Can you please help me in my haplotype analysis?

Question

[Fatemeh Nabizadeh]

Hello everybody Can you please help me in my haplotype analysis? I want to find out the relationship between my haplotypes and hormonal concentrations.

According to the data from SNP-analyzer, I have 3 haplotypes (2 SNPs): TT(h1)...TC(h2)...CC(h3) Every subject has 2 haplotypes, like this: h1,h2 or h1,h3

I'm confused since at last I have to report that just one haplotype affects the concentration of hormone. I do not know how to import my data into SPSS and how should I report.

Thanks in advance for your advice

[h.mon]

I do not know how to import my data into SPSS and how should I report.

As we don't know anything about your data, neither do we. What data do you have? How is it organized? Could you show a snippet of your data here?

Could you clarify if you really have an haplotype - that is, you have two sites with segregating SNPs, with the following possible haplotypes:

            haplotype 1    haplotype 2    haplotype 3
SNP 1           T              T              C
SNP 2           T              C              C

Or do you have one SNP with two alleles, and TT, TC and CC are the genotypes?

[Fatemeh Nabizadeh]

Thank you for your reply!

I have 2 SNPs which are in linkage disequilibrium. Each one containing 2 alleles (T and C). AND I have 4 genotypes: 1. SNP1 T/C...SNP2 T/C 2. SNP1 CC...SNP2 T/T 3. SNP1 T/T...SNP2 C/C 4. SNP1 T/C...SNP 2 T/T SNPanalyzer gave me 3 haplotypes as I mentioned; CT, TC and TT