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View Full Version : Geno 2.0 Next Gen is now sorting out the y-haplotree mess!



leo76
05-06-2016, 07:25 PM
See their announcement about it, from today. (http://i.imgur.com/FkOxjvq.png)

GoldenHind
05-06-2016, 08:28 PM
It's about time!

Amerijoe
05-06-2016, 09:11 PM
I second that!

ArmandoR1b
05-07-2016, 02:57 AM
I second that!Had it been more than two weeks that they said it would be fixed? I'm unable to look for your posts on that right now.

ArmandoR1b
05-07-2016, 02:59 AM
Has anyone seen a change yet? I also wonder if people that have transferred to FTDNA already will be able to transfer again and if the CSV file will have fewer false positives and false negatives.

leo76
05-07-2016, 04:39 AM
I don't know the answer to either of your questions, Armando. My terminal SNP/haplogroup assignment did not change. I think they got my right the first time.

jortita
05-07-2016, 04:54 AM
No change as of now on mine, even though a notification was posted

leo76
05-07-2016, 06:17 AM
Was yours in error, jortita?

GoldenHind
05-07-2016, 07:43 PM
No change as yet in the DF99 sample I wrote about on another Geno 2 thread where the person is erroneously classified as R-Z2970.

Ali16
05-18-2016, 01:24 PM
FTDNA will correct the false positives, no one needs to transfer data. All the data originates with FTDNA! But, let's hope they correct these results soon after all these months!!

GoldenHind
05-18-2016, 01:26 PM
No change as yet in the DF99 sample I wrote about on another Geno 2 thread where the person is erroneously classified as R-Z2970.

They have finally got this sample corrected.

The_Lyonnist
06-17-2016, 03:36 PM
I'm not at all Z138, only I1. When do I get the new results?

The_Lyonnist
07-19-2016, 07:33 PM
I'm not at all Z138, only I1. When do I get the new results?

WHEN ???

Amerijoe
07-19-2016, 08:52 PM
:\Here is some of the conversation with FTDNA and Geno 2 concerning errors. This test was originally transferred on 2/26/16.

Here are the results from the testing companies with my assigned maternal and paternal haplogroups.

23 and me J1c, R1a1a
DNAtribes. J1c, R1a1a1b2a2a=Z2123
FTDNA. J1c, R-Y15121*
Geno 2+. J1c4, R-Z94

I've contacted both Geno 2+ and FTDNA concerning the results. Also had 22 false positives. Correspondence listed below indicate they are aware of the problem.

Hello Joe,

For Kit B82688, I see the problem you are addressing. We are working on a resolution. FTDNA is not exactly the same as the Genographic project and we are working on getting the SNPs to resolve. The solution is not implemented but we expect it to be soon.



Thank you


Best Regards,

Tom
Family Tree DNA
www.familytreedna.com

Hello,

Thank you for contacting The Genographic Project, I have requested that the Raw Data regarding the results of your kit:XTJPA3P3XR be reviewed. As soon as I hear anything back from this investigation, I will notify you immediately.

I deeply apologize for any inconvenience this has caused you, your patience and understanding throughout this entire process has been greatly appreciated.

Best Regards,



Alyssa G
Information Specialist
The Genographic Project

Hello Joe,

The person in charge of the science end of the project is Dr. Miguel Vilar. He is well aware of the issues and differences.

I will see what we can do to help with your kit.



Best Regards,

Tom
Family Tree DNA
www.familytreedna.co
Last edited by Amerijoe; 03-17-2016 at 09:28 AM.

Here is the latest correspondence.

Alyssa G: I just came from your website and nothing has changed. Do you have me mixed up with someone else?

Please check your records for confirmation of changes and see if there is a mistake.

Regards,

Joe

MATERNAL LINE
J1C4
0.4%
Your maternal haplogroup is shared by 0.4% of all participants in the project

PATERNAL LINE
R-Z94
0.5%
Your paternal haplogroup is shared by 0.5% of all participants in the project


On Jul 18, 2016, at 4:59 PM, "[email protected]" <[email protected]> wrote:

## Reply ABOVE THIS LINE to add a note to this request ##
Request Update Your Ticket Number is: 75289

Hello,

Thank you for contacting The Genographic Project. Unfortunately there was an issue with the SNPs in the initial raw data for Y-DNA. We worked alongside Family Tree DNA to correct this issue, however, it did take much longer than we originally expected to make those corrections.

