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Author Topic: Analysis of Geno2 results  (Read 2443 times)
Peter M
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« on: December 11, 2012, 03:39:51 PM »

Sure, I know, there are plenty of spreadsheets, programs and things for the analysis of Geno 2.0 results available on the web already. And these are all respectable results of sophisticated and knowledgeable systems engineering. I DO know that.

But I like niches and there still might be just a little niche with the ultimately curious to get more information from their test results, so I've created Yet Another Geno2 Analysis Program. The whole thing including the way to submit your results for inclusion is described here: http://podvelde.home.xs4all.nl/Geno2/U106/

Currently the thing only works for Haplogroup R-U106/R-Z18 and Subgroups, but there's no reason why it would not be able to handle any haplogroup.

Please keep in mind that the thing is experimental until a reasonable number of test results have been processed and everything, including the procedure for adding new test results, is stable.

I guess it would be a good idea to have all discussions about this tool and its results in this topic (and open a new topic here should the tool ever be applied to any other haplogroup in future).

Any thoughts ??
« Last Edit: December 11, 2012, 03:41:06 PM by Peter M » Logged
razyn
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« Reply #1 on: December 11, 2012, 08:42:10 PM »

Any thoughts ??

Good luck with that.  I don't recall ever having seen colorized SNP results, as opposed to the commonly used colorized STR results.  It seems very logical, to me.  I'd like to see a big display, maybe a few hundred instead of three examples.

And I'd hate to have to play that Canto Ostinato on bass.  Or to conduct it.  Pianists, like most orchestral players, at least get to remain seated.
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Peter M
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« Reply #2 on: December 11, 2012, 08:57:47 PM »

Any thoughts ??

Good luck with that.  I don't recall ever having seen colorized SNP results, as opposed to the commonly used colorized STR results.  It seems very logical, to me.  I'd like to see a big display, maybe a few hundred instead of three examples.

And I'd hate to have to play that Canto Ostinato on bass.  Or to conduct it.  Pianists, like most orchestral players, at least get to remain seated.

It would work best if all Geno2 participants played along, but I'm afraid that due to all sorts of issues, that's not going to happen. Some people prefer their own small-scale manual approach using spreadsheets.

It has been played on many intruments but I've never heard anything about a bass. In the mean time I've heard version on one, two and four pianos. And then this was the short version. On the internet there's a 2.5 hour version somewhere, but I personally like this one much better. The images are nice as well, but for me all too familiar of course. $:-)

BTW, I've never seen minimal music being conducted. Seems a bit strange combination to me. $:-)
« Last Edit: December 11, 2012, 09:08:51 PM by Peter M » Logged
brunetmj
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« Reply #3 on: December 12, 2012, 04:12:50 PM »

Well let's start with the basics . I just received my results last night and see no section that's says " "download raw data" or similar. Where and exactly how do you get this data?
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brunetmj
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« Reply #4 on: December 12, 2012, 05:12:02 PM »

I got a message that downloading raw data takes a day or two after getting results back and it appears in the same section as doing the transfer to FTDNA
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Peter M
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« Reply #5 on: December 13, 2012, 10:37:08 AM »

Well let's start with the basics . I just received my results last night and see no section that's says " "download raw data" or similar. Where and exactly how do you get this data?

There's a good description with screen shots by CeCe Moore at: http://www.yourgeneticgenealogist.com/

If you scroll down to the section "EXPERT OPTIONS: TRANSFERRING AND DOWNLOADING" you'll see a description.

This ection actually describes TWO things: (1) downloading the final results to your earlier FT-DNA test results and (2) downloading the raw results (the ".csv file").

This article mentiones that it may take a little time before the .csv file is available for download. Lots of people have this problem currently.

People who are trying to analyse your results will be interested mainly in the .csv file, as that contains all raw testing data. If you send anything to anybody, make sure your .csv file is zipped, as that descreases the size of the file significantly.
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seferhabahir
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« Reply #6 on: December 13, 2012, 01:44:11 PM »

I am cross-posting this on a few forums to see if anyone who is keeping track of a large number of Geno 2.0 kits can help.

I'm looking at a side-by-side comparison of my (R1b) 3000 or so F-series SNPs and my cousin's (R2a) F-series SNPs. Almost all of them have the same values, which I assume means that R1 and R2 (all of R) would be either ancestral, or else derived (like P280 and P285 which define Haplogroup R in ISOGG). For the ones that have different values (about 30), I have to assume those are all derived SNPs, but either only for R1 (like  P233 or P236) or only for R2 (like P249 or P267), else the value would be the same.

