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How do I find a specific gene using 23 and me raw data?

Discussion in 'Genetic Testing and SNPs' started by Soundthealarm21, Feb 4, 2014.

  1. Soundthealarm21

    Soundthealarm21 Senior Member

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    There have been several genes I have wanted to look up, but I don't understand how to navigate the raw data. Does someone know how to find specific genes (ie PEX, HLA DRBQ, etc)?
  2. Sea

    Sea Senior Member

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    Sign in to your 23andme account.
    Click on your name on the top right hand corner of the screen.
    From the drop down menu choose Browse Raw Data
    Enter the Gene name into the search box.

    Start with some that you know are there like MTRR or MTHFR.

    Sometimes genes have more than one name and it may take a little extra searching to find how 23andme label a gene. Their searches are exact, no info is returned on a partial enquiry.

    If you know an rs number for a gene type that into the search box for a SNP and you will see how the gene name is displayed. By clicking on the gene name 23andme will list all the snps tested on that gene
    Soundthealarm21 likes this.
  3. lnester7

    lnester7 Seven

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    @ Sea how do I know if a gene is mutated from the raw data.
    ADAMTS2 178540975 rs1054480 A or G CC

    Reference Links:
    Entrez Gene
    Google Scholar (Gene)
    dbSNP Lookup GG
    Google Scholar (SNP)

    What does all this mean/???
    Last edited: Feb 4, 2014
  4. Valentijn

    Valentijn Activity Level: 3

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    The dbSNP link is the most useful. It should take you to http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs1054480 . G is the most common allele - is your "CC" result a typo?
  5. lnester7

    lnester7 Seven

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    Sorry My results are GG
    dbSNP genotype CC

    If results are different from dbSNP genotype does that mean is mutated? I am trying to understand the raw data since all the interpretation is Gone, I only find sites to interpret the methilations and Detox but not the other Genes. I am wondering about EDS since I look mutated? Or maybe I just don't understand well yet.
  6. Soundthealarm21

    Soundthealarm21 Senior Member

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    @Sea @Valentijn

    It's easier to spot the heterozygous ones. So the layout is this:

    Gene Position SNP Versions Genotype
    X X X C or T TT


    If under "versions" it gives a C and a T is the first one listed (the C in this case) the normal one and the second one (T in this case) the mutated version?

    Or am I misunderstanding?
  7. Valentijn

    Valentijn Activity Level: 3

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    No, they're always listed in alphabetical order by 23andMe. To see which one is rare, you need to go somewhere like dbSNP. And to see if an SNP is known to have any impact, you need to read the research. Sometimes there are useful summaries of the research for a SNP at snpedia.com .
  8. Valentijn

    Valentijn Activity Level: 3

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    dbSNP reports some genes backward. If it says REV near the top, then those alleles are reported backwards, and they'll also report the genotype prevalence backward at the bottom of the page. That SNP says "C/T (REV)" near the top, hence is backwards and the alleles are really A/G.
  9. Soundthealarm21

    Soundthealarm21 Senior Member

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    Whoops I apologize about the formatting! It bunched it together after I pressed post reply!

    Thanks @Valentijn !
  10. Sea

    Sea Senior Member

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    There are 2 strands in DNA (this is not the 2 alleles where you get one from each parent). One strand is designated forward (or plus) and the other reverse (or minus). I don't really understand the how or why but that isn't necessary to research our data.

    The one thing important to know is that when we know what an allele is on one strand we can know what it is on the other because they're always complementary pairs. If one strand is an A the other is a T. If one strand is C the other is G.

    23andme report all our snps on the forward strand of DNA. In dbSnp some snps are reported on the forward strand and some on the reverse. It used to be harder to tell which way they reported but as Valentijn said that info is now clearly displayed with a (FWD) or (REV) beside the alleles in dbSnp.

    The link to dbSnp from your 23andme raw data shows you how your alleles are reported at dbSnp. If it is reported on the forward strand at dbSnp then it will be the same as your 23andme alleles. If reported on the reverse then A and T will be swapped and C and G will be swapped. So for the one you noted above your data from 23andme is GG (on the forward strand as it always is from 23andme) and the dbSnp link shows you that your data is CC on the reverse strand.

