Гаплогруппа N в проекте 1K Genomes и HGDP

[Yurgan]

Вот чем завершилась работа Рэй Бэнкс по поиску новых снипов у N1c1 в проекте 1000 Genomes

Family Tree DNA today posted primer information for the candidate N1c1 SNPs I found. They only do this when there is a readymade primer is in what they call the Primer 3 database.
 
The news is extremely good as to readymade primers.
 
Almost all the ones that come from N1c1 seeming new subgroups were found in Primer 3.
 
They have listed primers for
Z1923
Z1924
Z1925
Z1926
Z1927
Z1928
Z1929
Z1930
Z1932
Z1934
Z1935
Z1936
Z1937
Z1938
Z1939
Z1940
Z1941
 
It is unlikely that $29 tests will be listed for all these.
 
On the spreadsheet I show the suspected subgroups to which these apply. So I would guess that 4 of these will be made available for $29 tests. The 5th subgroup, Z1942, is not listed for a primer. This is unfortunate because it seems to be a mother group for most if not all of the others.
The five subgroups are shown at
 
https://docs.google.com/spreadsheet/ccc?authkey=CIOag_UD&key=0Agq_ez43qXCjdFlxemtlUnZ1Qk01cVhMRVBFcm5WX3c&authkey=CIOag_UD#gid=59
 
It was not possible to determine the phylogenetic relationships of some of these because among the results for the 16 samples often one or two do not have conclusive reads. Especially in the case of Z1942, 100% good reads would have been needed to resolve relationships to the other 4 new subgroups.
 
So your customers will have to determine relationships here.
 
In addition among those SNPs found in all M178 persons, they found primers for
Z1950
Z1954
Z1955
Z1956
Z1957
Z1958
Z1960
Z1961
Z9162
Z1963
Z1965
Z1967
Z1968
Z1969
Z1970
Z1971
Z1975
Z1976
Z1979
I would be surprised if any of these turn up as $29 tests.
 
This area of the SNPs equivalent to M178 is a bit complicated and will need a lot more work should they ever make any of these tests available to rule in and out various possibilities regarding possible coverage outside M178.
 
There are probably no N1a persons in the 1000 Genomes Project. And the exact status of a few of those NO and N persons that were not confirmed N1c1 – all from China – is not presently determined. There is one Chinese L666+ man from China that was in the report I was using. The Family Tree info for L666 indicates it was found in a N1b man.
 
That L666 man is sample NA18613 . This man was probably negative for all the M178 SNPs I found, but that needs to be determined for sure if any use is made of these SNPs.
 
For sure these M178 SNPs did not show up in haplogroups outside haplos NO/N.
 
Although a few of the haplogroup N samples were not included in the old report from which I was working, it may be possible to use the chromosome browser to check for some of the results that would be of interest.
 
As you are probably aware, Family Tree does not announce when a specific SNP test becomes available. So you have to check every few days. It could take a month or more. Since they will likely be added at at once, I would recommend checking for just Z1938 and Z1939 as a determinant if any progress has been made. These two subgroups have a single SNP representing the subgroup and they will almost certainly make it into a $29 test.
 
The screening process is not really over. It is still possible that a SNP will be rejected because of past problems in that area of the chromosome, and the primer that arrives may not work when it arrives at the lab during the initial check there, and it will have to re-ordered.
 
In all the samples available, all but one of these men had the new L708 mutation (the other one had no read for that site), so they are actually N1c1d. The “no read” status of that single man is probably irrelevant since all the subgroups I identified did not rely on a single sample. However, I cannot find any evidence that any of them is L550+. L550 just does not show up among SNPs found. We can do the time-consuming check in the chromosome browser for each sample to see if it can load the status of these N1c1d men with regard to L550 but results are extremely likely to be negative.
 
The 1000 Genomes data also found L549 and L1026 as equivalent to M178, but I cannot guarantee that these two SNPs might be found in subgroups other that N1c1d. Your testing is probably determining this.
 
All indications are that the 4 or 5 subgroups I have identified will be really important major subdivisions.
 
I may have time tonight to start checking the samples for L550.
 
