Scope and Usage
Co-segregatation' refers to the correlation between the presence of a particular allele and the manifestation of a condition in a family pedigree. When an allele and a condition are only found together in family members, they are said to co-segregate.
When there are no individuals that have the allele without the condition or the condition without the allele, the allele and condition are said to co-segregate.
Attributes
| Name | Type | Cardinality | Description | IRI | Defined in |
|---|---|---|---|---|---|
| canonicalAllele | CanonicalAllele | 1..1 | Allele being tested for cosegregation | SEPIO:0000275 | FamilyCosegregationStatement |
| condition | GeneticCondition | 1..1 | Condition being tested for cosegregation | SEPIO:0000276 | FamilyCosegregationStatement |
| family | @id | 1..1 | Family in which segregation is being tested | SEPIO:0000282 | FamilyCosegregationStatement |
| phenotypePositiveAllelePositive | integer | 0..1 | Number of (non-proband) individuals with both the condition and the allele | SEPIO:0000292 | FamilyCosegregationStatement |
| phenotypePositiveAlleleNegative | integer | 0..1 | Number of (non-proband) individuals with the condition and without the allele | SEPIO:0000290 | FamilyCosegregationStatement |
| phenotypeNegativeAllelePositive | integer | 0..1 | Number of (non-proband) individuals without the condition and with the allele | SEPIO:0000291 | FamilyCosegregationStatement |
| phenotypeNegativeAlleleNegative | integer | 0..1 | The number of non-proband family members that have neither the allele nor the phenotype | SEPIO:0000289 | FamilyCosegregationStatement |
| inconsistentSegregationsObserved | @id | 0..1 | Whether phenotype positive/allele negative or phenotype negative/allele positive individuals are in the family | SEPIO:0000314 | FamilyCosegregationStatement |
| inconsistentSegregationCount | integer | 0..1 | The number of segregations inconsistent with allele pathogenicity | SEPIO:0000315 | FamilyCosegregationStatement |
| columns | string | 0..* | Column names for the pedigree data element | SEPIO:0000316 | FamilyCosegregationStatement |
| pedigree | string | 0..* | Detailed information about the family structure, affected status, and genotypes in pedigree/linkage format. | SEPIO:0000318 | FamilyCosegregationStatement |
| genotypeValues | string | 0..* | Map describing how genotypes are represented in the pedigree | SEPIO:0000317 | FamilyCosegregationStatement |
| affectedValues | string | 0..* | Map describing how affected status is represented in the pedigree | SEPIO:0000313 | FamilyCosegregationStatement |
| label | string | 0..1 | A name given to the resource. | RDFS:label | Entity |
| description | string | 0..1 | Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource. | DC:description | Entity |
| userLabelDictionary | UserLabel | 0..* | An optional label defined by the user. Used for custom entities or to clarify the preferred user label on existing entities with non-preferred labels. | SEPIO:0000422 | Statement |
| outcomeQualifier | string | 0..1 | Use “NOT” as the value of this property to assert that the statement is negated. | SEPIO:0000346 | Statement |
| evidenceLine | EvidenceLine | 0..* | supporting evidence | SEPIO:0000006 | Statement |
| contribution | Contribution | 0..* | The contributions (agent, time and role) made to this entity | SEPIO:0000159 | Statement |
| source | string | 0..* | A string indicating the source of a Statement | DC:source | Statement |
Instances
| ID | label | description | userLabelDictionary | outcomeQualifier | evidenceLine | canonicalAllele | condition | family | phenotypePositiveAllelePositive | phenotypePositiveAlleleNegative | phenotypeNegativeAllelePositive | phenotypeNegativeAlleleNegative | inconsistentSegregationsObserved | inconsistentSegregationCount | columns | pedigree | genotypeValues | affectedValues |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
