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Sunday, September 25, 2016

Y Chromosome

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22 comments:

  1. I'm a female and my data on my 24 looks a lot like this....

    what does this mean?

    rs13304893 24 18071765 C C

    what type of genes is this?

    ReplyDelete
    Replies
    1. It freaked me out a little when I first saw it, because no one had prepared me for this. But it turns out it's normal for female children to pick up tiny little bits of the father's Y chromosome. It doesn't hurt us as long as we don't get too much of it or the wrong bits. There isn't much discussion about it, presumably because there isn't much concern over it.

      The snp you cited is listed in the catalog as having NA (Not Applicable) significance. So, nothing to worry about.

      https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=13304893

      Delete
    2. I think it is probably safe to say that male children receive far more female DNA in their genomes, than the nominal bit of male DNA that gets sort of haphazardly stuck to female genomes.

      I've checked up on the various kinds of genetic gender anomalies, and none of them apply to this sort of very common and normal phenomenon. In other words, having this little bit of yDNA from fathers is not at all like having a Y chromosome of your own. So, nothing to worry about.

      Delete
    3. I was wanting to believe that until I saw this.

      http://www.malacards.org/card/46xy_sex_reversal_1


      I googled my first and second results on the Y chromosome and they matched


      rs104894959 24 2655375 G G

      rs104894968 24 2655442 A A



      I have as many results as the blogger does actually 125 out of 885 on my total y chromosome. I don't get though if it is a y chromosome why is the Y with so many spaces on it?

      But the good news is I did have all of my results on both of my XX's well a lot of them at least. Much more than this Y chromosome. And on gedmatch they uploaded my results as xyx chromosomes. Which means xxy I believe. And I looked up xxy sry negative means basically female just with perhaps a smaller uterus which I already know I have a small uterus. So no surprise there. I want to have a retalk with my doctor maybe one that actually knows about this type of stuff.

      Delete
    4. "And on gedmatch they uploaded my results as xyx chromosomes."

      Where did you see that on gedmatch? I've used that site extensively, but never noticed anything like that.

      Delete
    5. I uploaded my raw data to gedmatch and while it was uploading it said its uploading my x my y and x chromosomes. There is no way to see it on any gedmatch feature but when they upload the raw data they show what is being uploaded for it showed an x chromosome a y chromosome and then x chromosome. Basically youd have seen it while uploading your data to gedmatch.

      Delete
  2. This comment has been removed by the author.

    ReplyDelete
  3. I counted it's 136 results I have 125-127. I think I might have overlooked 1 or 2. But I looked at your first result. You have a result the 46xy reversal listed.

    rs104894959 24 2655375 G G

    You might have the same form. Especially if you have two xx chromosomes. There's no way to detect xxy with negative sry chromosomes besides by a dna test. Or in my case I did have precocious puberty. And I read about a girl with precocious puberty that had xxy with a negative sry.
    http://www.annclinlabsci.org/content/40/3/295.full.pdf


    I believe that with the condition from my experience that usually fertility is not affected.


    ReplyDelete
    Replies
    1. I don't know, none of it makes much sense to me. But, I've never had any symptoms that I'm aware of.

      Delete
    2. Its hard to understand to some extent if you don't know what Swyer's syndrome is. Swyer's syndrome is this basically

      https://ghr.nlm.nih.gov/condition/swyer-syndrome


      In the case of a person having xx chromosomes the symptoms are a lot more moderate because the only functional chromosomes are 2 x chromosomes. The whole condition for me is pretty rare because it only happens when you basically have 2 conditions in conjunction. Swyer's syndrome occurs 1 in 30,0000 and xxy syndrome sometimes called klinefelter's syndrome occur 1 in 600 so occurring simultaneous is like 1 in 20,0000. So its very that it happens and when it does very few symptoms are usually listed which makes the condition even less noticeable I also researched xxy syndrome and the mental side of it did seem similar to me when I was a kid.

      For me I had two of the symptoms for me and the precocious puberty and having a small uterus.

      Delete
    3. Your comments are much appreciated, thanks. I'm not sure if it applies to my case, though. There's never been any question that I'm a reasonably healthy female, apparently. You say your Y chromosome looks a lot like mine, and I can't argue with that, since I've not seen it. But I take your word for it. I just assume that there isn't enough yDNA material present in my own genome to cause any problems or have any real effect on my health.

      Here's something I found after a little bit of digging, which might help explain this phenomenon:

      "Normal females also possess two copies of pseudoautosomal genes, as each of their two X chromosomes contains a pseudoautosomal region. Crossing over between the X and Y chromosomes is normally restricted to the pseudoautosomal regions; thus, pseudoautosomal genes exhibit an autosomal, rather than sex-linked, pattern of inheritance. So, females can inherit an allele originally present on the Y chromosome of their father."
      https://en.wikipedia.org/wiki/Pseudoautosomal_region

      So, women can inherit small amounts of genetic material from their fathers which is not sex-linked. So, it doesn't affect their health at all.

      This discussion on the Ancestry forum (my data is from that company) also alludes to the phenomenon, explaining the role of pseudoautosomal genes. They suggest that there is nothing at all pathological about it, and that it is fairly common. However, the originator of the thread was quite confused and upset about it.
      https://boards.ancestry.com/thread.aspx?mv=flat&m=259&p=topics.dnaresearch.autosomal

      And since I haven't any troublesome or obvious symptoms, I'm not worried.

