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Table 5 Conditional probabilities of mating type and child genotype

From: TDT-HET: A new transmission disequilibrium test that incorporates locus heterogeneity into the analysis of family-based association data

Mating type = i

Pr(Mating type = i|D, pop = k)

Child genotype

Notation

Pr(Child genotype|D, Mating type = i, pop = k) (t= 1/2 when k= 2)

Pr(x abc |D, pop = k)

MM × MM (i = 1)

μ k,1

MM

x 222

1

μ k,1

MM × MNC(i = 2)

μ k,2

MM

x 212

t

μ k,2 t

MM × MNC(i = 2)

μ k,2

MN

x 211

(1 - t)

μk,2(1 - t)

MM × NN(i = 3)

μ k,3

MN

x 201

1

μ k,3

MN × MN(i = 4)

μ k,4

MM

x 112

t 2

μ k,4 t 2

MN × MN(i = 4)

μ k,4

MN

x 111

2t(1 - t)

2 μk, 4t(1 - t)

MN × MN(i = 4)

μ k,4

NN

x 110

(1 - t)2

μk,4(1 - t)2

MN × NN(i = 5)

μ k,5

MN

x 101

t

μ k,5 t

MN × NN(i = 5)

μ k,5

NN

x 100

(1 - t)

μ k,5 (1 - t)

NN × NN(i = 6)

μ k,6

NN

x 000

1

μ k, 6

  1. In this table, the high risk allele is M. Also, we define D to be the event that the child is affected. Note that 1 ≤ k ≤ 2. The last column is computed using the definition of conditional probability. Schaid and Sommer [63] also demonstrated this calculation. Note that Pr ( x a b c | D , pop = k ) = f B ( x a b c ; θ → k ) . Finally, t = Pr(heterozygous parent transmits an M allele to an affected child).