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seferhabahir
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« Reply #200 on: November 23, 2012, 03:03:46 PM »


Sounds like DF21 fared pretty well in the Geno 2.0 because it was discovered early enough to make the cut off.

For many of the rest of us, however, Geno 2.0 looks like a big dud.

Some current DF13+ guys might invest in it as a more extensive and slightly more expensive Deep Clade, with some added mtDNA and autosomal benefits. It's probably not too bad a deal for that.


Well, for me I think Geno 2.0 is a boon because there will be tens of thousands of people getting tested for L583 (and maybe even a few positives), whereas before the only testers, for the most part, were the ones that I personally encouraged to test.
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rms2
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« Reply #201 on: November 23, 2012, 03:09:04 PM »


Sounds like DF21 fared pretty well in the Geno 2.0 because it was discovered early enough to make the cut off.

For many of the rest of us, however, Geno 2.0 looks like a big dud.

Some current DF13+ guys might invest in it as a more extensive and slightly more expensive Deep Clade, with some added mtDNA and autosomal benefits. It's probably not too bad a deal for that.


Well, for me I think Geno 2.0 is a boon because there will be tens of thousands of people getting tested for L583 (and maybe even a few positives), whereas before the only testers, for the most part, were the ones that I personally encouraged to test.

That is a good thing, and Geno 2.0 should also add a lot of new L21+ guys to our growing army of ultimate world domination. ;-)

I don't see any reason for me to order it, however.

I am tossing over in mind whether it might not be a good thing for my dad, however. Too bad my one remaining maternal uncle passed away a couple of years ago. It would have been a great test for him.
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breckenheimer
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« Reply #202 on: November 23, 2012, 05:30:00 PM »

Besides the known Z, U, DF and L Y-SNPs in Geno 2.0, does anyone know what the CTS, F, PF, and YSC SNPs are?  Are they mt, X, Autosomal, or Y?  The name given seems to suggest they are Y, so perhaps some would be unknown and their placement in the tree to be discovered.

https://www.dropbox.com/s/j8yel8ddsq5o3rl/Geno-Y-SNPs.txt
« Last Edit: November 23, 2012, 05:31:50 PM by breckenheimer » Logged

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wing_genealogist
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« Reply #203 on: November 23, 2012, 05:41:55 PM »

Besides the known Z, U, DF and L Y-SNPs in Geno 2.0, does anyone know what the CTS, F, PF, and YSC SNPs are?  Are they mt, X, Autosomal, or Y?  The name given seems to suggest they are Y, so perhaps some would be unknown and their placement in the tree to be discovered.

https://www.dropbox.com/s/j8yel8ddsq5o3rl/Geno-Y-SNPs.txt

CTS undoubtedly stands for Chris Tyler Smith. He has worked with Spencer Wells on identifying more SNPs from the 1000 Genome data. It is believed he had access to the DNA, rather than simply access to the results, so he was able to verify many more SNPs than previously discovered (in the Z & DF categories).

YSC SNPs had been listed in Thomas Krahn's yMap program, and I believe it stands for Y SNP Candidate. It appears he was investigating potential SNPs.

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gtc
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« Reply #204 on: November 24, 2012, 02:22:56 AM »

Besides the known Z, U, DF and L Y-SNPs in Geno 2.0, does anyone know what the CTS, F, PF, and YSC SNPs are?  Are they mt, X, Autosomal, or Y?  The name given seems to suggest they are Y, so perhaps some would be unknown and their placement in the tree to be discovered.

https://www.dropbox.com/s/j8yel8ddsq5o3rl/Geno-Y-SNPs.txt

PF are believed to be the initials of Paolo Francalacci, the guy who provided Sardinian SNPs.

F is believed to be for Fudan University, Shanghai, from where Prof. Li Jin supplied East Asian SNPs.
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« Reply #205 on: November 24, 2012, 02:42:00 AM »

Below is a more detailed coverage of DF21, my terminal SNP, courtesy of David Reynolds.
The depth is fine as it includes DF5 which is four levels below L21. The main gap appears to be the "S" Series. Does this mean that certain labs are not releasing their data and are therefore not included in Geno 2.0 or did they not make the November 2011 cutoff date?

http://pinterest.com/pin/32721534764261989/


Sounds like DF21 fared pretty well in the Geno 2.0 because it was discovered early enough to make the cut off.

For many of the rest of us, however, Geno 2.0 looks like a big dud.

