Pedigree

This element is used to represent a pedigree to describe the family relationships of each sample along with their gender and phenotype (affected status). PED files are typically used by software for genetic linkage analysis. The phenopacket schema uses conventions similar to those of PED files 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.

The information in this element can be used 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.

Data model

Field Type Status Description
persons Person (list) required List of family members in this pedigree

The pedigree is simply a list of Person objects. These objects are meant to reflect the elements of a PED file.

Person

Definition of the Person element
Field Type Status Description
family_id string required Application specific identifier
individual_id string required Application specific identifier
paternal_id string required Application specific identifier
maternal_id string required Application specific identifier
sex Sex required See text
affected_status AffectedStatus required See text

Example

{
   "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": "FEMALE",
           "affectedStatus": "AFFECTED"
       },
       {
           "familyId": "family 1",
           "individual_id": "MOTHER",
           "paternalId": "0",
           "maternalId": "0",
           "sex": "FEMALE",
           "affectedStatus": "UNAFFECTED"
       },
       {
           "familyId": "family 1",
           "individualId": "FATHER",
           "sex": "MALE",
           "paternalId": "0",
           "maternalId": "0",
           "affectedStatus": "UNAFFECTED"
       }
   ]
}

AffectedStatus

This element is an enumeration to

Name Description
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.

If a Phenopacket is used to represent any of the individuals listed in the Pedigree, then it is essential that the individual_id used in the pedigree matches the id of the subject of the Phenopacket. It is allowable for the Pedigree to have individuals that do not have an associated Phenopacket. This is useful, for instance, if the 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.

The Pedigree object does not support reporting multiple phenotypes in one individual. The phenotype represented by the affectation status is whether the disease is present or not. If this is desired, then one would have to create full phenopackets for each individual in a family.