MTDNA file

[pamt523]

I had my testing done thru Living DNA and uploaded my raw data uploaded to GEDCOM Genesis. I can't find what to do with the MTDNA (CSV) file. Any ideas?

[KATM]

GEDmatch does not accept mtDNA or Y-DNA files, only autosomal.

The mitochondrial genome contains 16,569 base pairs, of which FTDNA tests all with their mtDNAFullSequence test. Living DNA says they use 4,000 locations:

Motherline: this test identifies your maternal ancestry by looking at more than 4,000 SNP locations on your mitochondrial DNA (mtDNA) that are encoded onto our custom Illumina GSA chip.

This is more than 23andMe, and perhaps National Geographic's Geno 2 chip, but does not compare with a Full Sequence test or even a mtDNAPlus test. The mtDNA testing comparison chart at ISOGG shows that Living DNA may have an mtDNA matching database sometime in the future.

As far as I know, mtDNA results from other companies are not transferable to Family Tree DNA, due to such differences in the chips and amount of base pairs tested. The only exception is National Geographic's Geno 2 test, when FTDNA did their lab work (for Geno 2 Next Generation, they no longer do the lab work; transfers are no longer possible). But due to the difference in chips, FTDNA will only show the haplogroup, but not matches for transferred Geno 2 results.

I have not heard of any other companies or services that accept transfers of mtDNA files from any source other than FTDNA's mtDNA tests, either, but perhaps someone else is aware of such a place. It is likely that there is no place to transfer your Living DNA mtDNA results.

If you are interested in double-checking your haplogroup, a website such as James Lick's mtDNA Haplogroup analysis could have been useful, except I don't see any sign that it accepts Living DNA files. Websites like mitosearch and mitotool seem to need at least the HVR1 and HVR2 results from FTDNA's mtDNAPlus test.

[pamt523]

Thank you

So, if you can't upload it anywhere, what is the point of this file? Sorry, just venting.

Trying to figure who accepts your data and who doesn't has been a crazy. I wish I would have checked into this further before testing with Living DNA. Thank you for your reply.

[pamt523]

What company would you test with?

So, what company would be your best pick to test with to find matches. Something that GEDMATCH would accept?

[ifiru]

The mt-dna CSV file is mt-dna matches file. It contains textual information of matches. Many companies needs raw data to upload. Mt-dna raw data is fasta.

[KATM]

The Living DNA mtDNA file has limited use, since it contains only a particular selection of markers that they've chosen to predict your mtDNA haplogroup. I suppose you could use it to see which markers they tested. Their prediction may or may not be for your specific, final twig on the mtDNA Phylotree. In order to really find out that "twig" (if you are interested), you would have to take the FTDNA mtDNAFullSequence test, which tests all the 16,569 base pairs, and is currently on sale. Only you can know if that is something you want to do. With the Full Sequence, you can do a few things with it, including use the websites I mentioned in my last post, and others posted below in this post.

I will say that 23andMe predicts mtDNA haplogroups the same way as Living DNA (by a selection of markers), and they predicted my mtDNA haplogroup as K1a3. This was the same haplogroup as what National Geographic's Geno 2 predicted for me (again, testing only a selection of markers). When I did the FTDNA mtDNA Full Sequence, I thought I might get a bit further out on the mtDNA tree, but it turned out that I was still K1a3. I do have one unique mutation, for what it's worth. This is just my experience; others have done the Full Sequence and their results did get them further out on their original branch.

Your other Living DNA information is what is of use in finding autosomal matches there. Perhaps one day they will provide mtDNA matches. You are correct about checking things out before testing, but consider it a lesson learned. Usually people test their DNA at one of the "big three" (FTDNA, 23andMe, or Ancestry), but now that there are several other companies, it complicates things. Always read the companies' privacy policies and terms of use before consenting to anything.

Besides using mtDNA Full Sequence results at the other websites I previously mentioned, another thing you can do with an FTDNA Full Sequence mtDNA Fasta file (the raw data file that irfu mentioned), is first to learn about Genbank, and then if you wish, upload your mtDNA Fasta file to Genbank to help science. You can read about how to do the upload at this page on Ian Logan's website: mtDNA Sequences at 'GenBank' (you can also read an interview with Ian Logan, although there is not a great amount of information about Genbank there). It is possible that your file might be helpful in adding another subclade to your haplogroup. Only the person whose mtDNA was tested can give permission to Genbank to use the file.

