Calculation of SNP effect using only homozygous genotypes

From: Khandker Kislam <kkislam_at_UALBERTA.CA>
Date: Wed, 19 Nov 2008 02:09:18 -0700

Dear Arthur and all,

In association analyzes using SNP marker we have three genotypes,
i.e., AA, AB and BB. I am using SNP with recoding these three
genotypes as(0=AA,1=AB,2=BB)

Using an animal model I have already estimated two effects successfully,

1) Allele substitution effect using command-- resp ~ mu SNP !r animal
This effect consider all three genotypes and is the effect of
substituting one allele in the population with the other allele.
2) Dominance effect using the command -- resp ~ mu at(SNP,1) !r animal
This effect is estimated as the non-additive genetic effects or the
deviation of the heterozygous from the mean of the 2 homozygous

But I don't know how to calculate another SNP effect (additive effect)
which use only two homozygous genotypes (AA and BB). This effect is
estimated as the difference between the 2 homozygous means divided by
2, i. e., [(AA-BB)/2] or [(0-2)/2]. This effect is different form the
allele substitution effect.

Thanks in advance for any advice.

Best regards,
Received on Fri Nov 19 2008 - 02:09:18 EST

This webpage is part of the ASReml-l discussion list archives 2004-2010. More information on ASReml can be found at the VSN website. This discussion list is now deprecated - please use the VSN forum for discussion on ASReml. (These online archives were generated using the hypermail package.)