Re: Calculation of SNP effect using only homozygous genotypes

From: <arthur.gilmour_at_DPI.NSW.GOV.AU>
Date: Thu, 20 Nov 2008 08:41:57 +1100

Dear Khandker

You have 3 SNP classes so there are only two degrees of freedom.
So fitting
 resp ~ mu at(SNP,1) SNP !r animal

fits them both. You will find the dominance effect as before and the SNP
regression will
give the effect you want.

You can verify this by fitting SNP as a factor (2 degrees of freedom) and
manually looking at the contrasts of interest.

May Jesus Christ continue to be gracious to you,

Arthur Gilmour, His servant .,
Principal Research Scientist (Biometrics)
NSW Department of Primary Industries
Orange Agricultural Institute, Forest Rd, ORANGE, 2800, AUSTRALIA
fax: 02 6391 3899; 02 6391 3922 Australia +61
telephone work: 02 6391 3815; home: 02 6364 3288; mobile: 0438 251 426


Khandker Kislam <kkislam_at_UALBERTA.CA>
Sent by: ASReml users discussion group <ASREML-L_at_DPI.NSW.GOV.AU>
19/11/2008 08:09 PM
Please respond to
ASReml users discussion group <ASREML-L_at_DPI.NSW.GOV.AU>


Calculation of SNP effect using only homozygous genotypes

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 Sat Nov 20 2008 - 08:41:57 EST

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