I you have any questions, please ask. Other feedback is welcome.
 
Ray Banks
Administrator, Haplogroup G Project
Content Expert for C, D and G at ISOGG

Так я не понял, будут эти снипы запускать в FTDNA или нет?

[mouglley]

Интересно, кто по национальности тот, кто N1c1, но не L708?

Есть ли у него 1026?

Вы думаете, они кого то, кроме нашего хакаса протестировали?

Замечательно, а какой у него номер?

[Yurgan]

Неплохо, но не для нас с Вами лично.

Но:

L392, L394, L395, L838, L839, они отнесли к
http://ytree.ftdna.com/index.php?name=Draft&parent=95065628
M178, P298, L1026
Хотя о L392, L394, L395 мы ничего не знаем

L839 приблизительно равен L708, а не M178

L729 есть и N1b

Не понял.

Я про дерево, где L729 показан только у N1c

[mouglley]

Уважаемый Eugene, не узнали, кто именно разбирал в той табличке снипы?
https://docs.google.com/spreadsheet/ccc?authkey=CIOag_UD&key=0Agq_ez43qXCjdFlxemtlUnZ1Qk01cVhMRVBFcm5WX3c&authkey=CIOag_UD#gid=59
Ray Banks или кто-то ещё?

[mouglley]

Я про дерево, где L729 показан только у N1c

Теперь понял.

Значит от находится выше места разделения N1c и N1b, но ниже N1?

[Eugene]

Уважаемый Eugene, не узнали, кто именно разбирал в той табличке снипы?
https://docs.google.com/spreadsheet/ccc?authkey=CIOag_UD&key=0Agq_ez43qXCjdFlxemtlUnZ1Qk01cVhMRVBFcm5WX3c&authkey=CIOag_UD#gid=59
Ray Banks или кто-то ещё?

Да, это Рэй.

[mouglley]

Или L729 встречался у кого-то из N1*?

[Yurgan]

Или L729 встречался у кого-то из N1*?

http://www.familytreedna.com/public/N%20Russia%20%20DNA%20Project/default.aspx

[mouglley]

Я правильно понял схему?
https://docs.google.com/spreadsheet/ccc?authkey=CIOag_UD&key=0Agq_ez43qXCjdFlxemtlUnZ1Qk01cVhMRVBFcm5WX3c&authkey=CIOag_UD#gid=59

[Yurgan]

Я правильно понял схему?
https://docs.google.com/spreadsheet/ccc?authkey=CIOag_UD&key=0Agq_ez43qXCjdFlxemtlUnZ1Qk01cVhMRVBFcm5WX3c&authkey=CIOag_UD#gid=59

Глобально, но есть ошибки в таблице

[mouglley]

Прошу дать Ваши замечания по результатам Вашего разбора 1000 Genomes.

Постараюсь учесть Ваши предложения прежде всего.

[Yurgan]

Кажестя, настал и на нашей улице праздник.
В FTDNA запущены снипы
 
Z1935, Z1936, Z1940, Z1941

Z1935 и Z1936 находятся под снипами Z1940 и Z1941
Эти снипы отсутствуют у L1022 и L550
Z1940 и Z1941 могут быть у всех представителей Финно-Карельской ветви N1c1
Z1935 и Z1936 либо у карелов либо у финнов Саво.
Надо срочно заказывать.

[Yurgan]

Всеми уважаемый Juhani  Väyrynen  (141818) заказал Z1935,Z1936,Z1940,Z1941
Посмотрим, широк ли охват этих снипов.

[shik]

Всеми уважаемый Juhani  Väyrynen  (141818) заказал Z1935,Z1936,Z1940,Z1941

Тоже заказал. Выбор дурацкий - хотелось бы Z1938, Z1942...

[Yurgan]

Всеми уважаемый Juhani  Väyrynen  (141818) заказал Z1935,Z1936,Z1940,Z1941

Тоже заказал. Выбор дурацкий - хотелось бы Z1938, Z1942...

Хорошо. Думаю, скоро будет больший, пока еще не ясно, какие снипы будут у карельской ветви, какие у савонской.