigree element.

Data model

Definition of the Family element

Field	Type	Multiplicity	Description
id	string	1..1	application-specific identifier. REQUIRED.
proband	Phenopacket	1..1	The proband (index patient) in the family. REQUIRED.
relatives	Phenopacket (list)	0..*	list of Phenopackets for family members other than the proband
consanguinous_parents	bool	0..1	flag to indicate that the parents of the proband are consanguinous
pedigree	Pedigree	1..1	representation of the pedigree. REQUIRED.
files	File (list)	0..*	list of files related to the whole family, e.g. multi-sample high-throughput sequencing files
meta_data	MetaData	1..1	Metadata about ontologies and references used in this message. REQUIRED.

Explanations

id

An identifier specific for this family.

proband

The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient. See Individual for further information.

relatives

Individuals related in some way to the patient. For instance, the individuals may be genetically related or may be members of a cohort. If this field is used, then it is expected that a pedigree will be included for genetically related individuals for use cases such as genomic diagnostics. If a phenopacket is being used to describe one member of a cohort, then in general one phenopacket will be created for each of the individuals in the cohort. If this field is used, then it is expected that a pedigree will be included for genetically related individuals for use cases such as genomic diagnostics. If all that is required is to record affected/not-affected status in a family, it is possible to use the pedigree element only.

pedigree

The pedigree defining the relations between the proband and their relatives. This element contains information compatible with the information in a PED file. Pedigree.individual_id MUST map to the PhenoPacket.Individual.id. See Pedigree for further information.

files

This element contains a list of pointers to relevant file(s) for the family as a whole. The file(s) MUST refer to the entire family. Otherwise individual files MUST be contained within their appropriate scope. e.g. within a Phenopacket for germline samples of an individual or within the scope of the Phenopacket.Biosample in the case of data derived from that biosample.

In the case of multi-sample high-throughput sequencing files the sample identifiers in the hight-throughput sequencing file MUST each map to a Pedigree.individual_id referenced in the pedigree field, in order that linkage analysis can be performed on the sample.

See File 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.