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Thread: Z2103, Z2104, Z2105, Z2106, Z2107, Z2108, Z2109, Z2110 & Sanger sequencing

  1. #1
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    Z2103, Z2104, Z2105, Z2106, Z2107, Z2108, Z2109, Z2110 & Sanger sequencing

    SNPs Z2103 and Z2105 have been available for the Sanger sequencing test from FTDNA for awhile. YSEQ recently added Z2104, Z2107 and Z2110/CTS7822 to their catalog of SNPs that can be tested. So I took the plunge and ordered all three from YSEQ. My goal is to have quality Sanger sequencing data for Z2103 through Z2110. Data that could be used for the ISOGG haplogroup tree if needed.
    Z2110/CTS7822 came in negative in just two weeks. YSEQ is good and quick.
    Z2104 is presenting some challenges because two sections of my genome are competing for attention. This SNP is in a homologous region that can recombine with a different chromosome. Z2104 YSEQ problem bhdiijah.png The double peak is highlighted in blue. Dr.Krahn in trying "Nested PCR" for additional filtering that may or may not work. We will know soon. Thanks to Thomas for this information and the extra effort.
    I was caught mentally flat footed by this.
    Fortunately Vince T had a post on another thread the other day that gave some clues on what this might mean for picking SNPs to test.
    Quote Originally Posted by VinceT View Post
    The 'X' call is an ambiguous call, i.e. heterozygous. It usually arises when the read alignment pattern stacks on a region that is highly similar or identical to other parts of the Y-chromosome, or to highly similar or identical regions existing in any of the other chromosomes. Often those calls tend to be in within the Y-centromere, in X-Y transpositions, or Y-palindrome arms.

    The '?' call on the other hand means that there are insufficient reads in the alignment to make a '+', '-', or 'X' call.
    Any hints or clues on how to better pick SNPs would be greatly appreciated?
    What are the good regions of the Y chromosome for Sanger sequencing? How far from the Y-centromere should the SNP be?
    Based on distance from the Y-centromere, are Z2104, Z2106, Z2108 and Z2109 in a more difficult region for Sanger sequencing? Conversely, are Z2103, Z2105, Z2107 and Z2110 in more suitable regions? Attached are the ISOGG YBrowse browser views of Z2103 thru Z2110 for comparison.

    Z-SNPs-Y-Browse.jpg or large view.
    Z2104 ISOGG YBrowse
    http://ybrowse.isogg.org/cgi-bin/gb2...7962..14167962

    Thanks!
    Last edited by Joe B; 02-27-2014 at 05:39 PM. Reason: Rewording
    L23+, L150+, Z2103+, Z2104+, Z2105+, Z2106+, Z2109+, Z2110/CTS7822-, L277-, L584-, CTS7763-

  2. #2
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    Quote Originally Posted by smal View Post
    Could you tell me chromosome positions for SNPs Z8127 to Z8159?
    CTS9906 is private for HG01515 (CTS9212).


    At the moment Z2104 and Z2107 are on the same level as Z2105 and Z2103.
    Just got the result for Z2107 from YSEQ. Negative
    Z2107 Allele T-
    anc: T der: C
    mutation: T to C
    ISOGG YBrowse Z2107
    Z2107 Details

    Negative for Z2107 is surprising. Assuming I read my results correctly.

    Here are my Sanger sequencing results so far for Z2103 - Z2110.
    Z2103+, Z2105+, Z2107-, Z2110-, L277-, L584-. Any thoughts on Z2106, Z2108 and Z2109?

    YSEQ is still working on the most difficult Z2104.
    Last edited by Joe B; 03-10-2014 at 06:00 AM.
    L23+, L150+, Z2103+, Z2104+, Z2105+, Z2106+, Z2109+, Z2110/CTS7822-, L277-, L584-, CTS7763-

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  4. #3
    Quote Originally Posted by Joe B View Post
    Just got the result for Z2107 from YSEQ. Negative
    Z2107 Allele T-
    anc: T der: C
    mutation: T to C
    ISOGG YBrowse Z2107
    Z2107 Details

    Negative for Z2107 is surprising. Assuming I read my results correctly.

    Here are my Sanger sequencing results so far for Z2103 - Z2110.
    Z2103+, Z2105+, Z2107-, Z2110-, L277-, L584-. Any thoughts on Z2106, Z2108 and Z2109?

    YSEQ is still working on the most difficult Z2104.
    If you look at the smal's tree, it seems that Z2107 is on the same plane of Z2104, CTS9416, PF7575, Y:6687319 and Y:14629851. It is possible that you are negative for all these SNPs and to be a true R-Z2103/Z2105*, but you could break these SNPs and to be positive for some of them. We wont be able to know this without testing each SNPs.
    Even more you should be negative for Z2106, Z2108 and Z2109. Interesting would be also the three SNPs of Chromo2: Y16050529 and the other two I posted in "R1b phylogeny".
    Last edited by Rathna; 03-10-2014 at 07:17 AM.

