.. _rstfamily: ###### 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 :ref:`rstpedigree` element. Data model ########## .. list-table:: Definition of the ``Family`` element :widths: 25 25 25 75 :header-rows: 1 * - Field - Type - Multiplicity - Description * - id - string - 1..1 - application-specific identifier. REQUIRED. * - proband - :ref:`rstphenopacket` - 1..1 - The proband (index patient) in the family. REQUIRED. * - relatives - :ref:`rstphenopacket` (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 - :ref:`rstpedigree` - 1..1 - representation of the pedigree. REQUIRED. * - files - :ref:`rstfile` (list) - 0..* - list of files related to the whole family, e.g. multi-sample high-throughput sequencing files * - meta_data - :ref:`rstmetadata` - 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 :ref:`rstindividual` 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 :ref:`rstpedigree` 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 :ref:`rstfile` 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 :ref:`rstmetadata` for further information.