LODscores

# LODscores - LOD SCORES Humans are the ultimate model...

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1 LOD SCORES 3/31/11 Humans are the ultimate model organisms whose genetics we eventually are interested in understanding. However, humans are impractical model organisms in the sense that we cannot control their matings and their family sizes (numbers of progeny) are quite small. Thus, sophisticated statistical approaches are often needed to study the genetics of human families. LOD scores offer the necessary statistical approach to analyze whether the limited data (i.e., offspring) for one or more human families support the conclusion that the gene for a trait and a known mapped marker are linked or are not linked. LOD stands for “log of odds ratio.” Given a set of data (e.g., the progeny of a family), one first calculates “ L :” L = (probability of the progeny assuming linkage with crossover) / (probability of the progeny assuming no linkage or independent assortment). Note that L is a true ratio that compares the odds of the progeny as analyzed with one model (linkage with crossover) versus the alternative model of no linkage. The LOD score is then calculated as: LOD = log 10 ( L ) If LOD > 3, then we conclude that the probability of linkage with crossover (the numerator) is sufficiently greater than the probability of no linkage (the denominator) to accept the “numerator” model (i.e., linkage with crossover). In contrast, if LOD < 3, then the “denominator” model is retained instead (i.e., the two genes are unlinked). Remember that we are dealing with logs, so a LOD = 3 reflects a 10 3 or 1,000 times greater probability of the numerator model over the probability of the denominator model (i.e., for linkage with crossover over no linkage).

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LODscores - LOD SCORES Humans are the ultimate model...

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