Some current DF13+ guys might invest in it as a more extensive and slightly more expensive Deep Clade, with some added mtDNA and autosomal benefits. It's probably not too bad a deal for that.





I did a quick analysis of the coverage of P312. It is not a pretty sight. There is far more orange than green.
I would estimate <50% of SNPs downstream of P312 are in the Geno 2.0 raw data file.
Glaring omissions are P312, DF27, DF13, as well as M269 upstream.
DF21 and U152 have good coverage, the rest have big gaps.
I counted 11,542 Y SNPs. I only hope that some of these compensate for the apparent gaps in P312.
I believe it will take at least until the end of January to update the ISOGG Tree.
Bottom line, I am not impressed.

http://pinterest.com/pin/32721534764263546/

There are indeed some very strange omissions, including L48.

We don't yet know where the CTS series SNPs (mined from the 1K Genome Project) sit on the tree, so there may yet be a new bonanza for R1b among those.
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rms2
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« Reply #206 on: November 24, 2012, 09:51:58 AM »

Below is a more detailed coverage of DF21, my terminal SNP, courtesy of David Reynolds.
The depth is fine as it includes DF5 which is four levels below L21. The main gap appears to be the "S" Series. Does this mean that certain labs are not releasing their data and are therefore not included in Geno 2.0 or did they not make the November 2011 cutoff date?

http://pinterest.com/pin/32721534764261989/


Sounds like DF21 fared pretty well in the Geno 2.0 because it was discovered early enough to make the cut off.

For many of the rest of us, however, Geno 2.0 looks like a big dud.

Some current DF13+ guys might invest in it as a more extensive and slightly more expensive Deep Clade, with some added mtDNA and autosomal benefits. It's probably not too bad a deal for that.





I did a quick analysis of the coverage of P312. It is not a pretty sight. There is far more orange than green.
I would estimate <50% of SNPs downstream of P312 are in the Geno 2.0 raw data file.
Glaring omissions are P312, DF27, DF13, as well as M269 upstream.
DF21 and U152 have good coverage, the rest have big gaps.
I counted 11,542 Y SNPs. I only hope that some of these compensate for the apparent gaps in P312.
I believe it will take at least until the end of January to update the ISOGG Tree.
Bottom line, I am not impressed.

http://pinterest.com/pin/32721534764263546/

There are indeed some very strange omissions, including L48.

We don't yet know where the CTS series SNPs (mined from the 1K Genome Project) sit on the tree, so there may yet be a new bonanza for R1b among those.

So, is it possible that some of those CTS SNPs are just L48, DF41, DF49, etc., by another name?
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wing_genealogist
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« Reply #207 on: November 24, 2012, 10:46:23 AM »

So, is it possible that some of those CTS SNPs are just L48, DF41, DF49, etc., by another name?

It may be possible that some of the CTS SNPs are SYNONYMOUS with the SNPs left off of the chip, but I would strongly doubt they are identical. Even if Tyler-Smith accidentally created a new CTS SNP name for one of these SNPs, I would expect Thomas Krahn (who was in charge of the Y-SNPs on the GenoChip) would have quickly discovered the error.
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mt-DNA - J1c2g with the following private mutations: 315.1C 522.1A 522.2C C9974T C16256T (FMS tested and submitted to GenBank)

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rms2
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« Reply #208 on: November 24, 2012, 05:02:08 PM »

So, is it possible that some of those CTS SNPs are just L48, DF41, DF49, etc., by another name?

It may be possible that some of the CTS SNPs are SYNONYMOUS with the SNPs left off of the chip, but I would strongly doubt they are identical. Even if Tyler-Smith accidentally created a new CTS SNP name for one of these SNPs, I would expect Thomas Krahn (who was in charge of the Y-SNPs on the GenoChip) would have quickly discovered the error.

Ah, well, that's a let down.
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Maliclavelli
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« Reply #209 on: November 27, 2012, 05:06:36 AM »

PF are believed to be the initials of Paolo Francalacci, the guy who provided Sardinian SNPs.