To correct these errors and update your results and raw data, your results had to be re-ran. This is why you may have seen your results disappear and reappear for a short while. The Genographic Project is using a more updated mtDNA tree than FTDNA, this is why you are seeing this difference between your haplogroup on both sites. ***As of now, your Genographic Project results are correct and up-to-date.***

I deeply apologize for any and all inconvenience this has caused you. Your patience and understanding throughout this whole process has been greatly appreciated.

Best Regards,



Alyssa G
Lead Information Specialist
The Genographic Project

Left their site just now and still no change.. Hopefully it will be corrected before Geno 3 comes out.

The_Lyonnist
07-20-2016, 04:16 PM
:\Here is some of the conversation with FTDNA and Geno 2 concerning errors. This test was originally transferred on 2/26/16.

Here are the results from the testing companies with my assigned maternal and paternal haplogroups.

23 and me J1c, R1a1a
DNAtribes. J1c, R1a1a1b2a2a=Z2123
FTDNA. J1c, R-Y15121*
Geno 2+. J1c4, R-Z94

I've contacted both Geno 2+ and FTDNA concerning the results. Also had 22 false positives. Correspondence listed below indicate they are aware of the problem.

Hello Joe,

For Kit B82688, I see the problem you are addressing. We are working on a resolution. FTDNA is not exactly the same as the Genographic project and we are working on getting the SNPs to resolve. The solution is not implemented but we expect it to be soon.



Thank you


Best Regards,

Tom
Family Tree DNA
www.familytreedna.com

Hello,

Thank you for contacting The Genographic Project, I have requested that the Raw Data regarding the results of your kit:XTJPA3P3XR be reviewed. As soon as I hear anything back from this investigation, I will notify you immediately.

I deeply apologize for any inconvenience this has caused you, your patience and understanding throughout this entire process has been greatly appreciated.

Best Regards,



Alyssa G
Information Specialist
The Genographic Project

Hello Joe,

The person in charge of the science end of the project is Dr. Miguel Vilar. He is well aware of the issues and differences.

I will see what we can do to help with your kit.



Best Regards,

Tom
Family Tree DNA
www.familytreedna.co
Last edited by Amerijoe; 03-17-2016 at 09:28 AM.

Here is the latest correspondence.

Alyssa G: I just came from your website and nothing has changed. Do you have me mixed up with someone else?

Please check your records for confirmation of changes and see if there is a mistake.

Regards,

Joe

MATERNAL LINE
J1C4
0.4%
Your maternal haplogroup is shared by 0.4% of all participants in the project

PATERNAL LINE
R-Z94
0.5%
Your paternal haplogroup is shared by 0.5% of all participants in the project


On Jul 18, 2016, at 4:59 PM, "[email protected]" <[email protected]> wrote:

## Reply ABOVE THIS LINE to add a note to this request ##
Request Update Your Ticket Number is: 75289

Hello,

Thank you for contacting The Genographic Project. Unfortunately there was an issue with the SNPs in the initial raw data for Y-DNA. We worked alongside Family Tree DNA to correct this issue, however, it did take much longer than we originally expected to make those corrections.

To correct these errors and update your results and raw data, your results had to be re-ran. This is why you may have seen your results disappear and reappear for a short while. The Genographic Project is using a more updated mtDNA tree than FTDNA, this is why you are seeing this difference between your haplogroup on both sites. ***As of now, your Genographic Project results are correct and up-to-date.***

I deeply apologize for any and all inconvenience this has caused you. Your patience and understanding throughout this whole process has been greatly appreciated.

Best Regards,



Alyssa G
Lead Information Specialist
The Genographic Project

Left their site just now and still no change.. Hopefully it will be corrected before Geno 3 comes out.

When ?

Amerijoe
07-20-2016, 05:28 PM
Here is the latest from geno project, hold on you're going to love this.

Joe,

As stated in my previous email The Genographic Project is using a more updated mtDNA tree than FTDNA, this is why you are seeing this difference between your haplogroup on both sites.

Best,


Alyssa G
Lead Information Specialist
The Genographic Project

Does anyone else know they were going deeper into mtdna than FTDNA?

Does this mean my matches at FTDNA are wrong, because they're all J1c?

Anyone else in this situation?

Cofgene
07-20-2016, 05:47 PM
They are not necessarily going "deeper". FTDNA is using the archaic version 14 of phylotree. The current release is 17 which came out this spring. This is one of the reference areas where FTDNA needs to get with it and update to the current reference releases.

vettor
07-20-2016, 06:06 PM
As far as myself, NAt-Geno has correctly presented me with my markers for Ydna and Mtdna correctly since March 2015.
It is the ONLY company that has done so.

