Allele frequency (p). The frequency of the risk allele (allele "A") in the population. The test locus is assumed to have only two alleles. Accepted values: 0 < p < 1. Example: if "A" has a population frequency of 1%, p = 0.01.
Total locus variance (Vq). This is the proportion of variance in disease liability that is attributed to the test locus. Accepted values: 0 <= Vq <= 1. Example: for a locus that explains 1% of the variance in disease liability, Vq = 0.01.
Background additive genetic variance (Va). Corresponds to the proportion of variance in disease liability that is attributed to the additive effects of other (untested) loci that also influence disease risk. Also known as background heritability or polygenic variance. Accepted values: 0 <= Va <= 1. Example: for a background heritability of 50%, Va = 0.5.
Shared environment variance (Vc). Corresponds to the proportion of variance in disease liability explained by environmental factors shared between relatives, such as home environment. Accepted values: 0 <= Vc <= 1. Example: if shared environment is thought to explain 10% of the variance in disease liability, Vc = 0.1.
Inheritance model. Model that determines how the genotype at the test locus influences disease liability. If a is the additive genotypic value and d the dominance deviation, then d = 0 for an additive model, d = +a for a dominant model and d = -a for a recessive model.
Number of families. Total number of families ascertained.
N affected offspring per family required for selection. As the name suggests, this is the number of affected offspring a family needed to have to be selected for the association study. The standard TDT design involves ascertainment of families conditional on having 1 affected offspring, disregarding the disease status of other relatives. If this was the case, then select "1" in this box. However, often, families are ascertained because they have multiple affected relatives (e.g. affected sib-pair design) - this is typical of linkage studies. Select "2" or "3" if families were ascertained conditional on having 2 or 3 affected offspring, respectively, even if not all affected offspring were genotyped and used in the TDT (see below).
Ascertain discordant parents? Specifies whether families were ascertained conditional on having one affected and one unaffected parent. Ascertainment of discordant parents is considered for two reasons. First, it can be used to assess the impact of family history (i.e. selection of families with multiple affected relatives) on the power of the TDT. Second, differences in allele frequencies between the affected and unaffected parents provide information about association which, under the null, is independent of the information provided by the parent-offspring transmissions. Therefore, both can be combined to provide a more powerful test of association while retaining a large degree of robustness to population stratification (parenTDT approach).
N affected offspring per family used for the TDT. The standard TDT analysis uses only 1 affected offspring per family. If this is the analysis you intend to use, choose "1" here. On the other hand, if you ascertained families with multiple affected offspring and intend to genotype (use in the TDT) all the offspring, then choose "2" or "3" here appropriately. Note that you can asses the impact of family history on the power of the TDT by selecting in this box a smaller number of offspring than those required for selection (specified above). For example, if you ascertained parent-offspring trios conditional on having an additional affected offspring, select "2" above (N affected offspring required for selection) and "1" here.
Type-I error. The type-I error rate used for power calculations.
Output format. Either a full or a very, very short output.