To determine which version of a mutation or polymorphism an individual has allele-specific PCR is used. In this method one primer is common to both reactions and anneals close to the mutation. There are two versions of the other primer. These are allele specific and anneal to the variation. The 3' end of the allele-specific primer is modified to only anneal to one of the alleles. For example:
- Mutation is T or C at one position;
- Number of reactions needed is two;
- Primer A1 ends in T, Primer A2 ends in C;
- The common primer, Primer B would be the same;
- Following PCR, these two sets of reactions are run on an agarose gel. The band pattern shows if the individual is homozygous for T or C, or heterozygous for T/C.