Linkage is the tendency of genes or other DNA sequences at specific loci to be inherited together as a consequence of their physical proximity on a single chromosome.¹⁵ It is possible to predict linkage by estimating the distance between genes or segments of DNA using recombination frequency. In this way, one can construct genetic maps called linkage maps.

Genetic recombination occurs when two homologous chromosomes exchange parts of their DNA. This often happens in gametes (egg and sperm) so that new combinations of alleles can be passed on to the next generation. Recombination occurs at random. If there is a large distance between two segments of DNA, there is a good chance that recombination will occur between them. However, if the two sequences are close together, recombination will rarely occur between them (the two sequences will tend to stay together rather than being split apart by recombination). In the latter case, the recombination frequency is low and the two DNA sequences are considered to be linked. High recombination frequencies are found for DNA sequences far enough apart that they are not in linkage with each other and are considered to be in linkage equilibrium.

The recombination fraction is defined as the proportion of recombinants that define genetic distance. Two loci that show 1% recombination are defined as being 1 centimorgan (cM) (in honor of Thomas Hunt Morgan, 1933 Nobel Laureate in Physiology or Medicine) apart on a genetic (or linkage) map. In general, genetic distance can be related to physical distance, with 1cM being approximately equal to 1Mb or 1 million base pairs of DNA.⁰⁷

The majority if the STR loci used to type biological fluids in forensic laboratories are not physically linked.  While some, such as D5S818 and CSF1PO, are on the same chromosome, none are genetically linked (i.e. they are all in linkage equilibrium with one another). Therefore, it is possible to multiply the genotypic frequencies over several loci to come up with a combined genotypic frequency for the entire profile.⁰³

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