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Thread: I'm interested in finding people with rs41302905 CT or TT

  1. #1
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    Red face I'm interested in finding people with rs41302905 CT or TT

    This is a SNP in the ABO gene.

    Most people will have rs41302905 CC. A few, however, will have rs41302905 CT, and an even smaller number may have rs41302905 TT -- although I believe that this will almost always reflect a chip error.

    Anyway, if you have either rs41302905 CT or TT, I'd appreciate it if you would post your results for rs41302905 and for two other SNPs: rs8176719 and rs8176747. It would also be helpful if you would post your ABO blood type (if known), and 23andMe's prediction of your blood type and subtypes, or whether the ABO Blood Type lab says "Can't be predicted".

    Here's what I'm expecting to find. If you have rs41302905 TT, you will probably get "Can't be predicted". However, your blood type will most likely be B. If you get rs41302905 CT, the lab may or may not be able to make a prediction. If you have rs8176719 DI, there's a good chance it will be able to make a prediction, and the prediction will be O -- with subtypes of some sort of non-deletional O (probably O303), and a deletional O (probably either O112 or O101).

    Now, if you really DO have rs41302905 TT, then you would expect to also have rs8176719 II, and you should get a prediction of O, with two non-deletional O alleles. This, I think, is extremely unlikely. But I'd love to hear from you if this is your situation!

    I also expect that if you have rs41302905 CT and still don't get a prediction, you most likely have rs8176747 GG. This call will prevent the ABO lab from "seeing" that your subtypes are B101 and O303. B101 would indeed have a "G" here, but O303 would have a "C".

    On the chip rs41302905 and rs8176747 are in exactly adjacent positions, and my speculation is that the combination of SNPs for B101 and O303 causes one or both of these positions to be misread as homozygous when it is actually heterozygous.
    Besides British-German-Catalan, ancestry includes smaller amounts of French, Irish, Swiss, Choctaw & another NA tribe, possibly Catawba. Avatar picture is: my father, his father, & his father's father; baby is my eldest brother.

    GB

  2. #2
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    Hey geebee, I'm in exactly that situation, as I think we discussed.

    rs41302905: CT
    rs8176719: II
    rs8176747: GG
    Result: "Can't be predicted."

    However my mother is O101/O303 and my paternal grandfather is B101/O112, and I serotyped B back in biology class. Since my father is also serotyped B while his mother (my grandmother, who was a nurse) was O, that only leaves the possibility that I am B101 + O303, since B101/O112 would not cause this problem.

    It would also be interesting to see the results of someone who is, say, A101 + O303, or some othe kind of B + O303.
     

    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

  3. #3
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    Finland Sami
    rs41302905 CT
    rs8176719 II
    rs8176747 GG
    Can't be predicted [but I know that I am B+]
    Genographic Project: N52850
    GenBank: EU784076
    Z62+ Z60+ Z59+ Z58+ P38+ P30+ P19+ M307+ M258+ M253+ M170+ Z73- Z140- P37.2- P259- P109- M72- M26- M227- M223- M21- M161- L803- L573- L338- L22- L211- L1248- L1247-

  4. #4
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    Thanks for the responses, AJL and Ilmari. I actually first learned I was not type B because of a college physiology class. We typed ourselves, and I was sure I'd done something wrong because I came up with O.

    Both my parents are B, and I guess they just assumed all of us (six) kids were. Later I ended up giving blood, and the Red Cross said I was O. And since then I've been tested on several occasions, with O as the result each time.

    I thought for a while I was the only one of us, but I have a sister who is also type O. Obviously she has to have the same two alleles I do, but I haven't gotten her to test at 23andMe yet. Most likely that won't happen until I offer to pay for it. (I'm from a cheap family.)

    With two other untested siblings, both type B, there are three possibilities for each of them. Either could be homozygous B101/B101 like my tested brother; B101/O112 like my tested sister; or B101/O303 like our father. My sister's B101 is clearly the one from our dad, and her O112 is from our mother. The B101/0303 combination could be what either of my untested B siblings has, which would reflect a B101 from our mother and an O303 from our father.

    I expect that if that turned out to be the case, that sibling would end up with "Can't be predicted". As far as I know 23andMe doesn't have a single instance of having called someone as B101 O303 -- but that's what I hope to find out. Maybe someone in that category will step forward!