Do I have this reasoning right? With no information about F-series SNPs, I'm trying to find out how many of my cousin's F SNPs might be relevant for a perhaps soon to be re-arranged R2a tree. He was given a new F-series terminal SNP called R-F1092 somewhere underneath R-M124. I don't know much about R2 except what I have stumbled across in the last couple days, and am wondering about the other twenty something F-series SNPs that look to be derived for R2. I would assume this situation is similar for the CTS and PF series SNPs as well? I haven't looked at those yet. It gives me a headache after a while.
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Peter M
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« Reply #7 on: December 14, 2012, 11:08:54 AM »

I am cross-posting this on a few forums to see if anyone who is keeping track of a large number of Geno 2.0 kits can help.

I'm looking at a side-by-side comparison of my (R1b) 3000 or so F-series SNPs and my cousin's (R2a) F-series SNPs. Almost all of them have the same values, which I assume means that R1 and R2 (all of R) would be either ancestral, or else derived (like P280 and P285 which define Haplogroup R in ISOGG). For the ones that have different values (about 30), I have to assume those are all derived SNPs, but either only for R1 (like  P233 or P236) or only for R2 (like P249 or P267), else the value would be the same.

Do I have this reasoning right? With no information about F-series SNPs, I'm trying to find out how many of my cousin's F SNPs might be relevant for a perhaps soon to be re-arranged R2a tree. He was given a new F-series terminal SNP called R-F1092 somewhere underneath R-M124. I don't know much about R2 except what I have stumbled across in the last couple days, and am wondering about the other twenty something F-series SNPs that look to be derived for R2. I would assume this situation is similar for the CTS and PF series SNPs as well? I haven't looked at those yet. It gives me a headache after a while.


I guess, your reasoning is right. In theory. I would be extremely careful in situations in which the number of SNPs you're studying is significantly bigger than the number of profiles you have available (with a call for each of those SNPs). Otherwise you'll have a high risk of e.g. looking at "SNP cascades" with little information (one of the issues with the 1kG samples).

BTW, my impression is if you're DF13 and your cousin is R2, then the two of you are relatively far apart, I might even say too far apart. You would be better off comparing to other people who are at least P312. Much more chance of finding something useful outside of the area where FT-DNA/NG are doing their "restructuring of the R-Tree".

On the positive side, you're looking at the difference between two samples and in that way overcoming another problem you haven't mentioned: that of non-functioning cells that always return an ancestral or derived call.

I would only be able to help if you manage to get a signifcant number of results together, I guess 5 at the very least, in your vicinity of the Y-tree. The software can determine the difference between those 5 given the SNP database and using R-U106 as a remote (!!) reference.
« Last Edit: December 14, 2012, 11:15:25 AM by Peter M » Logged
seferhabahir
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« Reply #8 on: December 14, 2012, 11:31:07 AM »


I guess, your reasoning is right. In theory. I would be extremely careful in situations in which the number of SNPs you're studying is significantly bigger than the number of profiles you have available (with a call for each of those SNPs). Otherwise you'll have a high risk of e.g. looking at "SNP cascades" with little information (one of the issues with the 1kG samples).

BTW, my impression is if you're DF13 and your cousin is R2, then the two of you are relatively far apart, I might even say too far apart. You would be better off comparing to other people who are at least P312. Much more chance of finding something useful outside of the area where FT-DNA/NG are doing their "restructuring of the R-Tree".

On the positive side, you're looking at the difference between two samples and in that way overcoming another problem you haven't mentioned: that of non-functioning cells that always return an ancestral or derived call.

I would only be able to help if you manage to get a signifcant number of results together, I guess 5 at the very least, in your vicinity of the Y-tree. The software can determine the difference between those 5 given the SNP database and using R-U106 as a remote (!!) reference.

David Reynolds has been able to help me out by confirming that the differences I found hold up using a larger number of Geno 2.0 samples in R1 and in other haplogroups. These now look to be real mutations in R2. Now the question is how many other R2 Geno 2.0 testers also have those, but for that I will have to wait for awhile.
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Y-DNA: R-L21 (Z251+ L583+)

mtDNA: J1c7a

Peter M
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« Reply #9 on: December 14, 2012, 12:07:22 PM »

David Reynolds has been able to help me out by confirming that the differences I found hold up using a larger number of Geno 2.0 samples in R1 and in other haplogroups. These now look to be real mutations in R2. Now the question is how many other R2 Geno 2.0 testers also have those, but for that I will have to wait for awhile.

