How to calculate linkage disequilibrium

Written by thomas bourdin
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How to calculate linkage disequilibrium
Calculating Linkage Disequilibrium. (Genetics image by rolffimages from Fotolia.com)

Linkage disequilibrium is an important concept in genetics which occurs when a genotype at one locus is dependent on a genotype at another locus. The dependence of these two genotypes means that the frequency of certain combinations of alleles may be different than what might be expected when considering the alleles separately. Linkage disequilibrium is an important concept to understand when studying genetic recombination, and can be calculated with a sufficient understanding of genetics and probability.

Skill level:
Easy

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Instructions

  1. 1

    Determine haplotype frequency. For example, if you have a two loci (A, B) , each with two alleles (A1, A2, B1, B2), than there will be four haplotypes: A1B1, A1B2, A2B1, A2B2. As an example, assume the frequencies are 0.5, 0.25, 0.15 and 0.1, respectively.

  2. 2

    Determine the allele frequencies in terms of haplotype frequency. For example, to find the frequency of allele A1, you would sum the frequencies A1B1 and A2B2 (in our example, 0.5 and 0.25, respectively, giving 0.75), and to find the frequency of allele B1, you would sum the frequencies of A1B1 and A2B1 (in our example, 0.5 and 0.15, respectively, giving 0.65).

  3. 3

    Multiply the frequencies of the alleles A1 and B1 from the previous step together. In equation form, this looks like (A1B1 + A2B2)*(A1B1 + A2B1). In the example above, the frequencies are of A1 and B1 are 0.75 and 0.65, respectively. Multiplying the numbers together gives 0.4875.

  4. 4

    Subtract the haplotype frequency of A1B1 from Step 1 by the value obtained from Step 3. The resulting number is the linkage disequilibrium. In our example, the haplotype frequency of A1B1 is 0.5 and the value from step 1 is 0.4875, resulting in a linkage disequilibrium value of 0.125.

Tips and warnings

  • A linkage disequilibrium value of zero indicates complete independence of the alleles, while a value of one indicates complete dependence.

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