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How to read 23andMe raw datas? Help

Discussion in 'Genetic Testing and SNPs' started by trollo, May 10, 2014.

  1. trollo

    trollo Senior Member

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    Italy
    hello. Somebody could please help me to understand how to read 23andMe raw datas?? I don't mean Genetic Genie results.

    as example this is my result for the snp A1298C:


    MTHFR 11854476 rs1801131 G or T GG

    Reference Links: dbSNP Orientation: Minus
    Entrez Gene dbSNP Genotype: CC
    dbSNP Lookup
    Google Scholar (SNP)

    what as example would it be that "dbSNP Genotype: CC" it would be this the risk allele??
    Thanks
  2. Sea

    Sea Senior Member

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    NSW Australia
    MTHFR The name of the gene
    11854476 The position on the chromosome
    rs1801131 Reference sequence number of the snp
    G or T The usual two alternatives for this snp
    GG Your genotype

    Clicking on any of these links will take you to information about the snp or the gene.

    Note how for this snp it says Orientation: minus.

    Your DNA has 2 strands with complentary alleles on each side. So if you have an A on one side it will have a T on the other. If you have a G on one side it will have a C on the other. These strands are called forward or positive and reverse or minus. It has something to do with the direction in which they are read.

    Anyway, 23andme use the forward strand for genotyping. Others sometimes use forward and sometimes reverse. So you are GG for this snp on the forward strand which means you will be CC on the reverse strand. You have to keep that in mind when looking at the research. The reference link is telling you that for this snp dbSNP are reporting for the reverse strand.

    It is not telling you anything about risk, simply what your genotype is for that snp according to dbSNP.

    For this snp A1298C means that at position 1298 (of the gene) instead of an A there is a C. This is reported on the reverse strand. Because 23andme look at the positive strand their two alternatives are G and T instead.
    Last edited: May 11, 2014
  3. trollo

    trollo Senior Member

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    Oh... now i understand. So basically the 2 alleles that characterize a SNP like GG are not the 2 nucleotides joined in the two complementary strands of DNA but are a sequence of 2 nucleotides on the same strand... is it right? Now i understand why i saw in a website that the risk alleles for VDR bsm were A/A while in the Genetic genie they say T/T. It s basically the same. Thanks, Sea.. very helpful response.

    But basically basing on the 23andMe raw datas i cannot deduce any info about the possibility that that SNP is an issue or not. Right?
  4. trollo

    trollo Senior Member

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    Ok i correct myself. Now i understood it. It s not a sequence of 2 nucleotides on the same strand, but the nucleotide (or nucleotides couple) that is in that specific point in each of the two different DNA strands of the two cromosomes. So basically that should mean that for every single nucleotide of a gene there is one 'normal' nucleotide and one 'unusual' or 'abnormal' nucleotide that it shouldn't be there. And if you have the wrong version you are anyway in some way a 'mutant' even if there is not any known functional issue related to that 'abnormality'. Is it right?
  5. Sea

    Sea Senior Member

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    NSW Australia
    You have 2 alleles at each nucleotide position because you get 1 from each parent.

    Most researchers are uncomfortable calling snps mutations unless they are known to be damaging. They are more often referred to as variations.
  6. Sporty

    Sporty

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    Essex, UK
    Hi all

    I've just received my initial results from 23andMe. Are these relevant for what I need? It only seems to be ancestry results from what I can make out.......
  7. trollo

    trollo Senior Member

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    Sporty please, open your own thread and ask for help there.

    Sea: variations means anyway that there is a normality and a variation from it ... does polimorphism basically mean that is a variation from normality??

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