Wednesday, December 12, 2012

My Geno 2.0 Results: Step-by-Step

As much fun as I have had posting and reading about other people's Geno 2.0 results in the last couple of weeks, I have to admit, there's nothing quite like getting my own (finally)!

OVER THIRTY-FIVE THOUSAND SOLD
According to the "infographic" below, I am one of 559,515 Genographic Project participants. (You can access this individualized image through the yellow "Share" button on the top right of the "Your Story" page.)


There were 524,384 participants from Geno 1.0, so judging from this, there are now 35,131 new Geno 2.0 participants. That is certainly a lot and we don't even know if that is the number of kits sold to date or just the number of results being returned now. This means at least 35,131 kits have sold since Geno 2.0's introduction in July of this year. (Pretty awesome!)

MY STORY




















MY MATERNAL LINE
My Geno 2.0 mitochondrial DNA haplogroup is U5b1b2 which is consistent with 23andMe's and mtDNA Community's label for me, while my full mitochondrial sequence at Family Tree DNA designates me as mtDNA Haplogroup U5b1.

If you click on the arrows on your map, you will be walked step by step through the migration pattern of your direct maternal line ancestors, ending with a heatmap of the frequency of your subclade (if available). Of course, being female, I don't have a Y-chromosome to explore, but as part of their results, males also receive their Y-DNA haplogroup subclade (terminal SNP), direct paternal line's migration route and heatmap.

















The next step that is recommended by National Geographic is to "Complete Your Profile" and "Contribute Your Story". These can be accessed through the Profile tab and the Our Story tab respectively, but for the first to be accessible, you need to opt into research participation under Profile > Account Settings. The default is "You are currently not participating", but if you check the box below and click on save...

 
...it changes to this:


Then, under Profile, go to "About Me", "About My Family" and "About My Ethnicity" and fill in the pertinent details.


Next, go to the Our Story tab at the top and you will see this:


If you scroll down below this, you will find this window, where you should enter information about your direct maternal ancestral line. This story should only include information on your mother's mother's mother's (etc...) line. Here's mine:


To see your story and the others that have been contributed, click on the "Read Stories" button on the opposite window under "Browse All Stories".


These are the other participants whose mtDNA haplogroup is U5b and have contributed their stories so far. There aren't very many people tested with mtDNA like mine yet as you can see from the "Universe" graphic above (the big blue circle with the red-orange center). The five dots are people whose mtDNA is most similar to mine.

Just for fun, here is peek at a few of the public Y-DNA stories. See anything interesting?



WHO AM I: AUTOSOMAL DNA AND ADMIXTURE
Next, let's take a look at my autosomal admixture results.


According to this, my admixture includes:
45% Northern European
35% Mediterranean
15% Southwest Asian
2% Northeast Asian

Which places me closest to...


Pretty cool since I am 25% Finnish, which as far as I know, is my biggest chunk of ancestry from any single area. My percentages don't match up exactly by any means. My Mediterranean component is significantly higher and my Northeast Asian component is lower than the typical Finn. The description for this latter component notes "... it is also found at a frequency of 5-10% in the Finns, likely introduced by the migrations of the Saami people from Siberia into Finland over the past 5,000 years." Since only one quarter of my ancestry comes from Finland, this discrepancy makes sense.

But, wait, hold on...


Iberian?! I don't have any known Iberian ancestry. Anyway, it doesn't look to me like I match it all that closely anyway.  (For details on how they reach these conclusions, read my earlier post.)

I'm not sure that this method of trying to match all of a person's ancestry to one population label works well for very admixed individuals like me. My individual components may appear to fit best with these two populations when taken as a whole, but this doesn't account for the mixed ancestry I have from multiple regions.

HOMINID DNA
This part of the test is definitely intriguing although I don't really know what to make of it.


The Neanderthal percentage is very close to my 23andMe Neanderthal result of 2.5%. The Denisovan seems on the higher end compared to other results I have seen, but investigating that will have to wait for another day.

EXPERT OPTIONS: TRANSFERRING AND DOWNLOADING
There seems to be much confusion regarding downloading the raw data file and transferring the results to Family Tree DNA, so I thought I would review the Expert Options section.

