Examples
Examples
The following examples demonstrate the way in which pedigrees of various complexity can be represented using the pedigree conceptual model.
Any pedigree more complex than would be represented with a PED file should use the conceptual model implemented within a compatible standard, such as FHIR or Phenopacket.
Basic Trio
A basic family trio consists of one male parent, one female parent, and a proband child. This would be represented as a Pedigree with three Individuals and two parent-child Relationships:
As a Phenopacket GA4GHPedigree message:
id: FAM1
narrative: A Phenopacket GA4GHPedigree of a trio with an affected child
date: 2022-06-23
individuals:
- id: 1
subject:
id: MOTHER
sex: FEMALE
- id: 2
subject:
id: FATHER
sex: MALE
- id: 3
subject:
id: CHILD
sex: UNKNOWN
relationships:
- individual_id: MOTHER
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: CHILD
- individual_id: FATHER
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: CHILD
index_patients:
- CHILD
Twins
The relationship between twins (TWIN1 and TWIN2) can be represented by adding another Individual, parent-child relationships and a twin Relationship to the Pedigree:
id: FAM2
narrative: A Phenopacket GA4GHPedigree of a couple with identical twins
date: 2022-06-23
individuals:
- id: 1
subject:
id: MOTHER
sex: FEMALE
- id: 2
subject:
id: FATHER
sex: MALE
- id: 3
subject:
id: TWIN1
sex: UNKNOWN
- id: 4
subject:
id: TWIN2
sex: UNKNOWN
relationships:
- individual_id: MOTHER
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: TWIN1
- individual_id: FATHER
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: TWIN1
- individual_id: TWIN1
relation:
id: KIN:010
label: isMonozygoticMultipleBirthSiblingOf
relative_id: TWIN2
The parent-child relationships for TWIN2 are not strictly necessary. Because the isMonozygoticTwinOf relationship is symmetric, it would be equally valid to have said that TWIN2 isMonozygoticTwinOf TWIN1.
Adoption
id: FAM3
narrative: A Phenopacket GA4GHPedigree of a child with an adoptive mother
date: 2022-06-23
individuals:
- id: 1
subject:
id: MOTHER
sex: FEMALE
- id: 2
subject:
id: BIOLOGICAL_MOTHER
sex: FEMALE
- id: 3
subject:
id: FATHER
sex: MALE
- id: 4
subject:
id: CHILD
sex: UNKNOWN
relationships:
- individual_id: MOTHER
relation:
id: KIN:022
label: isAdoptiveParentOf
relative_id: CHILD
- individual_id: BIOLOGICAL_MOTHER
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: CHILD
- individual_id: FATHER
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: CHILD
IVF
id: FAM4
narrative: A Phenopacket GA4GHPedigree of a child with an egg donor, gestational carrier, and biological father
date: 2022-06-23
individuals:
- id: 1
subject:
id: MOTHER
sex: FEMALE
- id: 2
subject:
id: SURROGATE
sex: FEMALE
- id: 3
subject:
id: FATHER
sex: MALE
- id: 4
subject:
id: CHILD
sex: UNKNOWN
relationships:
- individual_id: MOTHER
relation:
id: KIN:038
label: isOvumDonorOf
relative_id: CHILD
- individual_id: SURROGATE
relation:
id: KIN:005
label: isGestationalCarrierOf
relative_id: CHILD
- individual_id: FATHER
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: CHILD
Complete cancer family
Example BRCA1 pedigree. Source: https://visualsonline.cancer.gov/details.cfm?imageid=10436
id: FAM5
narrative: A Phenopacket GA4GHPedigree of a classic BRCA1 pedigree
date: 2022-06-23
individuals:
- id: 1
subject:
id: 1
sex: MALE
vital_status: DECEASED
- id: 2
subject:
id: 2
sex: FEMALE
vital_status: DECEASED
- id: 3
subject:
id: 3
sex: MALE
vital_status: DECEASED
- id: 4
subject:
id: 4
sex: FEMALE
vital_status: DECEASED
diseases:
- term:
id:
label: Ovarian cancer
onset:
age: P49Y
- id: 5
subject:
id: 5
sex: FEMALE
- id: 6
subject:
id: 6
sex: FEMALE
- id: 7
subject:
id: 7
sex: MALE
- id: 8
subject:
id: 8
sex: FEMALE
diseases:
- term:
id:
label: Breast cancer
onset:
age: P42Y
- id: 9
subject:
id: 9
sex: MALE
- id: 10
subject:
id: 10
sex: FEMALE
- id: 11
subject:
id: 11
sex: FEMALE
diseases:
- term:
id:
label: Ovarian cancer
onset:
age: P53Y
- id: 12
subject:
id: 12
sex: FEMALE
- id: 13
subject:
id: 13
sex: MALE
- id: 14
subject:
id: 14
sex: FEMALE
- id: 15
subject:
id: 15
sex: FEMALE
diseases:
- term:
id:
label: Breast cancer
onset:
age: P38Y
relationships:
- individual_id: 1
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: 5
- individual_id: 2
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: 5
- individual_id: 1
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: 6
- individual_id: 2
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: 6
- individual_id: 1
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: 7
- individual_id: 2
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: 7
- individual_id: 3
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: 8
- individual_id: 4
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: 8
- individual_id: 3
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: 9
- individual_id: 4
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: 9
- individual_id: 3
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: 11
- individual_id: 4
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: 11
- individual_id: 3
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: 12
- individual_id: 4
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: 12
- individual_id: 7
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: 13
- individual_id: 8
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: 13
- individual_id: 9
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: 14
- individual_id: 10
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: 14
- individual_id: 7
relation:
id: KIN:028
label: isBiologicalFatherOf
relative_id: 15
- individual_id: 8
relation:
id: KIN:027
label: isBiologicalMotherOf
relative_id: 15
index_patients:
- 14