Ancestry Modifies Their Autosomal DNA Chip

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For today’s consumer, this isn’t really much of a story, although it may be someday.

Ancestry published an article in their blog this week announcing that they have begun testing on a new AncestryDNA chip.

Currently, Ancestry uses the standard Illumina chip also used by Family Tree DNA which also functions as the base chip for the 23andMe product as well. 23andMe has a chip customized for medical testing, and Ancestry is now following suit as well with their new chip, soon to go into production.

The Illumina chip today holds roughly 700,000 locations, or SNPs that can be reported. Ancestry’s download today provides customers with roughly 682,000 locations, as compared to 23andMe’s 577,000 and Family Tree DNA’s roughly 690,000.

However, Ancestry is trading in some 300,000 of those SNPs currently on the standard chip and replacing them with new SNPs optimized for medical and ethnicity testing in addition to replacing some “low performing” locations with alternate locations. They couldn’t provide a breakdown in terms of percentages of how many are for medical, ethnicity or other SNPs.

What Does This Change Mean For You?

Today, nothing at all, according to Ancestry.

I asked if Ancestry had tested their clients who have tested on the new chip against the same client’s results from the current, soon to be, old chip – and Ancestry said they showed exactly the same matches.

So, the chip is backwards compatible in that the new chip will still provide matches to the old chip.

The difference may come in the future when more people have tested on the new chip. Only time will tell if those people will receive more and better matching with other people that have tested on the new chip.

Ancestry indicated that if they feel their clients need to update their test at some point in the future, then they will put together a plan – but until then, if then, there’s nothing to worry about.

Should You Retest?

Obviously the bloggers group wondered about this. If you retest today, you’ll have to handle both tests separately in your account.  There is currently no way to merge tests, so you’ll have an old one and a new one.  There is no “best of both worlds.”  There is no way to preserve stars or notes or anything you may have done to one account and transfer to a different account.  About the only thing you could do is, in time, to compare to see if you continue to have the same matches on both chips as more people test on the new chip.

Why The Change?

Ancestry was very clear that the changes today are really for future development and will have no effect on current accounts or matching. They are evaluating their future position in the medical arena.  With last June’s announcement of Ancestry Health, they have very clearly been sticking their toes in that water.  They hired Dr. Cathy Petti last July as well, an MD functioning a Chief Health Officer.

I’m not sure if this means Ancestry will one day offer health services to clients, similar to 23andMe, or whether it means that the firms they are currently or want to sell the DNA data to want more health related information, or perhaps both.  We will just have to wait and see.  Clearly they wouldn’t even be discussing this publicly and laying groundwork if they weren’t planning to do something!

Will You Still Be Able to Download?

Yes, your autosomal data file will be downloadable, just like it is today.

Will You Still Be Able to Upload to Family Tree DNA and GedMatch?

That of course will depend on those vendors making the necessarily format changes. This would be similar to the different vendors’ files being compared to each other today.  Comparing one vendor to another isn’t quite as good as comparing each vendor to its own files, but the matches are still good and it’s still a darned site better than nothing.

Both Family Tree DNA and GedMatch will need to see the new file formats first and have some time to work with them. We don’t know if quality of matching will be an issue given that nearly half of the SNPs are being replaced – but until we hear otherwise from either company, I’d presume that they will make every effort to accommodate the new file structure.

When Is The Change Being Made?

The new chips are arriving next week, but Ancestry will be running on dual platforms for a little while yet during the changeover. There really won’t be any external way to tell if your test was performed on a new (v2) or old (v1) chip – so if you want the new chip – wait just awhile to order to be sure the new chip is in full production first.


Ancestry’s change, to clients today, is superficial.  Your matching will still function. You don’t need to retest, unless you are simply curious. If you do want to retest, wait a few weeks to be sure the new test is completely in production – and remember, you’ll be managing two kits separately, so everyone will be asking you about you and your twin that they match.  I’m sure there will be a number of curious people who will test on both platforms.

These chip changes are for future development – and we’ll just have to wait for the future to see what those new developments might be.



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56 thoughts on “Ancestry Modifies Their Autosomal DNA Chip

  1. Just another roadblock thrown up by Ancestry to keep us from figuring out for ourselves who we match and where. They know GEDmatch will be slow to develop matching formulas for the new chip, so any close matches adoptees get from Ancestry will become useless until the problems are worked out.

