Hi everyone,
I want to determine the real genotype of my SNP in heterozygote patient but I can’t? Should I do the linkage disequilibrium analysis, if yes, please tell me how? I am new in SNP analysis, if no, can you help me with this problem??
I'll give you an example :
I have a sub-haplotype determined by six SNP : AAGCTG and GGGCTG !! How can I be sure wich matching is correct???
Hope my question is clear, thank you all.
I am not sure I am understanding the problem but to show each snp exists design forward primers ending with each 6base sequence and a reverse primer. The forward primers will only anneal to their correct sequence so if only one amplifies it is homozygous for that sequence but if both primers amplify then the sequence is heterozygous. The sequences including part of the snp and part normal sequence might make/break a restriction enzyme site which could also be used to distinguish the sequences but that is hard to say without seeing more sequence
@Paul Rutland thank you for your answer, but it's not really the problem. My issue is that each Sub-haplotype in my gene is characterized by 5 SNPs in diffrent positions. For example :H1J is AAGGT. When I did the experiment and got the results : heterozygote patient had AAGGT//AACGT. In this case , I can't define the exact alleles expression. Hope my question is clear now !! Thankk you
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