I am working on SNPs association with disease. I genotyped two SNPs per gene. Now one of the reviewer asked me to calculate Linkage disequilibrium r2 value for tw SNPs of TNFalpha an dtwo SNPs of Resistin gene. Someon eplease help me to know how to calculate r2 values?I have already constructed haplotypes for these polymorphism. As i construct haplotypes manually, i dont getr2 value automatically. Your early and detailed response will be highly appreciated. Thank you very much.
Hi Kanwai
You can use the 'pegas' package in R, or you can use 'Arlequin', or .... There is a lot of sotware that can do it.
Or you can do it by hand (see fior example, http://pbgworks.org/sites/pbgworks.org/files/measuresoflinkagedisequilibrium-111119214123-phpapp01_0.pdf).
But I have another concern, how do you obtain haplotypes manually? Do you have information on their parents? or sons?
Please be aware that some LD values can be obtained form genotypes (e.g. T2 in pegas package)
Hope it is helpful
Pablo
Hi Pablo and thanks. Let me try this by hand method as im not good at using software and time is very short. Regarding haplotype, i had gentrifying data for all my patients and control group for two respective SNPs. I made four possible combination and calculate them manually in excel sheet. Hope it make sense.
*genotyping data (not gentrifying data ), sorry for typo. I have done genotyping via RFLP-PCR technique.
Pablo G. Goicoechea
Hi Pablo,
I have tried your provided link and it worked to some extent. i wanted to calculate r2 value and i already have genotype and haplotype data for my four SNPs (two per gene). I calculated D value first and then directly calculated r value. I have calculated haplotypes separately for patient and control group. But my reviewer asked me to calculate r2 value for theses SNPs in my population. So what should i do now? Should i combine haplotype and allele frequency for both patient and control groups as both are from my population and then proceed? Secondly, i am confused about r2 value calculation.why there is square of r value in the last step? Can you please suggest me any easy to use software? I was unable e to download arlequin. You r help will be much appreciated. Thanks.
Hi Kamwal
No, keep your control and patient groups separated.
As explained in the link, r2 is calculated to remove the arbitrary sign that is included in the estimation of r (and D).
This link to Arlequin works fine http://cmpg.unibe.ch/software/arlequin35/Arl35Downloads.html
But again, I would be worried by your haplotype estimates. With only two SNPs from each gene the probabilities of the different haplotypes must be quite similar, making inferences very difficult. I would try to estimate T2 from genotypes (using pegas package in R).
Hope this helps
Dear Pablo G. Goicoechea
thanks you. Reviewer asked me to calculate pair wise linkage disequilibrium value r2 for two RETN SNPs and for two TNF SNPs in my population. So i will get four r2 values (two for patients and two for control group)? I am still confuse how to calculate these values.I think something is missing in my system that why i am unable to run arlequin.
Why are SNPs with: (i)call rate less than 90%, (ii) MAF less than 1%, (III) deviation from HWE (p10%) be excluded from analysis?
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