      Delete
  4. they say it's not enough people who have come forward to know the chances of infertility. And the fact that nobody has come forward kind of tells me that with the condition fertility and sexual development is not effected.

    https://www.ncbi.nlm.nih.gov/pubmed/11173857

    ReplyDelete
  5. Well I did the DNA test at ancestrydna and mine doesn't look like yours it just has a similar amount of data on mine being 127 results. But I have 2 genes listed with the site I linked that spoke of sex refers plus I have some of the few symptoms listed. See the first two results on my y chromosome are linked to to gonadal dysgenesis.
    http://s1.zetaboards.com/anthroscape/topic/8045324/1/#new

    I'm in no way saying anything about your data. I was just sharing what I learned about my own data. Yours is missing the second result I have which is actually the initial one I googled that matched the y reversal website I posted about previously. For me I do feel it may be the cause I need to talk to my PCP basically.

    ReplyDelete
    Replies
    1. Talking to your doctor about it is a good idea. Hope everything works out for you. I'd be curious to know what the doctor said about it, especially if it's nothing to be concerned about, but of course I respect your privacy. Again, I appreciate your comments.

      Delete
    2. Well on the link I left about the one with precocious puberty it said abnormalities can develop in the ovaries if I really have a y chromosome which it appears I do as I had the two genes mentioned on the other site about swyer's syndrome. There's more complications with swyer's syndrome than being xxy with the syndrome from the cases I've read though. With Swyer's syndrome you're infertile because you don't have ovaries and they have gonadal streaks which obviously have a higher risk for cancer I've had ultrasounds and I have ovaries so its probably not a high risk but I read in the case the girl with precocious puberty that had xxy chromosomes and was deemed fertile was followed closely for abnormalities like gonadalblastoma. So if its true for me I would like to make sure my Dr keeps an on eye on this.

      Delete
    3. BTW I looked at that ancstrydna thread just now I have a lot more than just 14 results on my y I have over 100 so its not a few results for me. Everything kind of makes sense for me the more I read about this. As a child I was dyslexic I had issues with low energy high anxiety and add And I was looking at the health risks of xxy syndrome everything was similar on the mental side of it. I was bad at sports and had poor motor skills poor writing and reading problems with language etc... As a kid.

      It does really seem that it is possible for me that these are conditions I was born with. I wish this was known when I was a kid. Supposedly early intervention is more effective in helping people to cope with the learning disabilities.

      Delete
    4. "I wish this was known when I was a kid."

      Yes, but better late than never, right? That's why I began investigating my DNA, to learn about myself. Knowledge is power, and you now have some insight into your early difficulties. I too learned things that made certain problems less puzzling for me. For example, I learned that I probably have had Crohn's disease and other digestive problems all my life. I knew something was wrong, but didn't know what it was exactly. Now I feel more certain about it.

      You might be interested in going to Interpretome:

      http://esquilax.stanford.edu/

      On that program (which is free by the way), you can upload your Ancestry data and run it through various applications which can reveal quite a lot about your personal health and ancestry. I ran mine through "Clinical" -> "Disease" in order to get my personalized GWAS variants report. The report is extensive, covers a lot of territory. It's important to use *Google Chrome* when doing so, if you want everything to come out nice and orderly (i.e. in alphabetical order, which is easier to read). Each snp they check for you includes links to scholarly references which give more information. You can find out a lot about your genes there, I think.

      Just a heads-up though: like me, you might see things on the report that are confusing at first, or even a little disturbing (if you happen to be very emotionally sensitive or nervous). But generally I found it to be fairly helpful, because for instance (just one example) I immediately adjusted my diet so that I don't have as many stomach aches anymore. That sort of thing.

      Also, just because you have 'risk' alleles on your genotype for certain conditions, doesn't always mean you will actually have that condition. It just means you could be predisposed to it, but there might be other (possibly unknown) factors involved, which could work either for or against you. Scientists are still in the process of investigating all the various genetic risk factors, so there is still a lot that is unknown. And some conditions have scores of known risk factors, while others have very few that have been discovered so far.

      Also, each risk factor (allele) is subject to a statistical potential. In other words, some have "NA" (negligible, or nothing much there to cause concern), while others are quite high risk for the individual. The report conveniently lists the estimated potential risk of each risk allele.

      If you haven't done that yet, I think you might enjoy doing so.

      Delete
    5. I should mention that the data from Ancestry needs to be in text mode for Interpretome. Just download your data from Ancestry first without opening it (just "save"). Then open it and save a separate text file from it to use for Interpretome. That way if you need the unopened file for something else, you won't have to wait another day (Ancestry only allows one download every 24 hours, as I'm sure you know already).

      Delete
    6. I went to my PCP today he referred me to 3 different doctors upon seeing all the results. But honestly I think the problem is the is a bit above what he sees everyday. Because like he and my gynaecologist didn't know anything about swyer's syndrome to begin with. What sucks more is I can't find a geneticist in my area so he referred me but without a geneticist. And he did say if it was true.

      Also my mom is getting hers done at 23andme. She has ulcerative colitis I think and I wonder if they'll pick up on it. I did remember uploading I think on dnaland or Prometheus a while back and looking something up that implied I had a propensity for some kind of colon cancer not sure if that's related to ulcerative colitis PR not but I know the colon cancer part already because my moms dad had colon cancer. I have also a melanoma risk but it said that was the same gene that I had to make blue eyes. And I don't have blue eyes I only had gray eyes as a baby so that's more recessive I guess.

      Delete
  6. This comment has been removed by the author.

    ReplyDelete
  7. hey wanted to let you know I actually did 23andme and they came up with the same conclusion that I had a y chromosome but they could not show the raw data they found exactly. My mom came up with no detected variants though.

    ReplyDelete
  8. Thanks for the update! If I find out anymore about it, I'll post the information here.

    ReplyDelete