OK, everybody happy !! $:-)
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brunetmj
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« Reply #10 on: December 14, 2012, 04:19:59 PM »

After transferring my data to FTDNA a whole new series of SNP's appears in the haplogroup tree page.
Are those the total amount tested by Geno2 ?
What I am getting at is there anything to be gained by submitting the cvs file to my project or could the list appearing at FTDNA suffice.
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eochaidh
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« Reply #11 on: December 14, 2012, 05:41:53 PM »

Wow! This Geno 2.0/FTDNA thing is all fouled up! Good thing none of us paid any money for it!

Wait a second....
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brunetmj
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« Reply #12 on: December 14, 2012, 06:34:49 PM »

@eochaidh

Oui! I started out as French Canadian but was pronounced English by the 23andme ancestry composition followed by a switch of nationalities to Danish.
I am not sure how to explain this to my mother!
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seferhabahir
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« Reply #13 on: December 14, 2012, 07:50:47 PM »

Geno 2.0 has my reference populations as Iranian and Sardinian (I think if one picks a geographic location exactly in between, it probably makes more sense). My mother is no longer alive, so I don't have the problem of explaining any of this.
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gtc
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« Reply #14 on: December 14, 2012, 11:18:11 PM »

After transferring my data to FTDNA a whole new series of SNP's appears in the haplogroup tree page.
Are those the total amount tested by Geno2 ?
What I am getting at is there anything to be gained by submitting the cvs file to my project or could the list appearing at FTDNA suffice.

Following data transfer, on your FTDNA haplotree page you will only see a subset of your positive Geno 2 SNPs, namely those that are currently offered for testing by FTDNA.  If you are a member of an FTDNA project, then your full set of positive Geno 2 SNPs can be seen on the SNPs view of that project.

It's anybody's guess what FTDNA will do with the haplotree view going forward as they add "new" SNPs to their testing menu, but there will need to be some mechanism to stop people ordering an individual SNP test for one that they are already positive for under Geno 2.
« Last Edit: December 14, 2012, 11:19:53 PM by gtc » Logged

Y-DNA: R1b-Z12* (R1b1a2a1a1a3b2b1a1a1) GGG-GF Ireland (roots reportedly Anglo-Norman)
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NealtheRed
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« Reply #15 on: December 15, 2012, 04:21:23 PM »

After transferring my data to FTDNA a whole new series of SNP's appears in the haplogroup tree page.
Are those the total amount tested by Geno2 ?
What I am getting at is there anything to be gained by submitting the cvs file to my project or could the list appearing at FTDNA suffice.

Following data transfer, on your FTDNA haplotree page you will only see a subset of your positive Geno 2 SNPs, namely those that are currently offered for testing by FTDNA.  If you are a member of an FTDNA project, then your full set of positive Geno 2 SNPs can be seen on the SNPs view of that project.

It's anybody's guess what FTDNA will do with the haplotree view going forward as they add "new" SNPs to their testing menu, but there will need to be some mechanism to stop people ordering an individual SNP test for one that they are already positive for under Geno 2.

I realize this may be too premature to say, but have there been any significant discoveries regarding the new SNPs gleaned from Geno 2.0? A number of folks in my project have uploaded their results, and I am wondering what I should be looking at.
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Y-DNA: R-Z255 (L159.2+) - Downing (Irish Sea)


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gtc
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« Reply #16 on: December 15, 2012, 07:21:38 PM »

After transferring my data to FTDNA a whole new series of SNP's appears in the haplogroup tree page.
Are those the total amount tested by Geno2 ?
What I am getting at is there anything to be gained by submitting the cvs file to my project or could the list appearing at FTDNA suffice.

Following data transfer, on your FTDNA haplotree page you will only see a subset of your positive Geno 2 SNPs, namely those that are currently offered for testing by FTDNA.  If you are a member of an FTDNA project, then your full set of positive Geno 2 SNPs can be seen on the SNPs view of that project.

It's anybody's guess what FTDNA will do with the haplotree view going forward as they add "new" SNPs to their testing menu, but there will need to be some mechanism to stop people ordering an individual SNP test for one that they are already positive for under Geno 2.

I realize this may be too premature to say, but have there been any significant discoveries regarding the new SNPs gleaned from Geno 2.0? A number of folks in my project have uploaded their results, and I am wondering what I should be looking at.

Things are in a state of flux at the moment, but the leaders at the various haplogroup projects seem to be making some headway with the handful of test results back so far.

