Inferring mode of inheritance by comparison of lod scores

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Abstract
One usually must assume a mode of inheritance when using lod scores for linkage analysis. In this study, we asked the question, “If one assumed mode of inheritance in a linkage analysis gives a higher lod score than another, does that indicate that the mode of inheritance that led to the higher lod score is more ‘correct’ than the other?” We simulated data under a variety of penetrances, assuming either dominant or recessive inheritance. We then analyzed those simulated data under the correct mode of inheritance, assuming a range of penetrance values, and under the incorrect model, also assuming a range of penetrance values. We found that, if there was enough information for a maximum lod score of at least 3.0, assuming the correct penetrance value or mode of inheritance in the analysis led to a higher lod score than assuming the incorrect penetrance or the incorrect mode of inheritance. These results cannot yet be generalized outside of the specific modes of inheritance and penetrance combinations that we have modeled. Also, penetrance was modeled as “random.” The effect of “reduced penetrance” caused by other genetic factors has not yet been tested. We also tested the effect of non‐standard ascertainment on drawing conclusions about mode of inheritance from linkage data. Even when families were ascertained only if the family was multiplex (i.e., more than one affected sib), assuming the correct mode of inheritance gave a higher lod score than assuming the incorrect mode of inheritance. This method has the promise of both simplifying and expanding the application linkage analysis. The explorations reported here are, however, preliminary, and the method should be used with caution.