ArmandoR1b
07-20-2016, 10:23 PM
:\Here is some of the conversation with FTDNA and Geno 2 concerning errors. This test was originally transferred on 2/26/16.

Here are the results from the testing companies with my assigned maternal and paternal haplogroups.

23 and me J1c, R1a1a
DNAtribes. J1c, R1a1a1b2a2a=Z2123
FTDNA. J1c, R-Y15121*
Geno 2+. J1c4, R-Z94

Your R-Y15121* from FTDNA is a much higher resolution result than any of the other tests including Geno 2+. That is one reason why FTDNA is much better.

Did you get the FMS test from FTDNA? If you did all you had to do was use the James Lick tool (https://dna.jameslick.com/mthap/) to get your PhyloTree Build 17 subclade which would have eliminated the need to spend money on Geno 2+ for that. Geno 2+ doesn't test all of the mitochondrial DNA that the FMS test does and Geno 2+ doesn't provide all of the results of what was tested while FTDNA does. http://www.isogg.org/wiki/MtDNA_testing_comparison_chart

Amerijoe
07-21-2016, 02:53 PM
Your R-Y15121* from FTDNA is a much higher resolution result than any of the other tests including Geno 2+. That is one reason why FTDNA is much better.

My original designation by FTDNA was R-M198, which is equivalent to my 23andme results R1a1a. At that point geno had a higher resolution R-Z94.

On 1/09/16 FTDNA Y111 placed me at R-Z93. On 2/04/16 FTDNA Backbone pack put me at my present designation R-Y15121. Yes, FTDNA can give you better resolution if you do the additional testing.

Also, did full mt at FTDNA resulting in J1c. Lick verified results. My test at geno was my attempt to establish ancestry, my mtdna results were not necessary for me at that point. My results for geno 2 were deeper for both mtdna and YDNA when comparing to FTDNA without additional tests. I assume it is not the case for all.

ArmandoR1b
07-22-2016, 12:44 PM
My original designation by FTDNA was R-M198, which is equivalent to my 23andme results R1a1a. At that point geno had a higher resolution R-Z94.

On 1/09/16 FTDNA Y111 placed me at R-Z93. On 2/04/16 FTDNA Backbone pack put me at my present designation R-Y15121. Yes, FTDNA can give you better resolution if you do the additional testing.
FTDNA will , not can, give better resolution if you do additional testing. Geno 2+ does not have that option. That's my point.


Also, did full mt at FTDNA resulting in J1c. Lick verified results.
If you recently uploaded your FASTA file from FTDNA to the James Lick site and only got J1c but not J1c4 then either the James Lick site has a problem or Geno 2+ is giving you a false positive. You can also look through your CODING REGION DIFFERENCES FROM RSRS at https://www.familytreedna.com/my/mtdna-results.aspx and look for A9632G T12083G which are the defining mutations for J1c4 which even Build 14 used by FTDNA had those as the defining mutations for J1c4. http://haplogroup.org/mtdna/jt/j/j1/j1c/j1c4/. If you don't have them you need to email Geno 2+ and let them know you have false positives from them.


My test at geno was my attempt to establish ancestry, my mtdna results were not necessary for me at that point.
Establish your ancestry how?


My results for geno 2 were deeper for both mtdna and YDNA when comparing to FTDNA without additional tests. I assume it is not the case for all.
Yes, the Geno 2+ by itself will give better results, but no matching, compared to the most basic tests at FTDNA however, as I stated before, Geno 2+ doesn't provide the option of getting higher resolution testing but FTDNA does. So if a person wants the best tests possible Geno 2+ is not the test to get.

wombatofthenorth
07-22-2016, 11:38 PM
FTDNA will , not can, give better resolution if you do additional testing. Geno 2+ does not have that option. That's my point.


That's a weird point though since how does testing with Geno 2.0 NG instead of FamilyFinder prevent additional haplo testing? It even lets you directly buy a SNP pack without needing a Y-STR test first (although some will want Y-STR anyway or to go YSTR and then BigY).



Yes, the Geno 2+ by itself will give better results, but no matching, compared to the most basic tests at FTDNA however, as I stated before, Geno 2+ doesn't provide the option of getting higher resolution testing but FTDNA does. So if a person wants the best tests possible Geno 2+ is not the test to get.

Why not? At FTDNA you never get the nice presentation of the haplogroup results and walk out of Africa (you do a touch at FTDNA but it's pretty poor compared to the Geno 2.0 presentation) and nothing about starting with Geno 2.0 NG prevents using the option of a later higher resolution FTDNA test!

wombatofthenorth
07-22-2016, 11:43 PM
My original designation by FTDNA was R-M198, which is equivalent to my 23andme results R1a1a. At that point geno had a higher resolution R-Z94.