I see from your signature that you are Z255 which places you under the major node of L21. If you're not already a member of that haplogroup project then I'd recommend your joining it, and also its associated Yahoo discussion group.
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Y-DNA: R1b-Z12* (R1b1a2a1a1a3b2b1a1a1) GGG-GF Ireland (roots reportedly Anglo-Norman)
mtDNA: I3b (FMS) Maternal lines Irish
rms2
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« Reply #17 on: December 15, 2012, 07:25:19 PM »

Neal is the Grand Poobah of the R-Z255 Project. I think that is his actual title. ;-)
« Last Edit: December 15, 2012, 07:25:31 PM by rms2 » Logged

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« Reply #18 on: December 15, 2012, 07:33:27 PM »

I run at least one major y haplogroup project, and I've got to confess that I am behind the eight ball on the Geno 2.0 stuff. I am kind of awaiting some word on just what is what, and that word is scarce.

It seems a shame to me that the Geno 2.0 does not include all the L21+ SNPs we know about. For that reason (mainly because it does not include my own current  terminal SNP), Geno 2.0 seems a trifle lame to me. I realize it's not, really, but it just seems that way to me. Maybe I'll feel differently if some groundbreaking stuff starts to emerge from the terracotta Chinese army of data so far assembled.
« Last Edit: December 15, 2012, 07:34:06 PM by rms2 » Logged

gtc
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« Reply #19 on: December 15, 2012, 07:51:40 PM »

Neal is the Grand Poobah of the R-Z255 Project. I think that is his actual title. ;-)

In that case, I dips me lid.
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Y-DNA: R1b-Z12* (R1b1a2a1a1a3b2b1a1a1) GGG-GF Ireland (roots reportedly Anglo-Norman)
mtDNA: I3b (FMS) Maternal lines Irish
seferhabahir
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« Reply #20 on: December 15, 2012, 09:15:39 PM »


It seems a shame to me that the Geno 2.0 does not include all the L21+ SNPs we know about. For that reason (mainly because it does not include my own current  terminal SNP), Geno 2.0 seems a trifle lame to me. I realize it's not, really, but it just seems that way to me. Maybe I'll feel differently if some groundbreaking stuff starts to emerge from the terracotta Chinese army of data so far assembled.


Lameness would be in the eye of the beholder, I suppose. I'm sure the next chip will have all the right L21 stuff. The terracotta Chinese armies at Fudan in Shanghai identified 38 new R2 SNPs, of which 29 can be found in my cousin's Geno 2.0 results (see above posts). I know this is an R1b forum, but R2 boards are very few and far between, and not a very hot topic for the Western European tester crowd.
« Last Edit: December 16, 2012, 02:40:57 AM by seferhabahir » Logged

Y-DNA: R-L21 (Z251+ L583+)

mtDNA: J1c7a

gtc
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« Reply #21 on: December 15, 2012, 10:24:05 PM »

The terracotta Chinese armies at Fudan in Shanghai identified more than thirty new R2 SNPs, of which 29 can be found in my cousin's Geno 2.0 results (see above posts). I know this is an R1b forum, but R2 boards are very few and far between, and not a very hot topic for the Western European tester crowd.

I think that's fantastic news! As a member of the huge R1b clan it's easy to forget that other clades have been wandering in the SNP wilderness for many years.

I also hope that haplogroup I gets a boost from Geno 2.
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Y-DNA: R1b-Z12* (R1b1a2a1a1a3b2b1a1a1) GGG-GF Ireland (roots reportedly Anglo-Norman)
mtDNA: I3b (FMS) Maternal lines Irish
rms2
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« Reply #22 on: December 15, 2012, 11:00:28 PM »

As I said, I know it's not really lame, it is just disappointing from my perspective. I am even wrestling with the idea of ordering it for my 82-year-old dad, but I don't know.
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« Reply #23 on: December 15, 2012, 11:24:24 PM »

My wife has some fairly wealthy cousins in Ukraine, one of whom is a surgeon (Sagalevich is the surname). I should get her to convince them to order the Geno 2.0 thing. They can afford it, and they are somewhat interested.
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eochaidh
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« Reply #24 on: December 16, 2012, 02:30:39 AM »

I am R1b-DF23 and expext to come out as an E-PF1197 or a J-PF21679. It will turn out that all of the people from County Wicklow and County Wexford, Ireland were from Sardinia and North Africa.

And my Autosomal matches will be Greece and Iran. I should have sent in a DNA sample from one of my cats. Both of them are Irish.
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Y-DNA: R1b DF23
mtDNA: T2g
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