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help translating an SNP from dnbSNP site

Discussion in 'Detox: Methylation; B12; Glutathione; Chelation' started by pgoody, Jun 4, 2013.

  1. pgoody

    pgoody

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    I've been trying to find out the frequency of major and minor alleles of a few snps from my 23andMe results, but I have been a bit confused by what comes up on dnbSNP. For example when I searched for rs6265 on 23andMe it shows "C or T" but when I look it up on dnbSNP (http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs6265) it shows both A and G as germlines. I have seen on at least one post on here that "A=T and C=G", so this made sense to me (using that logic), but then I read the MAF/Minor allele count was T=.229, and was confused as to why they used T to designate the minor allele and not either of the letters they referred to as the germlines. Does this mean that C/G is the major allele and that A/T is the minor allele with a .229 chance of having the minor allele?
     
  2. Sea

    Sea Senior Member

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    NSW Australia
    Sometimes the difference is in whether the alleles are reported in the plus or minus strand. 23andme is always reported on the plus strand. If the SNP you are looking at is reported on the minus strand your result can be inferred from your plus strand. Seems they always pair with the A/T and the C/G on opposite strands. So it's not the same as A=T, rather, if you have an A on the positive strand you will have a T on the negative strand. If you're looking at your browse raw data on 23and me click on the little plus sign to the left of the gene. The info that drops down includes whether it is in plus or minus in the dbSNP and will indicate what your genotype is in dbSNP.

    As for how they report the minor frequency I haven't quite worked that one out yet. It seems that there can be more than 2 possible alleles (eg an A could be replaced by a G or a T). If you click on the blue words MAF/minor allele frequency at dbSNP there is an explanation of how they report the minor allele. In the case of more than 2 reported alleles the frequency is of the second most common (in order to help distinguish between common SNPs and rare ones) .229 would equal 22.9%

    To look at frequency I usually go to the section with the coloured bars which represents the frequencies in different racial populations.
     
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  3. pgoody

    pgoody

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    So A,C, and G,T are not limited to positive and negative strands, yet they will certainly oppose eachother? For example just knowing you are AA would not determine if those are from the positive and negative strands, but it would tell you that there is a TT on the opposing strands? So since it is possible to have more than 2 variations then for example GC on the positive strand opposed by a CG on the negative strand is possible result?
     
  4. pgoody

    pgoody

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    By this do you mean that you scroll down and look at the bars on the dbSNP page that have percentages for the various allele groupings? I found issues with using that as a means to verify the minor from the major allele. If you look at this SNP (http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2020933) A is referenced as the ancestral allele and T is the minor allele with a probability of T=0.128. But if you scroll down T appears to be the most abundant allele amongst the populations. What gives?
     
  5. Valentijn

    Valentijn Activity Level: 3

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    All 4 can be on either strand. And yes, AA on one would mean TT on the other, and GC on one would mean CG on the other. So when 23andMe or older research isn't using the NCBI standard, it's pretty easy to translate.

    The first listed or major allele on NCBI is the "ancestral" allele. This doesn't mean a damned thing in practical terms .... it's often less common than the minor allele. I think it's mostly just a way to establish a standard for communication.
     
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  6. Sea

    Sea Senior Member

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    Yes that's what I mean and yes I also find things that seem to be contradictory. That's why I said I haven't quite worked that one out yet. The minor allele frequency is calculated from the 1000genomes project. The coloured bars are from HapMap which has a larger number of samples and they are separated by race. So, I think it is probably the more accurate representation, but I don't really know for sure.

    The ancestral allele just means they've been able to determine which one came first, but it's not necessarily the major frequency anymore.
     
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