As part of an association study, I have been investigating two
polymorphisms which lie within the same gene (in fact, only 70 bp
apart). I am attempting to ascertain whether the two
polymorphisms are in linkage disequilibrium, based on the
genotype frequencies in our study population. (As a separate issue
from any question of disease association.)
I have been using the commonly-cited equation to calculate
the linkage disequilibrium, D, where D = P11-p1q1.
However, there are difficulties in calculating P11,
the probability of the two most common
haplotypes occuring together, because it is impossible
to know from our data whether an individual heterozygous
for both mutations carries these muations on the same
chromosome. (We do not have any family data)
I have thus been trying to use the iterative method of
Hill to estimate P11, but it has not given me sensible answers.
My query (rather long-winded, apologies)is thus whether
there are any programmes available (preferably, though
not necessarily) over the internet which will calculate the
degree of linkage disequilibrium between two polymorphisms for
me given the genotypes which we have encountered.
Thank you.
H. Newbery
(hnewbery at liv.ac.uk)
