The LOD score (aka Z) gives an estimation of how closely two loci are linked (for example, a marker locus and a disease locus) and quantitates sample size (data reliability).
A LOD score less than 2.0 means the two loci are not linked; a LOD score between 2.0 and 3.0 is inconclusive; and a LOD score greater than 3.0 strongly indicates linkage. Lod scores are always reported in association with the recombination frequency (θ, theta), measured in Morgans, which describes linkage without accounting for sample size. Please review linkage analysis if any of these concepts are unclear.
|Step 1||Look at nothing more than affected/unaffected individuals and determine the mode of inheritance.|
Cross out individuals who cannot be identified as recombinants or nonrecombinants (uninformative individuals).
Determine whether each informative individual is recombinant or nonrecombinant. Considering an informative individual's haplotype, is it consistent with their parent's haplotype and the mode of inheritance?
|Step 4||Count how many recombinants and non-recombinants there are.|