    For both of you, I'm curious. Is the call of rs41302905 CT possibly a change? Were you maybe originally called as rs41302905 TT? That's still the call for my father, but if it were changed to CT it would clear up his discordancy with two of his kids.

    I think the rs8176747 GG is also iffy though. If it were CG, then your "Can't be predicted" would be resolved instantly. It would become B101 O303 in the ABO Blood Type lab, with no ambiguity.

    Lastly ... an interesting thing about B alleles. Other alleles besides B101 exist, but I'm guessing their pretty rare. Among all the B's I've looked at, I haven't seen one so far that was anything else. Also, with a single exception, the only other allele I've seen with O303 has been O112. I did find one person with O303 and O101, though.

    It certainly would be interesting to see an A allele with an O303. I wonder what it means that O303 seems mostly to occur along with B101? One would imagine it reflects the populations from which both came -- but what populations were they?
    Besides British-German-Catalan, ancestry includes smaller amounts of French, Irish, Swiss, Choctaw & another NA tribe, possibly Catawba. Avatar picture is: my father, his father, & his father's father; baby is my eldest brother.

    GB

  5. #5
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    I don't remember seeing a change but now that I think back, I vaguely remember that when they first released the tool they briefly predicted I was something I clearly am not (either A or O).

    My mother is O303 and O101. Although O101 is quite common, of course, the peak of O303 is in Scandinavia, where A is relatively quite common compared to elsewhere, though still in the minority. There's probably a fair pocket of O303/O101 around Scandinavia and a bit in the Baltic.

    Thinking to areas where B101/O303 overlap, my ugess is this would occur foremost in north-central Europe/northeastern Europe. B peaks in Eastern Europe to South Asia and East asia, while O303 was not found in a study of Japanese patients but seems to have a scattered presence in Western Europe with the peak in Denmark. You could probably find the B101/O303 combination anywhere in Western Eurasia, but the three of us (your father, geebee; ilmari; and myself) all have some indications of at least some ancestry from around Fennoscandia and something "a little further east." If I were to comapre this blood motif to a yDNA haplogroup, I would guess it might be something like the distribution of yDNA R1a-Z280:

    http://www.familytreedna.com/public/...ection=results
     

    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

  6. #6
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    ^What I'm remembering -- but only vaguely like yourself -- is that you said the lab predicted O2*/O2*. That would suggest the lab was reacting to rs41302905 TT. I also think I'm remembering correctly that at one time your 11 ABO markers were identical to my father's.

    Perhaps the v3 chip produced a better read of this marker, though not the adjacent one of rs8176747? My dad's still just on the v2 chip.

    The group of people sharing with me at a high enough level to see their ABO lab results in fairly small -- only 64, including myself and the other five profiles I manage. That group only includes two people outside of immediate family members with an O303 allele.

    One of these has exactly the same SNPs you do:

    rs41302905: CT
    rs8176719: II
    rs8176747: GG

    Of course he also has the "Can't be predicted". From his daughter I know that he doesn't know for sure what his blood type is, but his daughter is AB. It's pretty obvious to me her dad is type B, with subtypes B101 and O303. I know that originally, his rs41302905 was TT, but is now CT like yours and Ilmari's.

    I haven't yet found any direct times to Fenno-Scandia, but you're right that a small amount shows pretty consistently across various BGA tests -- including 23andMe's Ancestry Composition, FTDNA's Population Finder, and Ancestry. Not only that, but I would think my father's mtDNA haplogroup of H2a1 might be suggestive of something in that direction. Of course, his mtDNA result is only based on 23andMe's testing, so it's unlikely I'll ever be able to get anything more definitive than that.
    Besides British-German-Catalan, ancestry includes smaller amounts of French, Irish, Swiss, Choctaw & another NA tribe, possibly Catawba. Avatar picture is: my father, his father, & his father's father; baby is my eldest brother.

    GB

  7. #7
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    Quote Originally Posted by geebee View Post
    ^What I'm remembering -- but only vaguely like yourself -- is that you said the lab predicted O2*/O2*.
    Yes, that's rings a bell, now that you mention it! As for V3, no joy there since I upgraded V2>V3 and am still predicted "We think you have blood."
     

