Mitochondrial DNA Results from the Big Y Test

Say what? Mitochondrial results from a Y DNA test? You must be kidding? It’s April Fool’s Day, right???

“Not funny,” you say…

Keep reading:)

Felix’s Thought Logs, by Felix Chandrakumar, a software engineer from Australia, ran a nice article about the deliverable report from a company called YFull that does an analysis of the output of the fully sequenced Y chromosome files from either Family Tree DNA (Big Y) or Full Genomes (Full Y). I did find this report very interesting, but having said this, I would NOT go so far as to recommend this service. It’s free, and I know that’s enticing, but there really is no such thing as a free lunch.

YFull lists no terms of service. What are they doing with the DNA results, other than analyzing them for you? Are they also processing or retaining them in some other manner, for something else? There has to be a benefit of some sort to YFull, and they don’t tell us what that is. You can read more about YFull here. The YFull service is located in Moscow, Russia.

Until I fully understand what is being done with the files and results, I certainly will never recommend anyone send files to an unknown foreign entity under uncertain circumstances. Furthermore, Russia is outside the legal reach of people in the US if a dispute arises. There is no available recourse. Looking at the owners, and the websites they are involved with, are the DNA results being incorporated into those sites? Again, without terms of service and full disclosure, as consumers, we have no way of knowing.

Now that we have that housekeeping out of the way, let’s take a look at a very unusual report.

When reviewing Felix’s YFull results, I was very surprised to notice one screen in particular – his mitochondrial DNA.

Felix mito

This, of course, begs the question of how, on a Y chromosome test, can one obtain mitochondrial DNA results? To the best of my knowledge, there is no mitochondria on the Y chromosome.

mito y nucleus

In fact, the mitochondrial isn’t even in the cell nucleus with the X and Y chromosomes – it’s outside. So, how can the Y test be returning mitochondrial results?

I turned to Dr. David Mittelman, PhD, geneticist and Chief Scientific Officer for Gene by Gene, parent company of Family Tree DNA for answers.

Dr. Mittelman has been gracious enough to provide insights into how this happens.  See, no April Fools joke afterall!

Q. Dr. Mittelman, can you please confirm that the mitochondrial DNA and the Y chromosome are completely separate entities?

A. The mtDNA and Y chromosome are still separate entities :)

Q. Then how are mitochondrial DNA results being returned in conjunction with the Big Y test?

A. When you perform capture sequencing, you enrich for specific targets (in this case, the Y chromosome) but enrichment means you also get trace amounts of other sequences in the genome.

Q. Are these mitochondrial results high quality? Does the Big Y test cover all 16,569 mitochondrial DNA locations, like the full mitochondrial sequence test?

A.These mitochondrial results do not represent a high quality, high coverage sequence; and it does not give you the full mtDNA sequence — however in many cases you get enough markers to assign a haplogroup. You would probably prefer the complete sequence, however, if you want to use mtDNA for genealogical matching. Furthermore, since these are incidental findings, they are not reported on your mitochondrial page at Family Tree DNA, so no matching is possible. Only the specific mitochondrial tests designed for complete mitochondrial DNA coverage are reported on your personal page as results.

Q. If there are mitochondrial insertions, deletions or heteroplasmies, will the Big Y test be able to “see” those?

A. Yes but again the biggest limitation is coverage. At lower coverage and with fewer high quality reads, it is harder to resolve heteroplasmies and even some insertions and deletions. The BigY does not contain enough information to fully characterize all your variants in your mtDNA sequence, which is why we do not advertise it as such. It is exciting, however, to see that others are trying to extract value from the data. That is a key reason we make the raw data available. We are eager to see what complementary tools and insights other folks come up with.

Q. So, from what you’re saying, it sounds like the Big Y sequencing process may return an indeterminate amount of mitochondrial information, but it should not be relied upon as there is no guarantee that it is accurate or complete. In other words, they are simply incidental findings that are included coincidentally. Haplogroups predicted from this information may be incorrect or incomplete based on the quality or lack thereof of the incidental mtDNA data.

A. Certainly we did not design BigY to return your mtDNA sequence and I have not personally reviewed the accuracy of YFull, but it is possible for some customers to get some bonus mtDNA data. I think to gain more clarity it would be valuable to compare mtDNA data from the BigY to high quality, full mtDNA sequence from the same customers. Comparing that data would tell us more about the accuracy and value.

Following up on Dr. Mittelman’s suggestion, I checked with Felix about the accuracy of his mitochondrial results.

Felix has had his full mitochondrial sequence tested at Family Tree DNA. He reported that the YFull report found all of his 31 mutations, except for one in the coding region, and that another mutation, 315.1 was reported as 310. His haplogroup is accurate, but if some of the mutations missed were haplogroup defining mutations, it certainly could be, and probably would be estimated incorrectly. Not at all bad though, for an incidental freebie!

I want to thank Felix for being gracious enough to allow me to use his mtDNA results and Dr. Mittelman for his insights.

 

10 thoughts on “Mitochondrial DNA Results from the Big Y Test

  1. FTDNA uses NGS to test the complete mtDNA sequence.
    So FTDNA are using the same technology for both BigY and mtDNA.

    I don’t see why there would be a difference in quality.

    • The difference is in the “enrichment” step. If you target the Y, some mtDNA sneaks through, simply because there are thousands of copies for every copy of the Y.

      Felix’s difference at 310 is a difference in nomenclature. They put the C insertion at the beginning of a string of C’s. We’re used to seeing the C insertion presented as 315.1C (which practically everybody has).

  2. Hello,  I am genealogist for the past 40 years.  I am working with a family in Italy and we just got the full sequence back and the Haplo group is H 66.  Is this a rather new Haplo Group as I cannot find hardly anything on this group.  I will probably hire you to delve into this family.  Could you share anything with me about H 66, I would really appreciate it. Regards,m Geri

    ________________________________

  3. Hi! You write about a important topic when you warn about third party companies. You also mention that they don’t have any terms of service. I found them on the bottom of their page. They say the information will be used anonymously for YFull research, but not what this includes. Also that they do everything by the law – but not which law. Great blog – keep up the good work!! :)

    • The only law in Russia is Putin’s Law. Roberta is correct Russia is outside the legal reach of people in the US if a dispute arises. There is no available recourse.

  4. As I recall some other sites also do matching with DNA test results. I see many report adding their results to Gedmatch which you’ve mentioned before. How safe are sites like this?

    • Gedmatch does have a policy statement and they are a US firm, bound by US laws. As a consumer, we should always look at the terms of service for any of these types of companies or services.

  5. It’s currently a free analysis, although later they may charge a fee. I don’t care what they do with my Big Y partial sequence and partial mtDNA sequence. I know they aren’t going to weaponize it. Putin won’t be able to invade Georgia with it. They can’t use the data to get into my bank account. I don’t see a big deal here. If it furthers the understanding of the Y Tree, which is to my benefit, then why not let them have it?

  6. Well I am not a US but an EU citizen and I have tested at FTDNA. It would be unrealistically expensive for me to sue FTDNA if they would sell the ownership of my DNA data and samples to the ultimate evil, the-one-company-to-rule-them-all, Google…

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