I can confirm for certain, by a letter he wrote to a common friend, that PF is Paolo Francalacci.
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Maliclavelli


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Heber
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« Reply #210 on: November 27, 2012, 07:47:54 AM »

I have updated the Geno 2.0 coverage of P312 and its defining mutations back to R1b.
This would give an idea of the R1b Neolithic expansion described in Wei et al paper.
The P312 component would represent the Bell Beaker expansion described in the Patterson et al paper.
(I am assuming that P312 or possibly L11 is associated with the Bell Beakers).
Tyler Smith states "In all, we provide a nearly 10-fold increase in the number of Y markers with phylogenetic information, and novel historical insights derived from placing them on a calibrated phylogenetic tree."
 If this is correct and reflected in the Geno 2.0 test, then we are in for a treat for the holiday period when we should have a large number of Y results and my diagram will change dramatically.

http://pinterest.com/pin/32721534764284539/
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Heber


 
R1b1a2a1a1b4  L459+ L21+ DF21+ DF13+ U198- U106- P66- P314.2- M37- M222- L96- L513- L48- L44- L4- L226- L2- L196- L195- L193- L192.1- L176.2- L165- L159.2- L148- L144- L130- L1-
Paternal L21* DF21


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Solothurn
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« Reply #211 on: December 01, 2012, 08:22:50 AM »

Are there any Y SNPs tested on the GenoChip that the 23andMe V3 chip also has? I mean any terminal SNP that 23andMe haven't previously reported that Geno now do!

Hope that makes sense!
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gtc
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« Reply #212 on: December 01, 2012, 09:03:56 AM »

Are there any Y SNPs tested on the GenoChip that the 23andMe V3 chip also has? I mean any terminal SNP that 23andMe haven't previously reported that Geno now do!

Hope that makes sense!

Good question, but I don't know how we can tell at the moment.

The 23andMe data contains chromosome position details whereas the Geno 2 data that I've seen so far doesn't. That makes matching one with the other a tad difficult!

Maybe we'll get fuller info on the Geno 2 SNP set in due course.
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« Reply #213 on: December 01, 2012, 09:40:34 AM »

Thanks gtc

On CeCe's site there is:

"Dr. Tim Janzen, 23andMe Ancestry Ambassador and ISOGG Y-SNP Tree Committee Member, is currently working on creating a file that will include the SNP positions for all of the SNPs on the GenoChip that are also found on the 23andMe v3 chip. I will add the link here when it is completed (probably tomorrow)."

As you say in due course!


[/quote]

Good question, but I don't know how we can tell at the moment.

The 23andMe data contains chromosome position details whereas the Geno 2 data that I've seen so far doesn't. That makes matching one with the other a tad difficult!

Maybe we'll get fuller info on the Geno 2 SNP set in due course.
[/quote]
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Heber
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« Reply #214 on: December 01, 2012, 01:55:03 PM »

This was posted on 23andme:

"Here are some example analysis groups that will be helping to analyze the Geno 2.0results.

The R1b-L21 area is represented by
http://daver.info/geno/

The R1b-U152 area effort will occur here:
https://docs.google.com/spreadsheet/ccc?key=0Ago12PDVxPwwdGVOQWNuSlZad3gycHJOZFloeE85b2c#gid=0


The R1b-U106 area (including the royal Wettin lineage)
https://docs.google.com/spreadsheet/ccc?key=0Av9lu-SZDcLodFR1Ump6a0lCTmlqUTNjd3Jwd2VIbUE#gid=0"

I will focus my efforts on the defining mutations from M269 -> DF21 and peripheral SNPs, in an attempt to get some insights into Celtic Migrations and in particular the Gaelic Clan expansion. I guess there will be several iterations depending on the roadmap of the Geno 2.0 chip and depth of new SNPs discovered.

http://pinterest.com/pin/32721534764284539/


« Last Edit: December 01, 2012, 02:16:05 PM by Heber » Logged

Heber


 
R1b1a2a1a1b4  L459+ L21+ DF21+ DF13+ U198- U106- P66- P314.2- M37- M222- L96- L513- L48- L44- L4- L226- L2- L196- L195- L193- L192.1- L176.2- L165- L159.2- L148- L144- L130- L1-
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DavidCar
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« Reply #215 on: December 01, 2012, 09:35:49 PM »

Is anyone collecting and comparing kits in DF27?  I expect to get results from a cousin's kit in L176.2/Z262 in a month or so, and I want to compare his kit with a few others in that region.
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gtc
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« Reply #216 on: December 02, 2012, 08:31:56 AM »

Word from Charles Moore, an ISOGG Y-tree committee member and an R1b project admin, is that male Geno 2 tests will be delayed for another 1 to 2 weeks, because:

"[NG and FTDNA] 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."

and

"Although I was told to expect the results in one to two weeks, the publication
of the new tree itself is another matter. Spencer [Wells] and Bennett [Greenspan] 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."
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« Reply #217 on: December 02, 2012, 12:33:35 PM »

Maybe the SNPs such as L459 have been further defined.

