This element is used to represent a pedigree to describe the family relationships of each sample along with their gender and phenotype (affected status). The information in this element is for use by programs for analysis of a multi-sample VCF file with exome or genome sequences of members of a family, some of whom are affected by a Mendelian disease.
The phenopacket schema has implemented a PED-compatible data-model to promote interoperability between existing PED files and PED software, but does not actually store a PED file.
See the detailed description at the PLINK website for more information about PED files.
|persons||list of Person||1..*||list of family members in this pedigree. REQUIRED.|
The pedigree is simply a list of Person objects. These objects reflect the elements of a PED file.
The Person class represents a row from the PED file indicating the biological parents of the individual, their sex and their AffectedStatus.
|family_id||string||1..1||application specific identifier. REQUIRED.|
|individual_id||string||1..1||application specific identifier. REQUIRED.|
|paternal_id||string||1..1||application specific identifier. REQUIRED.|
|maternal_id||string||1..1||application specific identifier. REQUIRED.|
|sex||Sex||1..1||see text. REQUIRED.|
|affected_status||AffectedStatus||1..1||see text. REQUIRED.|
Here we show a pedigree in PED format, this contains two male siblings which share an abnormal (affected) phenotype and their two normal (unaffected) parents.
Below we show the same pedigree as a phenopacket Pedigree in YAML format.
pedigree: persons: - familyId: "family 1" individualId: "kindred 1A" paternalId: "FATHER" maternalId: "MOTHER" sex: "MALE" affectedStatus: "AFFECTED" - familyId: "family 1" individualId: "kindred 1B" paternalId: "FATHER" maternalId: "MOTHER" sex: "MALE" affectedStatus: "AFFECTED" - familyId: "family 1" individualId: "MOTHER" paternalId: "0" maternalId: "0" sex: "FEMALE" affectedStatus: "UNAFFECTED" - familyId: "family 1" individualId: "FATHER" paternalId: "0" maternalId: "0" sex: "MALE" affectedStatus: "UNAFFECTED"
This element is an enumeration to
|MISSING||It is unknown if the individual has the affected phenotype|
|UNAFFECTED||The individual does not show the affected phenotype of the proband|
|AFFECTED||The individual has the affected phenotype of the proband|
In a PED file, affected persons are encoded with “2”, and unaffecteds by “1” (a “0” is used if no information is available). Instead, Phenopackets uses an enumeration as shown in the table.
In a PED file, the sex of individuals is encoded as a “1” for females, “2” for males, and “0” for unknown. Phenopackets uses Sex instead.
The message is made up of a list of
Person elements (the Person element is defined within the Pedigree element).
Each Person element is equivalent to one row of a PED file.
The family ID and the individual IDs may be made up of letters and digits, and the combination of family and individual ID should uniquely identify each person represented in the PED file. The parents of a person in the pedigree are shown with the corresponding individual IDs. Individuals whose parents are not represented in the PED file are known as founders; their parents are represented by a zero (“0”) in the columns for mother and father. Finally, the sex and the affected (disease) status of the person are shown.
Phenopacket is used to represent any of the individuals listed in the
Pedigree, then it is essential that
individual_id used in the pedigree matches the
id of the
subject of the
Phenopacket. It is allowable
Pedigree to have individuals that do not have an associated
Phenopacket. This is useful, for instance,
Pedigree is being used to store the affected/not affected status of family members being examined by exome or genome
sequencing. In this case (i.e. where there are no associated phenopackets for the
Pedigree.individual_id), it is
expected that the
individual_id elements match the sample identifiers of the exome/genome file.