To transfer your results to Family Tree DNA, go to the Profile tab and then Expert Options:


Click on "Transfer to FTDNA":


Check the option for Geno 2.0 and enter your NatGeo Kit Number (found on your box and/or Profile> Account Settings> Geno 2.0 ID Code, where you have previously entered it to register). Then, check the box if you have a Family Tree DNA kit and enter your kit number and password as above. Click on "Next". On the next screen, you will be prompted to enter your address and it will look like you are going to be charged, but choose "Invoice" (instead of Credit Card) and keep going. Then, you will receive a screen to review that will show a cost of $0. Place the order and, if successful, you should get this:


and this:


 If you aren't sure if it worked, check your home page for this:


So far my account results don't show anything different, but I already have the mtDNA full sequence, so I'm not sure what would be imported anyway.  Many of the men importing their results are getting an extensive list of Y-SNPs on their Haplotree page like this:


Although importing Geno 2.0 results doesn't delete the results from the SNP testing that was previously performed at FTDNA, it will override what appears on the project pages.

Apparently, there is a delay for some accounts receiving the raw data download option and so far, mine hasn't appeared yet. When it does, it will be located under the "Expert Options" tab, just above the "Transfer Data to Family Tree DNA" option and look like this:


It is downloaded into a CSV file after clicking on the Download button.

I was hoping to be able to check my raw data file to see how my mtDNA heteroplasmy was reported, but apparently that will have to wait for another time. 

LOTS MORE TO COME...
Obviously, I don't have my own Y-DNA results to review, but I have been reading all of the reports from our citizen scientists who are already immersed in investigating those newly released results. I will be sure to report on their findings since this will, undoubtedly, be the area of the most groundbreaking discoveries.

In my next post, I will compare and review my admixture results from all four companies.

[Disclosure: I received a complimentary Geno 2.0 kit from National Geographic for review purposes. This has not affected my opinions or analysis.]

36 comments:

  1. Another very informative post. You are a great teacher!

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  2. I'll be very interested in what you find out about your heteroplasmy since that appears to be the only difference between your mitochondrial line and that of my paternal grandmother.

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  3. Excellent review, as usual, CeCe.

    Charles Acree

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  4. There's nine probes for 6260, so I'm really curious if the heteroplasmy shows up on any of them.

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    1. As you know, Jim, I was finally able to download my results and all probes for 6260 have been removed except one, which did not show my heteroplasmy.

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  5. I look at the migration map of National Geographic and wonder why the route from Europe to the eastern coast of North America isn't shown. There have been archeological discoveries showing the connection. This country wasn't just populated by peoples crossing the Bering Strait.

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    1. The Bering Strait "theory" was based on zero evidence and was discredited by Vine deLoria, Jr.

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  6. Thank-you for the information. I was able to transfer my results to familytree DNA following your instructions.

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  7. Dr. Jim in Springfield, Illinois - My results came back on December 12 as well. Transfer to FTDNA went smoothly and haplogroups updated immediately. I'm also an administrator so I could see it there as well.

    I also do NOT yet see the raw data button, so still something to look forward to. This is exciting.

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    1. An update 12/2/2012 - the raw results appeared in my profile as of today. Let the fun begin :-) --Jim

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  8. Your Geno 2.0 test says you are 3.6% Denisovan, yet from what I understand only Melanesians, Australian Aboriginals and a few nearby populations have Denisovan ancestry. Does this mean you are partially descended from one or more of these populations? If you are not it would seem that either the Geno 2.0 project is giving inaccurate information or those geneticists who claim that the previously mentioned populations are the only ones with Denisovan ancestry are wrong.

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    1. Peter,
      Thanks for your comment. I find this very strange as well. I definitely do not have any ancestry from those regions.
      I think this needs to be looked into further by the NatGeo scientists.
      CeCe

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  9. Your readers should be aware that the Geno test appears to be a disaster as far as Y-DNA SNP testing. I have several different SNPs that totally contradict each other as far as what Haplogroup branch of the tree I should be in. In checking with people at the FTDNA P312 project, several other people are getting SNP results that are the opposite of what FTDNA reported for those exact same SNPs. I would advise nobody to upload that data into FTDNA since it may just mess up your results shown there. Also, my Y-DNA Haplogroup that shows up on the Geno website disagrees with what is in the file that I downloaded from them.