MJost
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Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
brunetmj
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« Reply #218 on: December 02, 2012, 02:17:44 PM »

Quote
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.
What does layering out the tree mean exactly? Sorry I am just learning..
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« Reply #219 on: December 02, 2012, 02:56:44 PM »

"[NG and FTDNA] 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!

Hope good news for me.
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Maliclavelli


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ArmandoR1b
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« Reply #220 on: December 02, 2012, 03:10:13 PM »

Word from Charles Moore, an ISOGG Y-tree committee member and an R1b project admin, is that male Geno 2 tests will be delayed for another 1 to 2 weeks, because:

"[NG and FTDNA] 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."

What does layering out the tree mean exactly? Sorry I am just learning..

He is saying that some of the SNPs that were though to be of at the same level are actually of different levels. I am very interested in seeing the results and especially how they affect R1b, if they do.
« Last Edit: December 02, 2012, 03:12:19 PM by ArmandoR1b » Logged
Heber
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« Reply #221 on: December 02, 2012, 03:14:04 PM »

Quote
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.
What does layering out the tree mean exactly? Sorry I am just learning..

@Brunetmj

As per my post above, according to the Wei et al paper and Chris Tyler Smith  discovered a 10 fold increase in new SNPs in their work and especially an extreme expansion of R1b associated with the Neolithic. As we know that the majority of New SNPs relevant to R1b will carry the CTS prefix this will have the effect of creating several new layers on the existing tree. Some SNPs which today are known by several names will now become separate discrete new SNPs and several terminal SNPs eg M222 will get (four) new SNPs downstream. The effect will be that the tree will become bushier and wider.
« Last Edit: December 02, 2012, 03:24:09 PM by Heber » Logged

Heber


 
R1b1a2a1a1b4  L459+ L21+ DF21+ DF13+ U198- U106- P66- P314.2- M37- M222- L96- L513- L48- L44- L4- L226- L2- L196- L195- L193- L192.1- L176.2- L165- L159.2- L148- L144- L130- L1-
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seferhabahir
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« Reply #222 on: December 02, 2012, 05:02:21 PM »

"[NG and FTDNA] 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!

I wonder how many completed Y-DNA SNP results are stacked up awaiting whatever layering is being attempted (hundreds?? thousands??). Also, whether once they get their act together if they are going to give people whose DNA was used to test the chip an access code.
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Peter M
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« Reply #223 on: December 02, 2012, 09:27:04 PM »

Word from Charles Moore, an ISOGG Y-tree committee member and an R1b project admin, is that male Geno 2 tests will be delayed for another 1 to 2 weeks, because:

"[NG and FTDNA] 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."

and

"Although I was told to expect the results in one to two weeks, the publication
of the new tree itself is another matter. Spencer [Wells] and Bennett [Greenspan] 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."

If Spencer W. and Bennett G. have postponed publishing the (a ?) new Y-Tree for an unspecified amount of time, then why on earth would that be a reason for postponing publishing the test results of a fixed group of people (who, btw, paid for their test) for a fixed set of SNPs for (at least) one or two weeks ?? Something doesn't make an awful lot of sense to me.
« Last Edit: December 02, 2012, 09:28:18 PM by Peter M » Logged
gtc
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« Reply #224 on: December 02, 2012, 10:01:38 PM »

Word from Charles Moore, an ISOGG Y-tree committee member and an R1b project admin, is that male Geno 2 tests will be delayed for another 1 to 2 weeks, because:

"[NG and FTDNA] 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."

and

"Although I was told to expect the results in one to two weeks, the publication
of the new tree itself is another matter. Spencer [Wells] and Bennett [Greenspan] 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."

If Spencer W. and Bennett G. have postponed publishing the (a ?) new Y-Tree for an unspecified amount of time, then why on earth would that be a reason for postponing publishing the test results of a fixed group of people (who, btw, paid for their test) for a fixed set of SNPs for (at least) one or two weeks ?? Something doesn't make an awful lot of sense to me.


I agree with your sentiment regarding a paid service and how about delivering the goods but I guess they feel that they first need to update the Geno 2 FAQ in relation to the impact the results are having on the new Y-tree ahead of a predictable tsunami of questions in that regard.

And, on an closely-associated matter, Spencer Wells' paper on all of this is due (some might say overdue). Perhaps he wants to "stop the presses" so that he can make some changes.
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