GENO 2.0 - testing

Possible time of origin: Less than 18,500 YBP
Possible place of origin: Eurasia, most probably South Asia, or Central Eurasia.
Defining mutations: M420 (also includes M17, M198, SRY1532.2 and SRY10831.2)
Highest frequencies: Scandinavia, Central Europe, Eastern Europe, Central Asia, South Asia and Siberia. (See List of R1a frequency by population)

Moderator: Semargl


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PostPosted: Fri Apr 26, 2013 2:44 pm
Michał wrote:This, in turn, makes it possible that PF6557 is specific for all "Carpathian-Dalmatians", as the relative of 181827 is the first known (or rather predicted) 6.B2K member who ordered the Geno 2.0 test

You are not counting N112858 ?

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Location: Warsaw, Poland
YDNA:
R1a-L1280
MtDNA:
H2a2
PostPosted: Fri Apr 26, 2013 5:33 pm
lgmayka wrote:You are not counting N112858 ?

Thank you. You are absolutely right, I have overlooked his Geno 2.0 result indicating that PF6557 does not define the entire Carpathian-Dalmatian cluster.
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YDNA:
R1a-L365
MtDNA:
H11a2a2
PostPosted: Fri Apr 26, 2013 9:15 pm
Thanks Larry:

F2686 (under L365) is now available for order in FTDNA’s advanced menu.
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Location: Russia
YDNA:
R1a [CTS3402]
MtDNA:
U4a2g (FMS)
PostPosted: Sun Apr 28, 2013 3:02 am
#123791 Spain (Close to Volga-Carpathian cluster) CTS3402+, CTS11142+

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PostPosted: Sun Apr 28, 2013 11:04 am
Semargl wrote:#123791 Spain (Close to Volga-Carpathian cluster) CTS3402+, CTS11142+


Is #123791 the first confirmed positive for CTS11142? Or are there others?

Also, how much of category 6. B do you foresee CTS11142+ potentially encompassing?

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YDNA:
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PostPosted: Sun Apr 28, 2013 8:00 pm
T101 wrote:Is #123791 the first confirmed positive for CTS11142? Or are there others?

Apart from the 1KG-tested man from Finland (HG00366), this is the first CTS11142+ result known to us. Since HG00366 was additionally positive for CTS8841 (also included into the Geno 2.0 chip), we may suspect that CTS8841 is downstream of CTS11142.

T101 wrote:Also, how much of category 6. B do you foresee CTS11142+ potentially encompassing?

Definitely not much.
Without knowing the STR results from the 68-111 panel for kit 123791, it is hard to narrow down a group of potential CTS11142 members, but I would recommend this test to all those potential Carpathian-Dalmatian (6.B1) members who show some atypical STR results that are seen in 123791 (first of all DYF406S1=11 instead of typical 10, but also DYS385b=15, DYS458>15 and/or DYS565=12), especially if one's patrilineage originates from Eastern or North-Eastern Europe. The best candidate seems to be 193167, but maybe E5395 and 202194 from our project should also try this new SNP.
Semargl, what is your opinion?

Here is a new draft tree:
M417 draft tree 38.jpg
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Location: Russia
YDNA:
R1a [CTS3402]
MtDNA:
U4a2g (FMS)
PostPosted: Mon Apr 29, 2013 5:46 am
Michał wrote:
T101 wrote:Is #123791 the first confirmed positive for CTS11142? Or are there others?

Apart from the 1KG-tested man from Finland (HG00366), this is the first CTS11142+ result known to us. Since HG00366 was additionally positive for CTS8841 (also included into the Geno 2.0 chip), we may suspect that CTS8841 is downstream of CTS11142.

T101 wrote:Also, how much of category 6. B do you foresee CTS11142+ potentially encompassing?

Definitely not much.
Without knowing the STR results from the 68-111 panel for kit 123791, it is hard to narrow down a group of potential CTS11142 members, but I would recommend this test to all those potential Carpathian-Dalmatian (6.B1) members who show some atypical STR results that are seen in 123791 (first of all DYF406S1=11 instead of typical 10, but also DYS385b=15, DYS458>15 and/or DYS565=12), especially if one's patrilineage originates from Eastern or North-Eastern Europe. The best candidate seems to be 193167, but maybe E5395 and 202194 from our project should also try this new SNP.
Semargl, what is your opinion?

HG00366 sample of 1000 Genomes Project has a value dyf406s1=11.
I agree with you about the candidacy of the #193167/UFCTR Dmitriev.
Even more is the best candidate - #150175 Shirokov.
He is a member of the project "Russian Empire".

Also good candidates:
#175710 Glass "Polish Project"
#E5395/27P7M Kelly
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YDNA:
R1a [CTS3402]
MtDNA:
U4a2g (FMS)
PostPosted: Tue May 07, 2013 3:38 pm
Michal,
in geno2 found a new SNP located below the L1029.
#N25798 / Johansson / [L1029+] New SNP: F672+

SNP F672 previously been found in haplogroup O3

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YDNA:
R1a-L1280
MtDNA:
H2a2
PostPosted: Wed May 08, 2013 7:30 am
Semargl wrote:#N25798 / Johansson / [L1029+] New SNP: F672+

Unfortunately, he also shows three additional positive results for SNPs previously found in other haplogroups (CTS1366, CTS7141 and L797), while at the same time he is reported as negative for six markers upstream of R1a (CTS125, CTS5318, F332, P135, PF2745 and PF954), so I suspect that all these results should be considered as unreliable (and NatGeo should repeat his Geno 2.0 test). I've just got the csv file with his raw data, so will be able to say something more about those unusual results.

Posts: 748
Joined: Thu Mar 15, 2012 10:08 am
Location: Warsaw, Poland
YDNA:
R1a-L1280
MtDNA:
H2a2
PostPosted: Wed May 08, 2013 2:55 pm
Michał wrote: I've just got the csv file with his raw data, so will be able to say something more about those unusual results.

As for his five unexpected negative results, they all turned out to be "no-calls" (which means "no signal") instead of results indicating the presence of a specific signal corresponding to the ancestral allele (which would then indicate an absence of mutation at a given marker).

Also, all four unexpected positive results (as reported at FTDNA) are shown as "heterozygous states" in the Geno 2.0 raw data, which suggests that the signal corresponding to the ancestral (non-mutated) allele was not significantly different from the signal corresponding to the derived (mutated) allele, which strongly indicates that all these unusual positive results are simply "false positives". Additionally, he shows a similar unusual heterozygous result for another marker F3197 that is, however, not listed among his positive results at FTDNA. It should be noted that another R1a member who belongs to clade R1a-L260 (surname Skwarek) has also shown the presence of such unusual heterozygous result for F3197 (although he hasn't transferred his Geno 2.0 data to FTDNA, AFAIK, so I don't know if this unusual result has been recognized as positive in his case).

Basically, he shows a very large number of "no-calls" (about 2-5% of total), so I think his sample should be retested for no additional cost.
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