    Also, regarding Peter's question about Denisovan ancestry, my results came back with 5.6% Denisovan. My ancestors came over to the USA from the British Isles and Germany . I have zero Melanesian or aboriginal ancestry, so I question whether that test is as messed up as the Y-DNA testing.

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  10. Thanks for your reply Anonymous. Unfortunately there are people in Australia who are ordering the test because they see it as the only one which will be able to prove they have Australian Aboriginal or Melanesian ancestry given that no tests on the market have Australian Aboriginals as a reference population other than DNA Tribes, whose science has been questioned.
    These Australians believe that because only Melanesians and Australian Aboriginals are supposed to have Denisovan ancestry anyone who does not have such ancestry should have a zero come up in their Denisovan results, and if they do not get a zero it would be proof that they have a recent Australian Aboriginal or Melanesian ancestor.
    Yet the fact that many people such as yourself have positive results for Denisovan ancestry, . even though you know you do not have Australian or Melanesian ancestry, it makes the test worthless in regard to what people with Australian Aboriginal ancestry are looking for.
    As I have said, this means that either the Geno 2.0 Denisovan test is inaccurate and worthless or they have found a way of proving that persons other than Australian Aboriginals and Melanesians have Denisovan ancestry. If the latter is true I wonder if they have issued a press release announcing their discovery, because if they have I have read nothing about it, and I would have expected such an announcement would have made headlines internationally!

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    1. Peter, I was thinking the same thing about the fact that if these numbers are correct, it is quite a discovery on the part of NatGeo! You would think someone would have officially commented on it by now.
      CeCe

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    2. Thanks CeCe. I wonder if someone from NatGeo who may be reading this forum could clear the Denisovan matter up for us by either admitting that their test is inaccurate or announcing they have made a breakthrough and that many populations other than Melanesians and Australian Aboriginals also have Denisovan ancestry. Several people other than myself are having the test done for the sole purpose of proving they have Australian Aboriginal ancestry, and they are doing so as a result of my recommendation.
      However, because this forum has shown that persons such as yourself and Anonymous, who are without Aboriginal or Melanesian ancestry, also have Denisovan ancestry according to the Geno 2.o test, I now have egg on my face as I have assisted these folk in wasting their hard-earned money.

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    3. Interesting to hear of non-Aboriginal, non-Melanesian peoples with such high Denisovan results.

      I have no such heritage that I'm aware of, and my Denisovan result was 0.60%.

      The blurb on the Geno 2.0 site, in the Denisovan section, clearly states:

      "The Denisovan component of your Geno 2.0 results is the most experimental, as we are still working to determine the best way to assess the percentage Denisovan ancestry that you carry. Don’t be surprised if your percentage Denisovan changes over time"

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    4. Interestngly, through yesterday, percentages were not displayed for either my Neanderthal or Denisovan ancestry. After sending an email to customer support, now 2.0% Neanderthal and 2.4% Denisovan ancestry are displayed. My ancestors immigrated from the British Isles and Northern Europe, as my autosomal, mtDNA and Y-DNA results confirm.

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    5. Interestingly, through yesterday, neither my Neanderthal nor my Denisovan ancestry percentages were displayed. After an email to Geno customer support, now 2.0% Neanderthal and an unexpected 2.4% Denisovan are shown. My ancestors immigrated from the British Isles and Northern Europe, and my mtDNA, Y-DNA and autosomal DNA are all consistent with this origin.

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    6. Thanks Craig. The fact that they did not display your Neanderthal and Denisovan percentages and that you had to ask to see them seems to suggest to me that they know they have done the wrong thing by people by not telling them BEFORE they purchased the test that at least the Denisovan component is experimental, and from what I can see, worthless. I have asked them for my money back but have heard nothing from them and I probably won't.
      I was attracted to Geo 2.0 because it is being run by a non-profit organisation. I would however, be interested in knowing if those who work for them in the lab are paid on the volume of tests they process or whether they are on a fixed wage.
      If it's the former it would explain a lot of things. Employing a piece worker, such as a fruit-picker, is okay for the farmer because he can see what's in the worker's bucket, but when it comes to something like DNA tests the incentive for a piece worker to do things in a hurry at the expense of doing the right thing by the customer is enormous, and unlike the farmer who can directly view the content of the bucket we cannot oversee or check how the tests are performed.