On 1/09/16 FTDNA Y111 placed me at R-Z93. On 2/04/16 FTDNA Backbone pack put me at my present designation R-Y15121. Yes, FTDNA can give you better resolution if you do the additional testing.

Also, did full mt at FTDNA resulting in J1c. Lick verified results. My test at geno was my attempt to establish ancestry, my mtdna results were not necessary for me at that point. My results for geno 2 were deeper for both mtdna and YDNA when comparing to FTDNA without additional tests. I assume it is not the case for all.

What do you mean by you took the full mt at FTDNA? You mean the mtDNA full sequence? It would be a bit weird if you took that full sequence and ran the data with Lick and got a lower result. What did the Lick results say, any no calls on sub j1c SNPs? (does full sequence mtDNA even get no calls or do they, hopefully, make sure there are none?)

And when you get j1c4 is that what Geno shows on their page or is that just what the FTDNA transfer shows in the FTDNA page?

ArmandoR1b
07-23-2016, 11:34 AM
That's a weird point though since how does testing with Geno 2.0 NG instead of FamilyFinder prevent additional haplo testing? It even lets you directly buy a SNP pack without needing a Y-STR test first (although some will want Y-STR anyway or to go YSTR and then BigY).

It's not weird at all since the money towards Geno 2+ would be better used at FTDNA for a more precise and more recent SNP. Very little is gained with Geno 2+ testing over additional FTDNA testing.


Why not? At FTDNA you never get the nice presentation of the haplogroup results and walk out of Africa (you do a touch at FTDNA but it's pretty poor compared to the Geno 2.0 presentation) and nothing about starting with Geno 2.0 NG prevents using the option of a later higher resolution FTDNA test!

I don't care much for a "nice presentation of the haplogroup results and walk out of Africa" because we have ancient DNA to show which haplogroups and subclades have been found where and when, and a compiled list at http://www.ancestraljourneys.org/ancientdna.shtml, and academic studies of regions that show which haplogroups have been found where and at which percentage and I don't think many other people are willing to spend extra money almost solely for that "nice presentation". Starting with Geno 2.0 NG and then testing with FDNA just means more money spent in the end and without more precise results, no raw Y-DNA without a transfer, unreliable raw Y-DNA data after a transfer, incomplete mtDNA raw DNA, and many times more confusion or frustration or even misleading statements such as the one directly from Geno 2+ staff that the reason the customer has a different subclade than the FTDNA FMS test is because of a different phylotree. Geno 2+ staff didn't even bother to explain the defining mutations found in Geno 2+ for the J1c4 subclade or ask the customer to look at the FMS results and at the different phlylotrees. The cons of spending the money with Geno 2+ instead of FTDNA far outweigh the pros which are subjective.

Amerijoe
07-23-2016, 05:44 PM
Full mt, what would have happened if I called it the Full Mommy, banishment? I'm sorry for the error in terminology, but I suffer from a genetic defect known as speed thinking, resulting in shortened and incorrect terminology. My whole family suffers from it. Must be in the jeans, see what I mean?

I do appreciate all your help concerning the Geno debacle, but I am still working on it and hope for results shortly. Would I recommend Geno as a go to testing company, absolutely not, but for me it helped verify my haplogroups. Due to the absence of verifiable personal genealogy, I took the logical approach to test with most of them. Each company offers different testing protocol and some specialty testing as well. The differing protocols result in speculative analyses which should be considered in your search.

Each of us are unique with unique quests. Research as much as you can on the different DNA tests and testing companies. Once you feel comfortable with it, your path should become apparent.

wombatofthenorth
07-24-2016, 04:07 AM
It's not weird at all since the money towards Geno 2+ would be better used at FTDNA for a more precise and more recent SNP. Very little is gained with Geno 2+ testing over additional FTDNA testing.


That depends. I still say Geno 2.0 NG is the nicer starting point. It gives people a nice haplogroup start with the best presentation of it of any of the companies. For some people it's enough or it may be some time before they get enough money for the advanced full mtDNA and/or STR111 or BigY (the latter in particular is many hundreds of dollars plus an expensive STR test required first). And I think it leaves people a lot less confused than MyOrigins where people get results and are given zero context over what they mean, misleading maps, etc.

If you just want matching then FamilyFinder is more cost effective though.




