FamilyCosegregationStatement

A statement describing the observed correlation between transmission of a particular allele and a particular genetic condition, across a single family pedigree (i.e. the co-segregation of an allele and a condition as observed across a family pedigree).

SEPIO:0000247
Descended from Statement

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
pedigree string 0..* Detailed information about the family structure, affected status, and genotypes in pedigree/linkage format. SEPIO:0000318 FamilyCosegregationStatement
columns string 0..* Column names for the pedigree data element SEPIO:0000316 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
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
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 pedigree columns genotypeValues affectedValues inconsistentSegregationsObserved inconsistentSegregationCount

CGEX:FamSeg103

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.

CAR:CA010136

CGEX:GenCond020

CGEX:Fam363

(Family #001)

3

2

CGEX:FamSeg104

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.

CAR:CA010136

CGEX:GenCond020

CGEX:Fam364

(Family #002)

1

CGEX:FamSeg107

proband and 5 affected family members all homozygous for NM_206933.2(USH2A):c.1000C>G (p.Arg334Gly).

CAR:CA143213

CGEX:GenCond021

CGEX:Fam365

(Family #003)

5

CGEX:FamSeg108

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.

CAR:CA143213

CGEX:GenCond021

CGEX:Fam366

(Family #004)

CGEX:FamSeg196

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.

CAR:CA023690

CGEX:GenCond035

CGEX:Fam370

(Family #008)

0

2

SEPIO-CG:99011

(present)

CGEX:FamSeg197

The individual with HCM but without the allele is likely a phenocopy explained by environmental factors (obese, alcohol)

CAR:CA010777

CGEX:GenCond065

CGEX:Fam371

(Family #009)

3

1

SEPIO-CG:99011

(present)

CGEX:FamSeg076

CAR:CA090930

CGEX:GenCond056

CGEX:Fam373

(Family #011)

0

0

2

SEPIO-CG:99011

(present)

CGEX:FamSeg111

CAR:CA501226

CGEX:GenCond051

CGEX:Fam367

(Family #005)

2

CGEX:FamSeg113

CAR:CA006429

CGEX:GenCond002

CGEX:Fam368

(Family #006)

1

1

[[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]]

[“Family”,”Individual”,”Father”,”Mother”,”Sex”,”Affected”,”Genotype”]

{0: “Unknown”,1:”Reference”, 2: CA65}

{1: “Unaffected”, 2: “Affected”, 3: “Any Cardiovascular Abnormality”}

CGEX:FamSeg114

CAR:CA006429

CGEX:GenCond002

CGEX:Fam369

(Family #007)

2

3

[[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]]

[“Family”,”Individual”,”Father”,”Mother”,”Sex”,”Affected”,”Genotype”,”ObligateGenotype”]

{0: “Unknown”,1:”Reference”, 2: CA65}

{1: “Unaffected”, 2: “Affected”, 3: “Any Cardiovascular Abnormality”}

CGEX:FamSeg271

CAR:CA133141

CGEX:GenCond066

CGEX:Fam372

(Family #010)

0

2

SEPIO-CG:99011

(present)