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Thread: New Z251 SNPs from Full Genomes

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    New Z251 SNPs from Full Genomes

    The 42 high-reliability SNPs that were found in my test results (labeled FGC11962 - FGC12003 and likely downstream from S9294) are now in ybrowse, courtesy of Astrid Krahn at YSEQ. Of those 42 SNPs, 23 appear to be able to have primers developed for them. However, there is a huge likelihood that these are all indicative of the 251-11EE cluster and, therefore, likely not shared by any Z251 people outside of 251-11EE. To date, I don't see anyone with Big Y results having them. Since these SNPs are likely downstream from S9294, they would also not be seen in anyone who is L555+. But when kenmunn gets his FGC results back (soon, we hope) we will see what turns up.

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    Quote Originally Posted by seferhabahir View Post
    The 42 high-reliability SNPs that were found in my test results (labeled FGC11962 - FGC12003 and likely downstream from S9294) are now in ybrowse, courtesy of Astrid Krahn at YSEQ. Of those 42 SNPs, 23 appear to be able to have primers developed for them. However, there is a huge likelihood that these are all indicative of the 251-11EE cluster and, therefore, likely not shared by any Z251 people outside of 251-11EE. To date, I don't see anyone with Big Y results having them. Since these SNPs are likely downstream from S9294, they would also not be seen in anyone who is L555+. But when kenmunn gets his FGC results back (soon, we hope) we will see what turns up.
    Sorry but I'm delayed again. My DNA is apparently so old that it can't make it all the way to BGI in satisfactory condition! I have re-spit and re sent yet again and am now shown as batch # 9 in process. I don't know that it is actually at BGI or is receiving geriatric care by Justin before being sent on the trip. He mentioned some type of processing for some of the DNA samples that have a history of being problematic.

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    I'm taking a look at the FGC analysis files for these two kits

    Harrington (Z251>S11556>S9294)
    Yurzditsky (Z251>S11556>S9294)

    and observed that both kits show positive results (reliability varies) for

    09936670 C>A (PF362+)
    15210689 G>A (FGC11986+)

    For reference
    NA12340 (R-DF13) tested negative for PF362
    NA11831 (R-Z251) tested negative for S9294 and FGC11986

    FGC shows no known public kits with these two SNPs, so they may both be below S9294. I can't find a reference anywhere for a positive result for PF362, but obviously a Sardinian had one. I don't know if Big Y tests these locations, but for anyone S9294+ (or S11556+) from Big Y it would be worth looking at these locations in their BAM file.
    Last edited by seferhabahir; 04-15-2014 at 10:39 PM.

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    FGC11986 is now available as a stand-alone SNP test from YSEQ and might be considered by anyone who is Z251. It looks like there are two S9294 people separated by a large genetic distance (myself and Harrington) positive for it. It may or may not be below S9294. This seems to be the only potential common SNP since I could not find any of my other private SNPs in Harrington's FGC Full Y analysis, nor could I find any of Harrington's private SNPs in my FGC Full Y analysis. Wish we had Munn's results in hand.

    There is also a custom test of 23 of my private FGC SNPs (the ones for which primers could be created) plus S9294 available from YSEQ but that would likely NOT be of interest unless you are in the 251-11EE cluster. I'm guessing most of those are SNPs on the 251-11EE ancestral line and none of them (except perhaps FGC11986) would be shared with anyone outside the cluster. I asked YSEQ to develop this custom package for 251-11EE to help determine when L583 split up the cluster. I'm getting a non-L583 person to order it.

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    Quote Originally Posted by kenmunn View Post
    Sorry but I'm delayed again. My DNA is apparently so old that it can't make it all the way to BGI in satisfactory condition! I have re-spit and re sent yet again and am now shown as batch # 9 in process. I don't know that it is actually at BGI or is receiving geriatric care by Justin before being sent on the trip. He mentioned some type of processing for some of the DNA samples that have a history of being problematic.

    Well, when you eventually get them there are now more than 80 named SNPs that might be at or below S9294, since I now have 61 (19 more were found during a subsequent analysis in addition to the first batch of 41) and Harrington has 23. I guess we need to see if you are S11556 or S9294 as well. Your day will come.
    Last edited by seferhabahir; 04-26-2014 at 03:25 PM.

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    Quote Originally Posted by seferhabahir View Post
    Well, when you eventually get them there are now more than 80 named SNPs that might be at or below S9294, since I now have 61 (19 more were found during a subsequent analysis in addition to the first batch of 41) and Harrington has 23. I guess we need to see if you are S11556 or S9294 as well. Your day will come.
    There are a group of about 20 other potential testers who have the same STR pattern as I in our surname project. I hope to get a panel from Y-SEQ after getting my results so that we can determine different subgroups. Hope to have similar success to you.

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    Sample resting on site at BGI and hopefully cooperating with the analysis process this time. Looks like it will be around mid-September before I get to smile and announce the birth of any new SNPs. Beginning to feel like Sarah....

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    Quote Originally Posted by kenmunn View Post
    Sample resting on site at BGI and hopefully cooperating with the analysis process this time. Looks like it will be around mid-September before I get to smile and announce the birth of any new SNPs. Beginning to feel like Sarah....
    You could consider testing S9294 for only $25 at YSEQ while you are waiting just to see if you are...

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    Quote Originally Posted by seferhabahir View Post
    You could consider testing S9294 for only $25 at YSEQ while you are waiting just to see if you are...
    Just ordered S9294. Maybe I'll have some satisfaction while waiting for the big one.

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    Quote Originally Posted by kenmunn View Post
    Just ordered S9294. Maybe I'll have some satisfaction while waiting for the big one.
    FGC Batch 9 results looks like October 2014 based on a recent post. Any news on your S9294 YSEQ test?

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