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    7. As far as I know the Denisova cave is in Siberia, far away from Australia or Melanesia, so it seems absurd to me if the Denisovan component should be a clear sign of aboriginal ancestry. By the way, even "Oceanian admixture" is sometimes found in smaller amounts amoung Fennoscandians and other Northeuropeans without Oceanian ancestry. It's probably something very old and hitherto unknown. Look here:
      http://eurogenes.blogspot.fi/2013/11/first-genome-of-upper-paleolithic-human.html

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  11. CeCe

    Most of the people taking DNA tests at 23andme really don't know or are oblivious to how they make money off of us. See: http://www.theglobeandmail.com/news/national/time-to-lead/the-dna-dilemma-why-science-wants-your-genome/article5921666/

    Do you condone that type of activity at 23andme (where you are an Ambassador) or do you prefer more non-medical organzations such as National Geographic and their Geno 2.0?

    Pharma:
    For drug companies, today's genetic discoveries are paving the way for the treatments of tomorrow. But the era of personalized drugs custom-made to treat your cancer (or your baldness) hasn't arrived yet. Common conditions such as heart disease, diabetes, asthma and depression involve a complex web of many genes and environmental influences; these genes and the roles they play are still being identified. It may be that drugs of the future will be designed to target a number of different mutations involved in the same disease – which drug you're prescribed will depend on your DNA.

    That's why pharma giants are seeking partnerships with DNA testing companies, such as the California-based 23andMe, which recently forged a partnership with Genentech to leverage its database of genetic profiles.

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    1. First of all, I don't think 23andMe is profitable yet, so your main supposition is wrong. They aren't "making money off of us". At least, not yet.
      Secondly, yes I am supportive of crowd sourcing to increase the speed of life-saving discoveries in genetic medicine. Since my father suffered and died of Parkinson's Disease, I fully support and applaud 23andMe's research efforts. The quote that you posted here is all good news to those of us who hope to have more effective treatments for common diseases before we suffer from them. I sincerely wonder how that can be misconstrued as a negative. I, for one, fill out all 23andWe surveys and will continue to do so because that is my small contribution to the cause.
      Third, if a person chooses to opt out of 23andWe research and to forgo filling out the surveys, then their DNA is useless to 23andMe. As a result, the paranoid among us have options.
      Fourth, you cite my 23andMe Ambassadorship as if it is an accusation. I am very proud of that title and my relationship with 23andMe.
      Thank you for your comment,
      CeCe

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  12. Interesting to hear of non-Aboriginal, non-Melanesian peoples with such high Denisovan results.

    I have no such heritage that I'm aware of, and my Denisovan result was 0.60%.

    I noticed the following statement in the Denisovan results section of the Geno 2.0 results:

    "The Denisovan component of your Geno 2.0 results is the most experimental, as we are still working to determine the best way to assess the percentage Denisovan ancestry that you carry. Don’t be surprised if your percentage Denisovan changes over time"

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  13. Thanks for that octoberlady; I looked for the information re the Denisovan tests you just provided prior to paying for the test and could not find it, which would obviously be because I had no results and as such could not get access to the results section.

    It’s a bit late them telling us the Denisovan test is experimental AFTER we have paid for it. Surely they had a moral if not legal obligation to tell us BEFORE they took our money?

    Had I have known the info you gave re Denisovans from the results section existed I would not have paid for the test; nor would those other Australians who have done so with the objective of proving they have indigenous Australian or Melanesian ancestry, some of whom have done so upon my recommendation. I feel like I've been ripped off.

    I’m sick of companies not including as many populations as possible (such as that of Australian Aboriginals) in their reference populations. It’s a form of discrimination which cannot be excused as it would not be difficult for them to get samples; nor would it be too expensive. The only exception is DNA Tribes, but I question their science.

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  14. Has anyone been able to make sense of the mtDNA data downloaded from Geno 2.0?

    My mtDNA data from 23andMe are understandable. However, at least the mtDNA portion of the data downloaded from Geno does not make much sense. The data is reported in the csv format nnnnn,mt,N,N, wherein nnnnn is an integer up to 16527, and N is a DNA base C, A, T or G. Why (the same) N is duplicated in each entry is not clear. Furthermore, while nnnnn would be presumed to be mtDNA base number, the reported bases often do not match the CRS or my mtDNA according to 23andMe. Finally, many of the nnnnn values are repeated, often with the same N, but sometimes with different N.

