Transmission disequilibrium test

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In population genetics, the transmission disequilibrium test (TDT) was proposed by Spielman, McGinnis & Ewens (1993) as a family-based association test to compare transmission frequencies of an allele thought to be associated with a disease and its alternate allele using affected children born to parents heterozygous for the allele.

Non-transmitted allele
M1 M2 total
M1 m^2+\left(\frac{m\delta}{p}\right) m(1-m)+\left[\frac{(1-\theta-m)\delta}{p}\right] m+\left[\frac{(1-\theta)\delta}{p}\right]
Transmitted allele M2 m(1-m)+\left[\frac{(\theta-m)\delta}{p}\right] (1-m)^2-\left[\frac{(1-m)\delta}{p}\right] 1-m-\left[\frac{(1-\theta)\delta}{p}\right]
totals m+\frac{\theta\delta}{p} 1-m-\frac{\theta\delta}{p} 1

Stratification by parental mating type Wittkowski & Liu (2002) adjusts for a problem also seen in case-control association tests Sasieni (1997) namely that, due to the same confounders affecting penetrance, the effects of the two alleles transmitted to the same child are not independently observed, even though the alleles are independently transmitted.

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