    All that tells you is what your alleles are. To determine whether you have a mutation or not and whether it is of any significance or not you have to read about the snp at dbSnp and beyond.
  11. Sea

    Sea Senior Member

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    True it is easier to spot the heterozygous ones but without researching them we still won't know whether they will be of any significance to us or not. Many variations are of no consequence at all.
    Valentijn likes this.
  12. lnester7

    lnester7 Seven

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    Would you mind walking me trough it in this example??? I don't know how to translate that explanation to real example. So step by step once I am in dbSnp there is a lot of information but I don't see how to determain the mutation. When I read and reaserch the gene only says if the gene is mutated, does not explain for me how to know that or what values to compare to.
  13. Sea

    Sea Senior Member

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    http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs1054480

    If you click on any of the blue titles it takes you to an information page that explains the display.


    At the top of the page in the box under the heading Allele:

    Variation class SNV - single nucleotide variation in this instance. Sometimes it can be an insertion or deletion variation instead.

    RefSNPAlleles C/T (REV) - this tells you that on the reverse strand C or T are the usual results

    Ancestral Allele C - the ancestral allele is the original. It's usually, although not always, the most common and may or may not be the better one to have

    Clinical source - if an allele has significance data then there is often a link here to Variation viewer and OMIM with more information on the SNP and/or the gene

    Clinical significance N/A - in this instance there is no clinical significance data for this SNP. The kind of information usually found here would be "with pathogenic allele" in red if it has a known detrimental effect

    MAF/MinorAlleleCount A 0.252/549 - this is usually reported forward so the A here corresponds to the T above. This tells you that A(T) has a prevalence of 25.2% in the 1000 genome project data, and that A(T) was seen 549 times.

    Under the heading Gene View:

    If you click on the button "GO" it takes you to a table of SNPS for that gene. There is useful information here too.

    Yellow shows snps in the intron region - the effect of these is less known and mostly not significant.

    Green shows snps that don't change the gene product - sometimes these make a small difference to the speed of a gene's action but don't change what the gene does.

    Red shows snps that are "missense" meaning that the change in allele results in a change to the protein produced. This can result in a gene that does not do what it is supposed to or does not do it efficiently. The table includes if a change is known to be pathogenic.

    This table is one of the ways to find rs numbers for snps that 23andme have as i numbers because you can identify them by the position number instead.

    Back to the original page, still under gene view:
    Under the subheading Gene Model(s)
    Function - tells you this is a missense mutation

    Allele change - shows you the change from C to T. This is in red because it is a missense mutation.

    (Protein) position 1177, (MRna) position 3631 - useful to know for further research with an alternative naming convention

    Residue change - the protein coded by the original is Proline (Pro) and the mutation changes it to Serine (Ser)

    The table display has coloured boxes which you can click on for more information and links to research if there is any known. I can't use these on my ipad, only on the computer. Purple means known pathogenic. I can't remember what the other colours mean but they are significant.

    Under the heading population diversity:
    You can see how common the alleles are in populations of various ethnicities. An allele that is common overall may be almost non-existent in some races, or it may be rare overall but common in a particular populations. Some snps have been studied a lot simply because they are useful in determining ancestry rather than of any significance medically. A wide divide in prevalence here can be a clue to that.

    If a snp is well studied and known to be associated with something there will most likely be plenty of links on this page to follow up. Sometimes research records the rs number but often not, so it is useful to learn the alternative ways a snp might be displayed if your search doesn't turn up much.

    They are often written by the protein change - so in this instance you would find it as Pro1177Ser or P1177S
    Sometimes it is reported by the allele change - so by the gene position 3631 you would find it as C3631T or 3631C>T.

    Hope that goes some way to answering your question. I found it rather overwhelming when I first started looking but I am learning slowly. A year ago I didn't know any of this.
    lnester7 likes this.
  14. lnester7

    lnester7 Seven

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    @Sea Thank you so much, this is not for HH6 bunch :bang-head: Maybe I will keep looking at it and make any sense.
    Sea likes this.

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