    To provide just one example, 23andMe reports my mtDNA has G at position 750 in contrast to A in the CRS. The data from Geno lists 750 no fewer than 9 times. 6 occurrences are "G,G", and 3 occurrences are "C,C".

    The Geno results tend to intermingle complementary base pairs, e.g., C & G and A & T, suggesting that bases from both DNA strands are being reported. But then how can one determine, for example, whether a G is merely on the complementary strand rather than a SNP from C to G?

    Has the Genographics project published a user guide to explain how to interpret downloaded results?

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    1. Thanks Craig. I have on several posts set out why I believe the Geno project seems to be doing the wrong thing by us in regard to the Denisovan component. Another poster has argued that the Y component is in a mess and now you have explained some problems, as you see it, within the mtDNA section.
      So far we have heard nothing from anyone representing the Geno project, and because of this they are looking really bad.
      I would be grateful if our Genetic Genealogist, whose work I greatly admire, could contact the Geno folk and tell them they are copping a lot of criticism on her forum and that she would love to give them the right of reply.

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    2. I have gotten two Geno mtdna profiles in the last few months, and the problems still exist. They are apparently mtdna loci in the SNP column, as mentioned, but even assuming RSRS and the complementary value of the RSRS locus as opposed to the values reported by Geno, they both chart out as a peculiar branch of W3a1, which is unlikely and indicates there is no correlation between the results reported and the actual situation (except perhaps at top-level loci down to the Haplogroup level....?? Has anyone at National Geo or FTDNA ever clarified this situation....?

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  15. In looking at the results further, it appears that the seemingly unnecessarily repetitive N,N format for mtDNA is intended to accommodate the diploid autosomal DNA also included in the download file, because genes on the two chromosomes may have different base pairs. For mtDNA, the N,N format could also be used to report heteroplasmy, although this could be also reported using duplicate lines for a position.

    The apparent intermingling of complementary base pairs, e.g., C & G and A & T from the two mtDNA strands still is confusing, particularly as this does not allow identifying C/G or A/T polymorphism. If Geno is going to report bases from both mtDNA strands, they need to be distinguished, e.g., by specifying formats nnnnn,mt-L,N,N and nnnnn,mt-H,N,N, wherein "mt-L" denotes the so-called "light" strand and "mt-H" denotes the so-called "heavy" strand.

    For further visibility -- hopefully to the Geno staff, I may post a modified version of these comments on the Yahoo DNA-NEWBIE list.

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  16. I got 3.3 Neanderthal and 3.6 Denisovan. My ancestresses liked their men primal I guess. :)

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  17. hmm, I am guessing it doesnt take into consideration of migrations from wars or other circumstances in Europe. For Example as far as I know I am Spanish/Colombian/Dutch/German. The Spanish at one time occupied Holland. One of my Dutch ancestors could have been Spanish. Dont quote me on the history, I am not an expert. I guess I'm doing a little research to see if this is worth my 200$. What do you think?

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  18. Have a good read of the posts Reuben and think carefully before you spend your money.

    Sometimes people who are in opposition to certain products that are being sold on the net put in fake posts in order to give the said products a bad name. But in the case of this product the critical posts have raised legitimate questions based on what can be actually seen and questioned. And so far we have had nobody from Geno, or anybody else for that matter, having written back opposing these posts and defending the Geno procedures or the way they have marketed their product.

    I don’t have the expertise to defend other critical posts, but I am happy to clarify my criticisms regarding their Denisovan testing procedure and how they have, in my opinion, been misleading in that respect. The Geno folk have been made aware of this forum and the criticisms they have received on it, and the longer they go without posting a defence the worse they look.

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  19. I would like to say I was thinking of saving up the $200 to try the testing, but most of my interest is purely recreational. I know I have some Native American, but the amount varies from family member to family member, and I would like to know what my actual ancestry IS.

    After reading all of you comments about the misinterpretations of the Geno 2.0, I will say I am second-guessing my faith in the test.

    If anyone has a suggestion for a good test for me to get that would give a relatively accurate reading of my overall ancestry, I would greatly appreciate the help.

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    1. Hi Regina,
      I would recommend 23andMe for detecting relatively small amounts of Native American. Their Ancestry Composition is considered to be the most accurate "ethnic" breakdown.
      CeCe

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