    No doubt, they’re going to sell the new medical information, it’s all about cash flow at Ancestry.

  2. And just today I was asked to take a survey which seemed to be fishing for what I do with my raw data download. I pretty much told them they have no tools for me to use so my data has to go elsewhere, where is none of your business. They had Gedmatch and Family Tree as options.

      • I know 23 was another option I can’t recall if that one was there or not. Some other questions where how easy is it to download the raw data, why you download, where do you put the downloaded information. Choices were to get segment information or to use a chromosome browser. Next time I’ll take better notes! 🙂

      • I had that survey, too, but I don’t remember what the questions were. I did tell them we needed a chromosome browser.

      • Today I had a survey popup that was similar but did have some different questions from the one a couple weeks ago. One of the (new) questions was which additional tools/features have you used and the answers were segment matching comparison, ethnicity mapping, medical/health genetic evaluation, chromosome browser and lastly other with a box to type response. I took screenshots of each question if you are interested.

  3. Its all about information gathering, big brother, new world order, biogenetic warfare, pay offs or they call it foreign aid, continuity of government, that’s all.

  4. So we have Ancestry raking in the $$ selling our medical information while poor little GedMatch has to scramble to make Ancestry’s data compatible with everyone else. GRRRRR

    And if you really think you will be getting better matches, I have some nice ocean front property in south-eastern CO I can sell you.

  5. After reading the information that the “sell the DNA data” link above takes us to, I’m feeling REALLY uncomfortable with having given mine under the really naive assumption that it was all for the purpose of genealogy. Yeah, right! And it won’t make a bit of difference if I go in and delete my DNA file on Ancestry because I’m no longer either naive enough or stupid enough to believe that it’s not backed up more than once! And how many companies have it now? Welcome to the big bucks genealogy world!

  6. Has Ancestry cleared this with the FDA like 23andMe had to?

    Who are they going to sell the medical data to?

    What if I don’t want Ancestry to include my medical info?

    So many questions!

    P. Adamson

  7. Fewer genealogical samples will bring poorer matching. It’s all about the medical business. Any way we can leverage a customer revolt to at least get chromosome data?

  8. I have a kit that I ordered when they had a sale. For future use. Will it make a difference if I don’t collect it until after the new chip goes into use? In other words will the collection be the same?
    I too got the survey about my data.

  9. What happens to tests we haven’t sent in yet, on old chip or new? Or obsolete?

    Sent from my iPhone so please excuse typos and any bad proofing! Very small screen. 👀


    • Not obsolete. If you sent them right now, they could be on either platform. I’d wait a month or so (or maybe a little more) and then they would be on the new platform.

      • Unless you want to be able to upload your Ancestry results to FamilyTreeDNA and/or Gedmatch right away (or maybe at all), in which case you might want to send it in ASAP.

    • Based on the discussions, and I’m extrapolating here, not quoting Ancestry, I would say not anytime really soon. They have been focused on this chip change and the algorithm change, for now. I do know they are still planning on an ethnicity update.

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  11. Ancestry is Beta testing now and they tripled my possible ancestors. Interestingly one was my great grandfather. His second wife (my great grandmother) was already a match. Seems like they are using the genealogy of families as much as matching DNA, since none of the others had my grandmother listed as a family member. Also most had the wrong parents for my ggfather.
    . I did find one other new connection, same family, but on the maternal side. Maybe this chip will help other people more.
    My Heritage is asking for DNA results to be uploaded. Copying GedMatch?

  12. I’ve worked and worked on the two I’ve had for a long and can find no connection. I do have an NPE six or seven generatons back, though. One of the new ones is the son of a first cousin five times removed, so we probably do share DNA. If they had the parents of this first cousin five times removed in their tree, they should go to the DNA circle, which is a large circle. The wife of this NAD is also listed as a NAD and I have no genetic connection to her. I haven’t really looked at the rest of them, but nothing jumps out. Plus, I just got a new one … 23 now.

  13. Found another one! I am related to five of the twelve people on this NAD’s circle. Those five people are all closely related to each other and are related to me as fourth cousins and fourth cousins once removed. However, our relationship is on different line than the NAD. They do not have their trees back as far as our common ancestors.

