Friday, November 30, 2012

More on Geno 2.0: Third Party Resources and Images from a Second Set of Results

It turns out that an additional correspondent of mine received her National Geographic Geno 2.0 results in the last batch and she has kindly given me permission to share them. I have also received word that several third party tools are ready to accept GenoChip (Geno 2.0) raw data.

THIRD PARTY TOOLS
Mitochondrial DNA researcher James Lick's mthap tool (mtDNA haplogroup predictor) is now capable of processing the new GenoChip raw data. In fact, his tool returns an even more detailed subclade for the K1a1b1 result (shown below) than Geno 2.0 currently reports (K1a1b1f). This was also true for a K1 sample that was extended to K1e with Jim's tool.

Happily, reversing his earlier statements, Dr. Doug McDonald has successfully adapted his admixture analysis program to be able to work with the Geno 2.0 files. However, as expected, he reported that the results are inferior when compared to using 23andMe and Family Finder files due to the lower number of SNPs that he is able to incorporate in his program.

Dienekes announced today that he has created a converter to run Geno 2.0 files on his DIYDodecad tool.

After working with a raw data file, Mike Cariaso, cofounder of SNPedia, tells me that versions of Promethease 0.1.149 and later will be able to read the Geno 2.0 files directly.

Leon Kull reports that he is accepting Geno 2.0 files for inclusion in his HIR Search autosomal DNA matching database.

Y-DNA researcher David Reynolds compiled a list of Y-SNPs on the GenoChip from the raw data file. He explains on the ISOGG Facebook page, "While we don't know the exact location yet of most of the 12,000+ (e.g., the CTS, F, PF SNPs), this will answer the questions about which DF/L/Z etc SNPs are included."

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).

Dr. Ann Turner (we all know who she is and needs no introduction from me!) has informed me that she is ready to share the spreadsheet method that she has been working on to facilitate Geno 2.0 raw data usage with third party applications. She tells me, "GenoConvertTemplate.xlsm contains a macro to convert the GenoChip raw data download to the format used by 23andMe, which many 3rd party utilities can handle. It uses Build 37 numbers for the chromosomal locations of the SNPs." She would like to test it with additional Geno 2.0 data files, especially from people who have also tested at 23andMe and are willing to share both files with her. Please contact Ann directly for access or to donate your raw data (you can write to me for her email address if you don't have it).

Mitochondrial DNA researcher and mtDNA Haplogroup K Project administrator  Bill Hurst has spent quite a bit of time examining the data as well. After working with two files, he commented (in agreement with Jim Lick) that so far he "was impressed by the full coverage of the test, even while testing only 19% of the mtDNA."

I had full confidence that our amazing community of researchers/citizen scientists would come through for us and they have, even more quickly than imagined! Thank you to all those who have contributed so far to this groundbreaking project. (There's a long way to go yet!) I would be remiss if I didn't note that this expedient work could not have happened without the generosity of both Sharon and Anna in sharing their early data. Thanks go out to both of them from all of the community!

The researchers listed above are still looking to examine more raw data files, so if anyone reading this has received their results and would like to contribute to the cause, please contact me or any of the researchers directly. If you have a third party tool that is accepting Geno 2.0 raw data and is not listed, please comment below or email me to be added. I will continue to update this list as I receive more info, so please check back periodically.

**To access your Geno 2.0 raw data for use with these tools, go to "Expert Options" under the Profile tab and download the .CSV file to your desktop.**


MORE RESULTS FROM GENO 2.0:

YOUR MATERNAL LINE
Here are the newest set of mtDNA results:























WHO AM I?
These are her autosomal results:

Note: Clicking on a percentage brings up information about that population
National Geographic has recently clarified that the matching reference populations listed as first and second (shown in this screen shot) are not in order of closest matching, but simply the top two.

Interestingly, her Denisovan ancestry component is significantly lower than the other account that I reviewed.



OUR STORY
It looks like there are a few more "stories" in the community section now:


There are a total of 30 as of today (more than when I looked yesterday!).


TRANSFERS
I tried to transfer her data to Family Tree DNA (found in Expert Options under the "Download Data" button),


but I got this:

"The kit you entered already has a Population Finder, new PopFinder data cannot be transferred"

It appears that if you already have a Family Finder test from FTDNA (which includes the Population Finder feature), then you cannot transfer your Geno 2.0 results at this time. I'm surprised by this since Family Finder (PopFinder) and Geno 2.0 are very different products. Further, this customer does not have a mtDNA test in her FTDNA account, so she should be able to transfer her mtDNA results at the very least. One project administrator has already reported that a woman has transferred her results into an FTDNA Project, so contrary to earlier reports, women are not automatically blocked from transferring their Geno 2.0 results to FTDNA. I'm quite confident that National Geographic or FTDNA will clarify this issue for us soon.

MORE TO COME...
I'm sure this will be only one of my many future posts on Geno 2.0, so stay tuned.

14 comments:

  1. I can do comparisons of Y-Data between kits just to flag the differences. I'm assuming at this point that for the Y-Data, columns D and E will be identical.

    David

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  2. "One project administrator has already reported that a woman has transferred her results into an FTDNA Project, so contrary to earlier reports, women are not automatically blocked from transferring their Geno 2.0 results to FTDNA."

    That was an mtDNA K transfer. The odd thing is that no results were actually transferred. No autosomal; no mtDNA. She has a blank FTDNA personal page with an "N" series kit number. She can order any FTDNA test, of course.

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    Replies
    1. Thanks for the clarification and additional information, Bill. By the time I wrote this it was much too late to ask you if I could say it came from you so I just anonymized it to be safe! ;-)

      Delete
  3. My question is: Where is the community section at? I've been looking for it but can't find it.

    ReplyDelete
  4. Thank you, I'll look for it.

    ReplyDelete
  5. Scroll down to >> Browse All Stories >> click on Read Stories

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  6. Well, I tried to look for it. I did not see Browse All Stories. I did read you are able to participate if you create your profile, which I did. But there was no link to any community pages. The only have About, Check your Results, Profile under setting, News etc. No tab for Our Story either. I'm referring to their website, unless you are referring to Facebook?

    Luis

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    Replies
    1. Hi Luis,
      No, I am referring to the website. You must need to have your results to access it at this time. Perhaps that will change as we progress.
      CeCe

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  7. Does anyone know if the result pages print as seen on screen, or has the Nat. Geo. web team designed a printable version? I ask because I'd like to print my elderly father's results (when they are available), to make it easier for him to review. Many times printing a screen version is not optimal.

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    Replies
    1. I don't know, but that is a good question. I did not see the option anywhere. Perhaps they will add it. You should email them with the question/suggestions.
      Thanks!

      Delete
  8. Thank you CeCe for this great and very infomative article. Please continue sharing all the Geno 2.0 information you get with us !

    One remark though. Your comment about Dr McDonald is a bit misleading. From what he posted on the Rootsweb genealogy-dna mailing list I understood that at the moment, what he is able to do is use his current program with Geno 2.0 files, and so only use the 57785 markers the Genochip shares with FF/23andme chips, and none of the new Genochip SNPs. Under those conditions it is perfectly normal for the results to be inferior. They may not be so when he is able to take advantage of all the new AIMs of the Genochip...

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    Replies
    1. Good point, Itai. Thanks for the clarification.
      CeCe

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  9. Thank you, CeCe.

    That's what came to my mind after I wrote my last comment. I'll wait for my results.

    Luis

    ReplyDelete