I have a bunch of SNPs of interest and I have proxies to those SNPs. How can I automatically (as I need to do it for hundreds of SNPs) identify which variant of the proxy (A, C, G, or T) corresponds to which variant of the original SNP? Should I use the frequency of occurence of variants and assume that the low frequency variant of the proxy corresponds to the low frequency variant of the SNP?
Hi there,
I think you are talking about haplotypes (i.e. allelic combinations at multiple loci on the same chromosome). An easy and convenient way to analyse this is to use Haploview and look at the 'haplotype' tab. If you are more interested in strong pairwise allelic associations, I suggest you do LD analysis (estimating r-squared) within Haploview to tell you which SNPs (proxy and original) show the highest allelic associations. For instance if r-squared is 1, there are only two allelic combinations (haplotypes) and therefore the proxy SNP is indeed a 'proxy' for the original SNP.
A Method I wrote quite a while ago to make Haploview input files is available here:
Method Haploview input file instructions: haplotype analysis, taggi...
Hope it helps.
Naser
P.S. related post:
https://www.researchgate.net/post/Anyone_has_an_easy_tutorial_of_how_uploading_excel_sheet_on_HaploView_software_for_LD_analysis_in_several_SNPs
I want to work SNPs of RA in case-control study. I checked LD of SNPs. Should i exclude the proxy SNPs which are in LD with selected SNPs?
why we exclude proxy SNPs?? If any SNP of our interest show positive association, then proxy SNPs which are in LD may also positive association ???
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