  14. I just got my results back and it was done with the new V2.0 chip. The amount of the SNP’s is almost the same as before. It’s almost 670.000.

    It works well with gedmatch, livewello and promethease. Actually I’m pretty surprised about the amount of data on promethease. With 23andme I had over 20.000 results, ancestry v1.0 usually had over 10.000 results and with the new ancestry v2.0 chip I have over 40.000 results! That’s twice as much as with 23andme.

      • It says it in the raw data file – v2.0. Yes, I was very surprised about the amount of medical related SNP’s. In fact it’s nearly 48.000 on promethease.

        Unfortunately I wasn’t able to transfer my raw data to FTDNA. The upload tool on FTDNA keeps saying that it’s only compatible with 23andme v3 and – liars :-)))

        Ancestry received my kit May 2nd and started to process it in the lab on May 18th.

      • Here a few more info on the new chip:

        Total SNP’s: 668.942
        Autosomal: 637.639
        Number of Y chromosome SNPS: 1.691
        Number of X chromosome SNPS: 28.892
        Number of mtDNA: 195

    • Someone sent me a list of the 195 mtDNA SNPs. They do not include any SNPs in the HVR, and the coding region chips seem to be selected for medical significance. They are not useful for assigning haplogroups.

  15. I downloaded a relative’s raw results from Ancestry today and with his permission attempted to upload to gedmatch (successfully) and FTDNA (unsuccessfully). The error message reads, “We only accept autosomal raw data files from Ancestry DNA & 23andMe V3 (sold from about Jan 2011 to Oct 2013).”
    So am I correct in assuming that the Ancestry chip has changed? How can we find out if the upload will eventually be possible? Their customer service is useless. Thanks for any guidance you might be able to give me.

  16. I had the same problem as “Pat M.”and “S O” above. I *just* got my AncestryDNA results back and tried to upload them to FTDNA and I get the same error message “We only accept autosomal raw data files from Ancestry DNA and 23andMe V3 (sold from about Jan 2011 to Oct 2013).” Ancestry received my sample May 2, started processing it May 14 and the results were available May 31st.

    I guess this means my data was processed on the new platform. I wonder if this applies to another test for family that I sent in and had processed on exactly the same days. I’m reluctant to try to upload their results to find out though because FTDNA definitely uploaded and is sitting on my data even though the error message popped up after the fact. I sent their customer service a message asking them to please advise what they plan to do with my data (try to process it or if they can’t) because I DEFINITELY do not want them holding onto my raw data if they can’t process it. I’m hoping I hear back. I noticed on their support forum that other people just started having this problem as well. Thanks in advance for any guidance or insight you might be able to share.

  17. Update- FTDNA’s customer service just sent me this response:

    “There is a current known issue that stops participants from successfully uploading their AncestryDNA data. Our IT team is aware of this and is working on a fix. There is no current ETA on the completion, but it is high priority. I appreciate your continued patience.”

    I guess I’ll just sit tight…

  18. That explains it. I got my file yesterday and ftDNA wouldn’t accept it. I saw the header and the V2 marker but didn’t know when the switchover was. I’m not holding my breath though.

  19. Does anybody have v2 results they are willing to share with me? You can remove personal data by search and replacing all ‘A’, ‘C’, ‘T’, ‘G’ with blanks. I’m interested in determing how much overlap the new v2 results have with 23andme v3, v4 and FTDNA. I will gladly share the results once calculated. Unless someone is one step ahead of me and has already done this and is willing to share? 🙂

      • HI Sebastian,

        I have figured out some of the answers to my question. There is a discussion in the GEDmatch forums if anyone is interested:

        To give an overview, what I’ve found is this:

        “Here is what I can come up with for chr 1 to 22 SNPs:
        Total: 638k (-45k from v1)

        comm with v1: 408k
        comm with 23andMe v3: 437k (-223k)
        comm with 23andMe v4: 308k (+7k)
        comm with FTDNA: 410k (-260k)

        Novel SNPs between the all the above:

        AncestryDNA v1: < 1k
        AncestryDNA v2: 180k
        23andMe v3: 44k
        23andMe v4: 67k"

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  21. Starting to test my oldest relatives and have a sibling, parent, and myself on ancestry. Should I be testing both Ancestry (v2 which is my sibling and parent’s kits) and FTDNA for my oldest relatives?

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