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Linkage disequilibrium

hnewbery at liverpool.ac.uk hnewbery at liverpool.ac.uk
Thu Apr 9 04:29:37 EST 1998

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)

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