I have a question about LOD score calculations. I have been teaching
the LOD score method in my intermediate genetics class. We calculate
our first z value based on the number of recombinants in the
population. So if we have 1/10 recombinants, the theta value is 0.1
and the probability of a recombinant birth is theta/2 = 0.1/2 = 0.05
and the probability of parental birth is (1 - theta)/2 =
(1 - 0.1)/2 = 0.45. I next have my students pick one theta value that
is create than the observed recombination frequency and on that is
less. What we have always seen is that the theta associated with the
actual observed recombination gives the highest LOD score, and is
therefore the best estimate of the linkage distance. I know it is
best to have a LOD > 3.0. I tell the class this what is looked for in
clinical situations, but for our in class examples, I always have them
choose the theta that give the largest LOD score as the best estimate
of lnkage distance. In the real world of human linkage estimates,
does the theta value that represents the observed frequency of
recombinants always give the highest LOD score.
You can see what I teach at the following URL:
http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/linkage/linkage6.htm
I also have a homework assignment that has the students calculate the
linkage distance based on the simualted marker data. If you go to the
following URL:
http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/topics.html
go to the line labled "Molecular Markers" and select "Quiz" you will
see the assignment. The question is #2.
Any help clarifying this for me will be greatly appreciated. You can
respond here or directly to me via e-mail.
Phil McClean