Effect of transmission model specification on lod score analysis (2)

If the transmission model specified for lod score analysis differs from the true model then the lod scores obtained will be different from those the true model would have produced. The nature of the differences is somewhat random and unpredictable, but certain general rules apply.

If the penetrance is set too high and/or the phenocopy probability too low and/or the disease mutation frequency too low (i.e. the genetic effect is set too large):

In general the lod score curves produced will be more sharply curved and have a greater magnitude.

By contrast, if the penetrance is set too low and/or the phenocopy probability too high and/or the disease mutation frequency too high (i.e. the genetic effect is set too small) then flatter lod score curves of a smaller magnitude tend to be produced.

If the transmission model is grossly misspecified (e.g. recessive instead of dominant) then lod scores may be completely negative, even with linked markers.

modspec1.html, modspec3.html