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  6. #4
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    Quote Originally Posted by Rathna View Post
    If you look at the smal's tree, it seems that Z2107 is on the same plane of Z2104, CTS9416, PF7575, Y:6687319 and Y:14629851. It is possible that you are negative for all these SNPs and to be a true R-Z2103/Z2105*, but you could break these SNPs and to be positive for some of them. We wont be able to know this without testing each SNPs.
    Even more you should be negative for Z2106, Z2108 and Z2109. Interesting would be also the three SNPs of Chromo2: Y16050529 and the other two I posted in "R1b phylogeny".
    Key words from smal are "at the moment" as the tree is evolving. I'm always looking at smal's tree. http://www.anthrogenica.com/showthre...ll=1#post26401
    I have added NA20532 and NA20866 into Semargl database.
    Quote Originally Posted by smal View Post
    There are five Z2103 sequences from the 1000 genomes project with the therminal SNPs:
    Z2106, Z2107 - NA20532
    CTS7763, CTS8966 - NA18645
    Z2108, Z2109 - NA20866
    CTS7822/Z2110 - HG01277
    CTS9212 - HG01515

    But there are no sequences for the L584 and L277 branches. Now we will have the L584 sequence. That's great. We also really need to have the L277 sequence to construct a correct tree of the Z2103 branch.
    Not picking on you smal! Just another useful post from you.
    Does anybody know if the phylogeny of Z2103 - Z2110 is settled or presumed? My guess is based on the lack of data that it is presumed and not proven.
    Reminder that we do have a L584 waiting on Big Y results.
    Last edited by Joe B; 03-10-2014 at 09:36 PM.
    L23+, L150+, Z2103+, Z2104+, Z2105+, Z2106+, Z2109+, Z2110/CTS7822-, L277-, L584-, CTS7763-

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  8. #5
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    Quote Originally Posted by Pillar_of_fire View Post
    Thanks Joe, on the topic on Mike W's R1b, my husband is Z2103+, Z2105+, L584-, L277- all Sanger sequencing. Waiting for Big Y for N112116.
    Hello Fire,
    This thread is better for N112116. Your husband is a good man as we both have YCAII=18-23, see 257842. I'm sure it's just coincidental. One thing we do have in common is mml2303-a- uas, the unassigned speculative rating in Mike W's Early R1b Haplotypes spreadsheet.
    Smal's tree has the most detail for R1b-Z2103/Z2105. . Smargl is a good source too.
    FTDNA has been a little slow to offer many of these SNPs la carte. As you can see from this thread, YSEQ is worth looking at. They use a dry sample which may make it easier for shipping too.
    We do have a brand new Bulgarian R1b-Z2110/CTS7822, brygian. http://www.anthrogenica.com/showthre...ll=1#post34575

    So, Bulgarian Rakia doesn't turn the ice white?
    Last edited by Joe B; 03-22-2014 at 03:35 AM.
    L23+, L150+, Z2103+, Z2104+, Z2105+, Z2106+, Z2109+, Z2110/CTS7822-, L277-, L584-, CTS7763-

  9. #6
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    Bulgaria
    Mastika does http://en.wikipedia.org/wiki/Mastika

    N112116 has no matches on any level even in the limits of the accepted GD (he is tested up to 67). Knowing the number of R1b I expected at least one or two....

    So the BIG Y will be a eye opener, but we will have to wait - just received the update. too bad - don't know in which percentage my kits are.....

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  11. #7
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    Quote Originally Posted by Pillar_of_fire View Post
    Mastika does http://en.wikipedia.org/wiki/Mastika

    N112116 has no matches on any level even in the limits of the accepted GD (he is tested up to 67). Knowing the number of R1b I expected at least one or two....

    So the BIG Y will be a eye opener, but we will have to wait - just received the update. too bad - don't know in which percentage my kits are.....
    High GDs and funky STRs are a hallmark of this clade. Doing the Big Y is big news!
    L23+, L150+, Z2103+, Z2104+, Z2105+, Z2106+, Z2109+, Z2110/CTS7822-, L277-, L584-, CTS7763-

  12. #8
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    Z2104/PF7575 results came it today. Positive
    Z2104 Allele T+
    anc: C der: T
    mutation: C to T

    My Sanger sequencing tested SNPs are Z2103+, Z2104+, Z2105+, Z2107-, Z2110-, L277-, L584- and would seem to indicate that Z2104 and Z2107 are not on the same plane.
    YSEQ 39 = FTDNA 257842
    Attached Images Attached Images
    Last edited by Joe B; 03-29-2014 at 04:43 PM. Reason: Copied format on #9
    L23+, L150+, Z2103+, Z2104+, Z2105+, Z2106+, Z2109+, Z2110/CTS7822-, L277-, L584-, CTS7763-

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  14. #9
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    YSEQ 39 = FTDNA 234905 (L277+) Z2104+

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  16. #10
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    Quote Originally Posted by smal View Post
    YSEQ 39 = FTDNA 234905 (L277+) Z2104+
    Considering how diffucult Z2104 was to test, we are very fortunate to have two Z2104 results today.
    L23+, L150+, Z2103+, Z2104+, Z2105+, Z2106+, Z2109+, Z2110/CTS7822-, L277-, L584-, CTS7763-

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