In a linkage analysis,given that you do not know the distance between a marker and the disease locus,the calculation is reiterated for many values of θ.How,then,is one LOD score selected from these data?

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Quizplus · Accepted Answer

The LOD score is a measure of the likelihood of linkage between a marker and a disease locus, with higher LOD scores indicating stronger evidence for linkage. Therefore, the LOD score associated with the highest θ value (which represents the highest likelihood of no linkage) is chosen as the best estimate of the LOD score for that particular marker-disease pair. This is because the highest θ value represents the scenario in which the marker and disease locus are farthest apart on the chromosome, and if linkage is still detected at that distance, it is more likely to be real than if linkage is only detected at closer distances where recombination events are more frequent. Additionally, taking into account information from surrounding markers may help to confirm or refine the estimated θ value for the marker being analyzed, but the ultimate choice of LOD score is still based on the highest θ value tested.

In a Linkage Analysis,given That You Do Not Know the Distance