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From: "Ray Banks" <>
Subject: [DNA] Revised Y Tree & Geno 2.0
Date: Tue, 18 Dec 2012 22:54:43 -0700


I note problems regarding my eight men who have transferred their Geno 2.0 results to Family Tree DNA. Four of them are being prompted in the haplotree section to order SNPs for which they were found negative in Geno 2.0.

A fifth is prompted because he was not tested for all the listed equivalent SNPs to test for the one equivalent he did not test and its subgroups though he would have – under the old system – automatically been kept away from the subgroups because he was negative for the other equivalents.

And all this prompting and categorization is operating apparently off the two-year-old Y tree and no attention is being made to the fact that the persons were found positive in Geno 2.0 for new intermediate subgroups that would that have been recognized in ISOGG and the FTDNA draft tree much of the last year.

Presumably all this will be rationalized when the new tree is released. I had reported several days ago that prior SNP test results were erased in the FTDNA display when someone transferred Geno 2.0 results. They quickly corrected this. And the Geno Project over the weekend seems to have corrected the problems preventing some men from transferring results.

I have processed all the F-series SNPs released today in the Geno 2.0 paper
http://arxiv.org/abs/1212.4116

So with all the Geno 2.0 SNPs now known, it appears that one of the seven major haplogroup G subgroups (P16/P18) is a real winner with almost 100 new SNPs specific to that group included in Geno 2.0. At the opposite extreme, L293 men do not seem to have anything, and L293 itself is not tested. The men in the largest groups, L497/Z725, Z1903/Z724 and L13 have a few new SNPs each, mostly items that Family Tree decided not to turn into $29 tests because of lack of readymade primers or bad chromosome locations. There could be additional SNPs for which these initial testers were individually negative, but they are unlikely to have much coverage.

In the Geno 2.0 article today it indicates in figure 3 that they had only 82% success rate in “validating SNPs defining Y-chromosomal...haplogroups”or as explained in the text “to test the ability of the GenoChip to infer Y-chromosome...haplogroups” They indicated there were 431 such Y haplogroups, but did not list them. They felt GenoChip can capture many of the remaining haplogroups and that they are conducting a larger genotyping effort to validate them. I do not know what to make of this. My guess is that they were expecting equivalent SNPs would do the same job as some SNPs deliberately omitted. Perhaps someone has a better explanation of this.

Ray Banks


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