Likelihood Ratio (LR) calculations in Parentage Assessments
Genetic parentage assessment is an indispensable tool in animal breeding and husbandry, especially for checking parent animals and ensuring correct breeding lines. A key statistical tool in this context is the likelihood ratio (LR). The concept quantifies the probability of two competing hypotheses about the parentage of an animal. The calculation of the LR in animal breeding must take into account that there may be doubts about the identity of both parents.
Basic principles
The likelihood ratio (LR) compares the probabilities of two competing hypotheses
- H1: The stated parents are the biological parents
- H2: The stated parents are not the biological parents
'Evidence' is collected and statistically evaluated for each of the hypotheses. The total of all the evidence results in the likelihood ratio. In the case of high values, these are output as logarithms to the basic number 10 (log10). An LR of 6 then means an LR of 1:1,000,000.
If the LR is negative, the evidence speaks against the specified parent animals.
Application of DNA data
To evaluate the two hypotheses, all animals involved are analysed for a defined set of DNA markers. Their overall number and information content must be sufficient to allow an evaluation to be made with an acceptable degree of certainty.
The respective allele findings of the markers of the offspring are checked to see whether they can originate from the two parent animals. If no exclusion situations are found, the LR of the two hypotheses is calculated for each marker:
- H1: The match is given because the declared parents are the biologically correct ones. The value for H1 would then always be 1.
- H2: The match is given because by chance the declared parents have the same allele values as the biologically correct parents. The fact that this coincidence can occur results from the general frequency of the two alleles of the offspring, which are also found in the two parents.
At Generatio, we consider 3 different starting situations that allow us to recognise the individual contribution of each parent and to evaluate cases where only one parent is present:
- Both parents are equally weighted. The value is referred to as the co-parentage index
- LR of the mother without taking the father into account / Fatherless maternity index
- LR of the father without taking the mother into account / Motherless paternity index