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what is a risk allele

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#1 SF_HK



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Posted 01 March 2020 - 02:22 AM



Im new to SNPs.  Would appreciate if someone can help me understand a few concepts on SNPs.


1. What doe sit mean when research papers mention for e.g. minor allele 'T' is a risk allele for rsxxxx (C>T). So does this imply risk for homozygous for TT and risk for heterozygous CT, but no risk for CC?


2. If rsxxx (C>T) is studied by taqman PCR, the vic/fam dyes would be for C or T. A SNP is classified if present in more than certain percentage of the population. Can someone have A or G instead of CT for this particular SNP, in which case there would be do data determined by qPCR?


Thank you, I would appreciate any help.

#2 bob1


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Posted 01 March 2020 - 06:01 PM

1) it means that there is more risk associated with that particular SNP. It is not necessarily that there is no risk for the CC, it's just that the presence of a T at that position is higher risk.

2)There could possibly be a A or G at that position, but it would be an independent SNP. Occasionally in the literature you will see a SNP reported with abundance of each nucleotide at particular positions (for a completely made up example e.g. C 80%, T 15%, G 5%), but it really depends on the allele and the disease it is associated with. You would not detect the A/G mutation with your TaqMan assay - These days you most likely would be doing some sort of deep-sequencing to determine this. Formerly it would have been Sanger sequencing, or perhaps denaturing-HPLC for a well defined allele.

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