I don't care much for a "nice presentation of the haplogroup results and walk out of Africa" because we have ancient DNA to show which haplogroups and subclades have been found where and when, and a compiled list at http://www.ancestraljourneys.org/ancientdna.shtml, and academic studies of regions that show which haplogroups have been found where and at which percentage and I don't think many other people are willing to spend extra money almost solely for that "nice presentation".


that depends and the link you provide gives very, very different info



Starting with Geno 2.0 NG and then testing with FDNA just means more money spent in the end and without more precise results,


That depends for some it may be enough and there may be no more money spent in which case it's actual less money since FamilyFinder but basic mtDNA plus STR+SNP packs totals up more money.
If someone doesn't care about presentation or any context to MyOrigins or anything and just wants the most complete mtDNA and Y info then yes it is just more money spent in the end and some time wasted, but that won't be the case for everyone, I'd bet far from it.



no raw Y-DNA without a transfer, unreliable raw Y-DNA data after a transfer, incomplete mtDNA raw DNA,


And with FamilyFinder alone you don't even have any of that at all.

Plus some of the Geno money goes to research while the money for the other tests puts none of it back into field research.

ArmandoR1b
07-25-2016, 11:31 AM
That depends. I still say Geno 2.0 NG is the nicer starting point. It gives people a nice haplogroup start with the best presentation of it of any of the companies. For some people it's enough or it may be some time before they get enough money for the advanced full mtDNA and/or STR111 or BigY (the latter in particular is many hundreds of dollars plus an expensive STR test required first). And I think it leaves people a lot less confused than MyOrigins where people get results and are given zero context over what they mean, misleading maps, etc.


If you just want matching then FamilyFinder is more cost effective though.

So people should be told ahead of time exactly what I have been saying which is if they are not going to spend more than $200, don't care for matching for Y-DNA, mtDNA or autosomal DNA, and want a "nice presentation" to go with Geno 2+. If they are going to end up trying to get closer to their actual terminal SNP, want matching, want access to reliable raw data, less of a need to communicate with the company, haplogroup projects many times with forums, and so on then there is no question that there is no need to go with Geno 2+ first because in the end it is just spending more money.


that depends and the link you provide gives very, very different info
That info is from academic studies. Geno2+ doesn't even publish where they are getting their info from so we have no idea what the sample sizes are or how reliable it is.



If someone doesn't care about presentation or any context to MyOrigins or anything and just wants the most complete mtDNA and Y info then yes it is just more money spent in the end and some time wasted, That's been part of my point all along. Reliable results and matching for Y-DNA, mtDNA and autosomal DNA are also important. Those can't be had without spending extra over what Geno2+ provides. People need to know this ahead of time when possible. They need to know that Geno 2+ is a limited test and there are other options out there with better results if they are willing to spend the extra money.


but that won't be the case for everyone, I'd bet far from it.
I'd bet that more people would be more interested in a more accurate and higher resolution test with matching from get go. Sometimes they don't even know it.


And with FamilyFinder alone you don't even have any of that at all.
So you are missing my point. It's if people want higher resolution results. Not if they only want Family Finder matching and ethnic results.


Plus some of the Geno money goes to research while the money for the other tests puts none of it back into field research.
For some people that is important, but they should also know that they are getting and what they are not getting from the test.

wombatofthenorth
07-27-2016, 10:47 PM
That info is from academic studies. Geno2+ doesn't even publish where they are getting their info from so we have no idea what the sample sizes are or how reliable it is.


My point wasn't that it was contradictory but that it was providing information about entirely different stuff (maybe I didn't find the correct part of the website?).



I'd bet that more people would be more interested in a more accurate and higher resolution test with matching from get go. Sometimes they don't even know it.


Look at the database size for Ancestry, FamilyFinder, Geno 2.0 and they are all huger by an order of magnitude over the size of the full mtDNA database size and it gets even more extreme comparing to BigY, probably getting closer to two orders of magnitude difference. Pushing FamilyFinder as the safest starting place and with Ancestry not bothering with haplos anymore just means that we will get less data on haplogroups. Look at the haplgroup discussion forums here. There hasn't even been a single post in more than a year for some groups since so many just get an Ancestry or FamilyFinder test and never find anything out. At least with 23 and Geno 2.0 including haplos in their basic test, and basic tests are all most people ever end up doing, it gets more data out there.



So you are missing my point. It's if people want higher resolution results.


Yes, if you want the most detailed SNP results you'll need one of the extra tests.
Although some will just want to save money and get the SNPs and not care about anything else, I still think some might not mind having gotten all the background info from Geno 2.0 first so I still wouldn't bash it down so much.