Which factor most significantly contributes to 'allelic dropout' in PCR-based sequencing assays?

Correct answer: A polymorphism under the primer binding site

Allelic dropout occurs when a variant (polymorphism) in one allele is present within the primer binding sequence. This mismatch prevents the primer from annealing efficiently during PCR, leading to preferential amplification of only the other allele and resulting in a false homozygous call.