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DELAYED Geno 2.0

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  • Charles Moore
    I have been officially informed as a member of the ISOGG Y-Tree Committee that Geno 2.0 results are not expected to be released for the male participants for
    Message 1 of 35 , Dec 2, 2012
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      I have been officially informed as a member of the ISOGG Y-Tree Committee that Geno 2.0 results are not expected to be released for the male participants for another one to two weeks. This news ultimately comes from Spencer Wells and Bennett Greenspan.

      However, there is a lot of good hiding behind this delay. They are being continually surprised, particularly in Haplogroups I, J, and R, that SNPs previously thought to be multiple SNPs defining the same subclade levels, are in fact actually layering out the tree. Yeeha!

      The large number of tests of a large number of SNPs are apparently revolutionizing the Y tree. Even some major classification levels, potentially affecting some long-known ancestral naming conventions such as "R1b" could potentially be at risk of being changed by the layering taking place.

      I was not given any specifics, but we can look at subclade levels on the R1b-U106 Comprehensive Tree where there are a large number of SNPs with the background painted green or yellow, and see the potential layering that might take place over time as more guys get tested for Geno 2.0. The clade defined by Z5 is one potential example where layering might take place.

      Although I was told to expect the results in one to two weeks, the publication of the new tree itself is another matter. Spencer and Bennett decided to further delay the publication of the new tree for the simple reason of the fact that it is changing too rapidly as a result of all the tests they are running. Despite the frustration of the delay, this is really great news. I imagine that these guys fully realize that they have to pull these triggers regardless, but it really is terrific that this chip is having this significant effect on the tree, and that a sufficiently large number of initial "blind" testers signed up, to cause all of this revolution to occur.

      I was not told whether any list of SNPs or locations or an update to TK's draft tree or yMap would accompany the release of the results, or not. Obviously if not, that would be rather frustrating if we have to wait for publication of the tree to understand where the CTS SNPs are located. So on this point, I am merely "hopeful".

      Nevertheless, the bottom line is that we have a lot of SNPs already in our group, painted green or yellow on the tree, that Ray will be reporting on his spreadsheet as soon as the results are released and we send him our raw data. So we might begin to see some of that potential layering taking place as Ray updates his sheet.

      So it is unfortunate about the delay, but we might have a nice Christmas present.

      Ray reports that at least 18 of our testers are now waiting in QC, otherwise known as the Alcatraz of DNA, from which there is no escape, until Uncles Spencer and Bennett say so.

      It sounds like it will be worth the wait.

      Charles
    • Charles Moore
      21 of our 48 Geno 2.0 testers have now made it into Quality Control. So, I m guessing that by the time the results are released around the end of this week or
      Message 35 of 35 , Dec 3, 2012
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        21 of our 48 Geno 2.0 testers have now made it into Quality Control. So, I'm guessing that by the time the results are released around the end of this week or next week, according to the current expectation, it looks like about half of our testers might be ready to have their results released.

        I'm playing in the sandbox with my little STR friends. Thanks to sister CeCe for standing guard, and to Don for his nice compliment.

        Ray and I established a "spreadsheet philosophy" here, with respect to organizing haplotypes. That is that whenever testers choose to join public Y DNA projects, they have made their data public. The FTDNA projects all organize the basic data the same way, because there is no flexibility in the FTDNA system for how the ht data is organized, other than the basic "Subgrouping" divisions. So members are free to reorganize the ht data and present it back to the group in spreadsheets posted into this Forum's Files or Links sections in ways that we think present the data "better", usually mostly by arranging the rows of hts in a more sensible way than the automatic ordering at the project itself. The yahoo forum format that R1b-U106 Project Co-Admin Mike Maddi chose for our forum has worked out terrifically well for us, specifically because of those Files and Links sections. So, Ray and I have always freely shared our spreadsheets and swapped data back and forth, and helped find errors, and made suggestions to help one another. The clustering work that Christiaan has done in the very difficult Z326 area has definitely been helpful, as the hts in that group appear to have been poured into a blender. So basically our "spreadsheet philosophy" is "free sharing" and try to help one another. And I definitely appreciate Don and others applying their skills to the effort.

        I think Geno 2.0 is going to help us subgroup the haplotypes by layering some of the clades with lots of SNPs where I've colored the background yellow. Those are the SNPs that have previously been untestable. Whether any new CTS SNPs or other SNPs will define new clades for us, we have no idea. New .x occurrences of SNPs otherwise found elsewhere on the Y tree are a shot in the dark, and I think we will have to require that a second tester show up with such a .x occurrence in order to be more certain that it isn't just a false positive on the chip. We do have to realize that although the initial indications are that this chip is high quality, nevertheless it is not the quality of Sanger sequencing at FTDNA. But it does bring us the chance to test thousands of SNPs, and layer out the group.

        I am reasonably optimistic with respect to a new clade level in the Z326 group defined by Z319 etal. This clade was discovered in a 1000 Genomes tester from Barbados, which was settled by the English. So I am hoping those SNPs will help us to finally layer this large group.

        The STRs are calling, and I can't resist their favorite games, like Chicken and Egg, Hide and Seek, and the one I really don't care for, which is called Go Fetch. So, off I go....

        Charles
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