identified in 1 individual with HCM. Segregation analysis determined 5 other members of the family also carried this variant. However, only 3 of those family members had HCM (aged 48-75). The 2 other family members were young and asymptomatic. So from this paper, only count 3 segregations. The two apparently refuting segregations can be ignored due to the age-dependent penetrance of HCM. |
(Family #001) |
3 |
2 |
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In LMM internal family, c.1351+1G>A was identified in 1 individual with HCM. Variant also found in individual’s sister - who also had clinical dx of HCM. |
(Family #002) |
1 |
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|
proband and 5 affected family members all homozygous for NM_206933.2(USH2A):c.1000C>G (p.Arg334Gly). |
(Family #003) |
5 |
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|
c.1000C>T identified in het state in 1 individual with Usher. Individual compound het with Gly1840Val USH2A variant - confirmed in trans. Gly1840Val called Pathogenic. Individual has 3 affected sibs all of whom are compound het with 1000C>T & Gly1840Val. One additional sib only carried 1000C>T and is unaffected. |
(Family #004) | |||||||||||||||||
|
observed in one case diagnosed with Familial Hypercholesterolemia, characterized by elevated LDLC levels. Two siblings of the proband also have elevated LDLC levels but neither carry the 313+2T>C variant. |
(Family #008) |
0 |
2 |
(present) | ||||||||||||||
|
The individual with HCM but without the allele is likely a phenocopy explained by environmental factors (obese, alcohol) |
(Family #009) |
3 |
1 |
(present) | ||||||||||||||
| (Family #011) |
0 |
0 |
2 |
(present) | ||||||||||||||
| (Family #005) |
2 |
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| (Family #006) |
1 |
1 |
[“Family”,”Individual”,”Father”,”Mother”,”Sex”,”Affected”,”Genotype”] |
[[Fam006,Fam006.1,0,0,1,2,0/0], [Fam006,Fam006.2,0,0,2,1,0/0], [Fam006,Fam006.3,Fam006.1,Fam006.2,2,3,0/0], [Fam006,Fam006.4,Fam006.1,Fam006.2,1,2,1/2], [Fam006,Fam006.5,Fam006.1,Fam006.2,2,1,1/1], [Fam006,Fam006.6,Fam006.1,Fam006.2,1,2,1/2]] |
{0: “Unknown”,1:”Reference”, 2: CA65} |
{1: “Unaffected”, 2: “Affected”, 3: “Any Cardiovascular Abnormality”} |
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| (Family #007) |
2 |
3 |
[“Family”,”Individual”,”Father”,”Mother”,”Sex”,”Affected”,”Genotype”,”ObligateGenotype”] |
[[Fam007, Fam007.1, 0, 0, 1, 3, 0/0, 0], [Fam007, Fam007.2, 0, 0, 2, 1, 0/0, 0], [Fam007, Fam007.3, 0, 0, 1, 3, 0/0, 0], [Fam007, Fam007.4, 0, 0, 2, 1, 0/0, 0], [Fam007, Fam007.5, 0, 0, 1, 3, 0/0, 0], [Fam007, Fam007.6, Fam007.1, Fam007.2, 2, 3, 1/2, 1], [Fam007, Fam007.7,0, 0, 1, 1, 0/0, 0], [Fam007, Fam007.8, Fam007.1, Fam007.2, 2, 1, 1/2, 1], [Fam007, Fam007.9,Fam007.3, Fam007.4, 1, 1, 0/0, 0], [Fam007, Fam007.10, 0, 0, 1, 1, 0/0, 0], [Fam007, Fam007.11, Fam007.5, Fam007.6, 2, 2, 1/2, 0], [Fam007, Fam007.12, Fam007.5, Fam007.6, 1,2, 0/0, 0], [Fam007, Fam007.13, Fam007.5, Fam007.6, 2,1, 1/1,0], [Fam007, Fam007.14, Fam007.5, Fam007.6, 1, 1, 1/1, 0], [Fam007, Fam007.15, Fam007.7, Fam007.8, 1, 2, 1/2, 0], [Fam007, Fam007.16, Fam007.8, Fam007.9, 1, 2, 1/2, 0], [Fam007, Fam007.17, Fam007.8, Fam007.9, 1, 2, 0/0,0], [Fam007, Fam007.18, Fam007.8, Fam007.9, 1, 2, 0/0, 0], [Fam007, Fam007.19, Fam007.10, Fam007.11, 1, 2, 0/0,0], [Fam007.20,Fam007.10, Fam007.11, 1,1,1/1,0]] |
{0: “Unknown”,1:”Reference”, 2: CA65} |
{1: “Unaffected”, 2: “Affected”, 3: “Any Cardiovascular Abnormality”} |
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| (Family #010) |
0 |
2 |
(present) |