LOD score

LOD score is a statistical estimate that is used in the field of genetic linkage analysis to test for linkage between genes. It was first introduced by Newton Morton, a pioneer in the field of human genetics. The LOD score compares the likelihood of obtaining the test data if the two loci are indeed linked, to the likelihood of observing the same data purely by chance.

Calculation

The LOD score is calculated using the formula:

LOD = log10 ( (1 - θ)^nθ^u / 0.5^n )

where:

• θ is the recombination fraction (the probability that a chromosome segment will cross over in a single generation)
• n is the number of recombinant offspring
• u is the number of non-recombinant offspring

A LOD score greater than 3 is generally taken to indicate sufficient evidence for linkage, while a LOD score less than -2 is taken to indicate evidence against linkage.

Applications

LOD scores are used in genetic mapping to locate genes relative to one another on a chromosome. They are also used in gene hunting to identify genes associated with diseases.

Limitations

While LOD scores are a powerful tool in genetic analysis, they have some limitations. They require large, informative families and accurate phenotype data. They are also sensitive to errors in the estimated recombination fraction.

See also

• Genetic linkage
• Genetic mapping
• Gene hunting

LOD score Resources
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