Say what? Mitochondrial results from a Y DNA test? You must be kidding? It’s April Fool’s Day, right???
“Not funny,” you say…
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.
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.
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.