    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

  8. #8
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    On a side note -- but I believe it has some relevance for this issue -- I ran a comparison of my 23andMe and Ancestry files in one of David Pike's utilities (http://www.math.mun.ca/~dapike/FF23utils/diffs.php). Here's some of what I found:

    669639 SNPs appear in both files

    0.238 % (1592) of these 669639 common SNPs are NoCalls (i.e. NoCall in at least one file)

    0.018 % (121) of the 669639 SNP results differ

    83 differing SNPs are both homozygous
    6 differing SNPs are homozygous in File1 but not in File2
    31 differing SNPs are homozygous in File2 but not in File1

    The 83 SNPs that are both homozygous are likely to just be flips, but the important thing in the context of this thread is that there were 37 SNPs homozygous in one file, but heterozygous in the other. I would suspect that, all other things being equal, a heterozygous read is probably a bit more reliable than a homozygous one. The reason is that if you get a homozygous read, it really only tells you that just one allele was detected. It may have been the only allele to detect, but even if a second, different allele happened to be present but undetected, the detected allele would be reported as a pair of matching alleles -- except in cases in which it is known that there is only one SNP at any given position, as in the case of the Y chromosome.

    Unfortunately, while rs41302905 is one of the SNPs Ancestry reports, for me it seems to have been a no call (assuming that's what 0 0 means here). I couldn't find rs8176747 or rs8176719 in my Ancestry raw data file. However, I counted a total of 27 ABO SNPs in the Ancestry file -- all of which are included at 23andMe. With the exception of the "no call" at rs41302905, all of the SNPs matched between the two companies.

    By way of comparison, I also used one of David Pike's utilities to search for discordancies between my father's 23andMe file and my own. Not including the X and mtDNA -- which of course would not be expected to match between father and son -- I came up with some 23 discordant SNP pairs.

    What this means is that the number of differently-called SNPs (not including the flips) is actually greater than the number of parent-child discordancies, although when I compared the two sets of results I didn't find any common SNPs. (SNPs which were different between the two different company's files AND also discordant between my father and me.)
    Besides British-German-Catalan, ancestry includes smaller amounts of French, Irish, Swiss, Choctaw & another NA tribe, possibly Catawba. Avatar picture is: my father, his father, & his father's father; baby is my eldest brother.

    GB

  9. #9
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    Quote Originally Posted by geebee View Post
    83 differing SNPs are both homozygous
    6 differing SNPs are homozygous in File1 but not in File2
    31 differing SNPs are homozygous in File2 but not in File1[/indent]

    The 83 SNPs that are both homozygous are likely to just be flips, but the important thing in the context of this thread is that there were 37 SNPs homozygous in one file, but heterozygous in the other. I would suspect that, all other things being equal, a heterozygous read is probably a bit more reliable than a homozygous one. The reason is that if you get a homozygous read, it really only tells you that just one allele was detected. It may have been the only allele to detect, but even if a second, different allele happened to be present but undetected, the detected allele would be reported as a pair of matching alleles -- except in cases in which it is known that there is only one SNP at any given position, as in the case of the Y chromosome.
    I suspect you're on to something here. I remember when 23andme reported a transversion on my mtDNA as a more likely transition. (Likelihood isn't everything!)
     

    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

  10. #10
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    ^Yes, I've come to the conclusion that people should actually first look at genotyping error as a possibility, before considering mutations, microdeletions, etc. There are certainly times when the latter may account for "unusual" results, but it is obvious that testing errors do occur.

    Where two companies report the same SNP differently, I suppose someone who wants the results to always be correct might try to argue it's chimerism, or something like that. But it's clear that the changes are really two minor to be that. Besides, if I'm right that you and Ilmari, as well as the other individual I mentioned, all had rs41302905 TT before you had CT, that in itself shows that errors do occur.

    By the way, AJ, is it possible to me to edit the post title, so I can change that silly "interesting" to the "interested" it's supposed to be? I can see how to edit a post, but not the topic title.
    Besides British-German-Catalan, ancestry includes smaller amounts of French, Irish, Swiss, Choctaw & another NA tribe, possibly Catawba. Avatar picture is: my father, his father, & his father's father; baby is my eldest brother.

    GB

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