The power and pitfalls of omics part 2: epigenomics, transcriptomics and ME/CFS
Simon McGrath concludes his blog about the remarkable Prof George Davey Smith's smart ideas for understanding diseases, which may soon be applied to ME/CFS.
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Help Understanding the Different Ways to Describe Genotype

Discussion in 'Genetic Testing and SNPs' started by aaron_c, Apr 15, 2015.

  1. aaron_c

    aaron_c Senior Member

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    Hi Yall,

    I just looked up Rs662 on 23andme (A PON1 snp) and found that I have the TT genotype according to them, but the AA genotype according to dbSNP. The snpedia page lists my options as either A or G. Other genes on 23andme do not have different genotypes for 23andme and dbSNP.

    I understand that in DNA A will always be paired with T and G will always be paired with C, so it makes sense that they are saying the same thing in different languages, as it were, but I don't understand why they are sometimes different and sometimes the same. In particular, it makes it difficult to know what is happening when there are three possible nucleotides (I think I have seen this happen...but perhaps I did not understand what I saw.)

    I would appreciate any explanation yall can offer.

    Thanks a lot!
     
  2. halcyon

    halcyon Senior Member

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    The base pair notation for an allele will depend on which side of the DNA strand it was sampled from. As you mentioned, T pairs with A and G pairs with C, so A and T would be synonymous. 23andMe says C or T, snpedia says A or G, these are saying the same thing. TT = AA.
     
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  3. Valentijn

    Valentijn Senior Member

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    @aaron_c - 23andMe always uses the forward alignment.

    dbSNP can use either forward or reverse alignment. Near the top of the dbSNP page for a SNP, there is a bit which says "RefSNP Alleles:", then the alleles, and (REV) or (FWD). If it says (REV), then the alleles need to be switched: C=G, and T=A.
     
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