Case-control phased Haplotype logistic regression on SPSS

Question

[Guilherme]

I have phased haplotypes based on 13 SNPs, which generated 17 unique haplotypes on my case-control data. I've done the logistic regression association test on SPSS for the genotypes (independently), coding each SNP with and additive mode (0, 1, 2).

Now that I have the haplotypes (generated with PHASE program), I would like to perform a logistic regression analysis but I don't know exactly how to code those haplotypes on my database...

Below Is my database with the 13 SNPs coded as 0, 1, 2

Answer 1

[pbpanigrahi]

I am assuming you are asking how to encode the haplotype into 0, 1, 2? If that is the case then use

• 0/0 -> 0
• 1/1 -> 1
• 0/1 -> 2

Let us know if this is what you are asking?

Thanks

Priyabrata

[Guilherme]

Hi Priyabrata,

Not exactly. This is something that I've already done as you can see on the image above. Each polymorphism were coded as 0/1/2 based on their genotype combination (e.g AA = 0, AG = 1, GG = 2).

I have determined the phase (with PHASE program) of these 13 polymorphism, generating 17 unique haplotypes distributed across my case-control study...Now I want to do a regression analysis to see if one of those (or more) 17 haplotypes might be associated with my disease (taking into consideration on the regression model, the two PCs in order to control for population stratification). The two PCs can be seen on the last two columns of the picture above...