Advantages of linkage analysis include that the power to find a QTL can be easily quantified, and that the approach is minimally influenced by allelic heterogeneity.
Disadvantages of the approach include that it requires the study of related individuals and typically localizes relatively large genetic loci (e.g. 10–15 megabases).
Such a large locus often harbors many genes and requires additional analytic methods to determine the gene of interest.