Announcement

Collapse
No announcement yet.

SNP + or -

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • SNP + or -

    Just prior to ordering the BigY test it was recommended to take an S17250 SNP test. I received my results back and it should this for the marker:

    S17250 ChrY 15531354 15531354 A+

    I was told that this meant S17250+.

    Could one of you fine folks point me in the direction of understanding how + and - is determined for the SNPs. So far I have M423+ CTS10936+ S17250+?
    What is the significance of these + and how is that decided? Is there a list somewhere of the SNP alleles and which nucleotide is normally there?

  • #2
    Originally posted by singingfalls View Post
    Just prior to ordering the BigY test it was recommended to take an S17250 SNP test. I received my results back and it should this for the marker:

    S17250 ChrY 15531354 15531354 A+

    I was told that this meant S17250+.

    Could one of you fine folks point me in the direction of understanding how + and - is determined for the SNPs. So far I have M423+ CTS10936+ S17250+?
    What is the significance of these + and how is that decided? Is there a list somewhere of the SNP alleles and which nucleotide is normally there?
    In the case of S17250 the G value is ancestral/negative and the A value is derived/positive. Prior to the advent of the A mutation at that chromosomal position, everyone would have been G. At some point in the past, there was a mutation from G to A at that position in an individual and now his direct male descendants carry that A mutation.There are places where you can look up what the ancestral/derived states are for different SNPs, the easiest place to use is http://isogg.org/tree/ISOGG_YDNA_SNP_Index.html, for more advanced use another place is http://ybrowse.y-chromosome.org/gb2/gbrowse/chrY/?

    Comment


    • #3
      According to Yfull S17250 is currently estimated to have formed about 2,300 years before the present.

      Comment


      • #4
        Thank you for your replies. Very helpful. And the significance of plus or minus? Does that refer to the reference SNPs? +=yes you have it. -=no you do not have it?

        Comment


        • #5
          Correct. + means you have the mutation and are descended from the first man it which it arose. - means you belong to the rest of humanity*

          * There are a few exceptions such as SNPS that are coincidentally recurrent and some that can recombine.

          Earl.

          Comment


          • #6
            Great. Thanks again for helping me sort that out.

            Comment


            • #7
              Originally posted by Earl Davis View Post
              [----] There are a few exceptions such as SNPS that are coincidentally recurrent and some that can recombine.

              Earl.
              Earl, where can I learn about that?

              Thank you - Mr. W.

              Comment


              • #8
                Originally posted by Earl Davis View Post
                Correct. + means you have the mutation and are descended from the first man it which it arose. - means you belong to the rest of humanity*

                * There are a few exceptions such as SNPS that are coincidentally recurrent and some that can recombine.

                Earl.
                Of keen interest to me is the complex and unsettled history of the I2a clade and its subclades. Its variances over Europe and time contribute to the confusion surrounding its origins. It makes for difficult searching. Some of the literature definitely points to a possible recurrence of I2a after the ice age? On top of that it seems there is little known of beginnings of the particular clade of which I am a part; I2a (I-P37) Dinaric North. Invariably when I2a is mentioned the information drifts more toward your part of the world. I sprang for the BigY in the hope of adding in some small way to the compendium of knowledge related to this clade. I have a voracious appetite to know.

                Comment


                • #9
                  Originally posted by dna View Post
                  Earl, where can I learn about that?

                  Thank you - Mr. W.
                  Assuming it's the recombination on the Y you are interested in try googling terms like;

                  homologue parts of the Y chromosome

                  or

                  Pseudoautosomal region


                  To give an idea of this in practice I have an SNP called BY127 which was discovered under DF27. It was later also found in L21 people. As DF27 and L21 are both sons of P312 this sould not have been possible. The simple assumption was that it was a recurrent SNP but when Thomas Khran took a look at it he said

                  "The region around BY127 is 97.9% identical to ChrY:15226203..15227256.
                  We don't recommend testing for this marker because such markers are
                  prone to parallel and back mutations due to recombination events in
                  between the homologue parts of the Y chromosome.

                  In this case we have a so-called parallel repeat. It is similar to a palindrome, but the direction of the segments point into the same direction (not reverse complement)"

                  Comment


                  • #10
                    Originally posted by Earl Davis View Post
                    Assuming it's the recombination on the Y you are interested in try googling terms like;

                    homologue parts of the Y chromosome

                    or

                    Pseudoautosomal region


                    To give an idea of this in practice I have an SNP called BY127 which was discovered under DF27. It was later also found in L21 people. As DF27 and L21 are both sons of P312 this sould not have been possible. The simple assumption was that it was a recurrent SNP but when Thomas Khran took a look at it he said

                    "The region around BY127 is 97.9% identical to ChrY:15226203..15227256.
                    We don't recommend testing for this marker because such markers are
                    prone to parallel and back mutations due to recombination events in
                    between the homologue parts of the Y chromosome.

                    In this case we have a so-called parallel repeat. It is similar to a palindrome, but the direction of the segments point into the same direction (not reverse complement)"
                    Thank you.

                    From the example provided, it appears to me that parts of Y chromosome are subject to gene conversion.

                    Earlier I was imagining that the pseudoautosomal regions were already excluded, but learned about gene conversion only now.

                    Thank you! - Mr. W.

                    Comment

                    Working...
                    X