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 Familyelement¶Field Type Status Description id string required application-specific identifier proband Phenopacket required The proband (index patient) in the family relatives Phenopacket (list) optional list of Phenopackets for family members other than the proband pedigree Pedigree required representation of the pedigree hts_files HtsFile (list) optional list of high-throughput sequencing files meta_data MetaData required Metadata about ontologies and references used in this message
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.
hts_files¶
This element contains a list of pointers to the relevant HTS file(s) for the family as a whole. For a Family these
files MUST be merged/multi-sample files with appropriate genotype information. For a multi-sample file, the sample
identifiers 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 HtsFile for further information.