With your other mtDNA information:
mtDNA can contain mutations about medical conditions. If you wish, you can get a report from Ann Turner, an ISOGG member (interview here) and medical doctor who provides this service. She does not use the mtDNA Fasta file, but would need the .pdf of your mtDNA certificate from FTDNA. Note that FTDNA does not address medical issues for mtDNA. This ISOGG page, "Custom mitochondrial DNA reports", has a description of her service, and also contains a link to a copy of the type of report she provides.[/LIST]

[KATM]

So, what company would be your best pick to test with to find matches. Something that GEDMATCH would accept?

It looks like GEDmatch accepts the following files to their main database: Ancestry, FTDNA, WeGene, and MyHeritage (as well as 23andMe versions 2,3 and 4). For 23andMe v.5 and Living DNA files, due to the chip used, they must use GEDmatch Genesis, as you found out. Once you create a GEDmatch account, there are instructions on how to obtain your file from each company, and then how to upload to GEDmatch. WeGene is focused more on the Asian market than the other companies. Ancestry, 23andMe, and FTDNA are based in the U.S. I believe that MyHeritage is based in Israel.

I'm not saying that you should not test at Ancestry, because they do have the largest database for autosomal matches. I don't know much about MyHeritage, but that could be another option. Both can be uploaded to the main GEDmatch.com database, and FTDNA. Which company/companies you choose to test with depends on what you want from your DNA testing: are you looking for matches, and want to be in as many places as you can to find them (thus possibly needing the ability to transfer from one company to another); or not as interested in matches, but more interested in ethnicity predictions.

But right now, I would generally recommend FTDNA, and here is why:
Both 23andMe and Ancestry's DNA tests have changed over to a new chip for the current versions of their tests (similar to the one used by Living DNA, what's called a "GSA" chip). They are using customized GSA chips. There are far fewer markers on the GSA chips in common with the older "OmniExpress" chip versions. I'm talking about 23andMe v. 5, and Ancestry v. 2, as these GSA chips are what you would be tested on if you tested right now with those companies.

There are problems transferring the newer chip version files to FTDNA (and for 23andMe v. 5, to GEDmatch). In the case of 23andMe v. 5, FTDNA cannot even accept the file at all, because there is just not enough there to compare for matching. And with Ancestry's v. 2 chip, you would not get matches beyond about 3rd-4th cousin at FTDNA, and those potential matches would not see you, because of the limited overlap of markers. You can see a comparison of autosomal SNPs tested by each company at ISOGG's Autosomal SNP comparison chart. You can also see how the different autosomal DNA testing companies compare at ISOGG's Autosomal DNA testing comparison chart (I think this page is a bit dated on the number SNPs). This is why you had to use GEDmatch Genesis to upload your Living DNA results - they can't be used with the regular GEDmatch database.

Soon, FTDNA will have to change over to a similar chip. This is due to the fact that the company (Illumina) that provides chips to all of the commercial consumer DNA testing companies, will no longer produce the older "OmniExpress" chips, so everyone must use their new chip. But I have read that FTDNA has requested their own customized version of the GSA chip, which will still provide something like twice as many markers than any of the other companies using the GSA chip will have.

Another concern with the new GSA chip is something called imputation. You can read about it at Roberta Estes' blog in her articles "Concepts – Imputation," and "Imputation Matching Comparison." Imputation is currently being used by MyHeritage and DNA.Land, but because of the need to use new chips from Illumina, some degree of it will be used by most, if not all, testing companies in the near future.

Roberta also has other articles that may help you decide which company (or companies) would be best for you:

• "Which DNA Test is Best?" which includes the chart "Genealogy Autosomal Vendor Feature Summary Chart" and other charts for different features.
• "Autosomal DNA Transfers – Which Companies Accept Which Tests?" - in which we see a chart that shows that only FTDNA, MyHeritage and GEDmatch accept transfers from others. The Ancestry, 23andMe, Living DNA, WeGenes and National Geographic's Geno 2 tests currently do not accept any transfers.

Finally, it is probably best to actually do the test at any given company, versus transfer results from elsewhere, if you can afford it.

[chr]

I believe the raw formats for mtDNA out of the Illumina sequencing machine would be a FASTQ-file, which contains many short unaligned sequences plus the corresponding quality information.

Then this could be aligned to the reference genome and then output as a SAM file (or BAM, the binary version with smaller file size). This would still contain the (average 2000x for mtDNA?) multiple coverage and therefore I would still call it a raw format.

I'm not an expert on this but just an interested person, so please correct me if I'm wrong.

The FASTA file that can be downloaded from FTDNA is a boiled down single sequence without distinct multiple coverage. It's not raw data anymore.

I asked FTDNA support whether I can obtain raw data (I mentioned preferably SAM/BAM format) from them, but unfortunately they denied.

I'm not aware that there is a public web service where the above mentioned mtDNA raw data can be easily (re-)analyzed. There are some open source linux command line tools available for processing, that would most likely be difficult to install and use.