08 August 2011

mtDNA tests

There are a lot of people getting interested in Genetic Genealogy: using DNA to find out about ancestry - but it is not always easy to find basic information about what these tests can do.

mtDNA: What can I test and where?
There are several testing companies, but they offer very different tests, on different levels, at different prices. Make sure you look around and ask people to get the best offers.

The mitochondria consist of 16569 SNPs that can be tested. Typically these are tested in three steps: (from Family Tree DNA’s FAQ)

Mitochondrial DNA (mtDNA) has two major parts, the control region and the coding region.

The control region is often called the hypervariable region (HVR). Hypervariable means fast changing. In mitochondrial DNA, the control region is the fast changing part. The control region may be further divided into two Hypervariable regions, HVR1 and HVR2.

* HVR1 runs from nucleotide 16001 to nucleotide 16569.
* HVR2 runs from nucleotide 00001 to nucleotide 00574.

The coding region (CR) is the part of your mtDNA genome that contains genes. Because it does contain some genes, the coding region is believed to be slower mutating than the control region. Often, it is the mutations that are found in the coding region that are used to define haplogroups.

* The coding region runs from nucleotide 00575 to nucleotide 16000.

The only complete test that will assign you with certainty to your haplogroup and subgroup is a Full Sequence test. This is offered by Family Tree DNA ($299 or less) and Genebase ($528).

The reason for this is that a lot of (but not all) of the mutations that define the different subgroups are placed in the Coding Region, which is only analysed in a Full Sequence test (FMS, FGS, "Mega").

It is possible to buy the complete test at once, or to do it step-wise and upgrade. If you are most interested in the deep ancestry and anthropology of your group, a HVR1 level test will find that. For genealogical purposes it is almost always necessary to do a Full Sequence test, FMS.

What about 23andMe?
This company offers one type of test only, which include an analysis of about 2500-3000 SNPs on the mitochondria. This will often be enough to find out haplogroup and a few subgroups, but it is not a complete test, and it does not easily compare with tests from other companies, as the SNPs tested are spread over the mtDNA. If you already have an mtDNA-test from 23andMe, only the Full Sequence at FTDNA (all 16569 SNPs) will be useful to learn more. 

Timeframe for Matches

HVR1 only:
The common direct maternal ancestor could have lived up to 50 000 years ago.

HVR1 + HVR2:
The common direct maternal ancestor could have lived many thousand years ago

FMS/Full Sequence test:
The common direct maternal ancestor could have lived from recently to about 3000 years ago.

Consequently: to use mtDNA for genealogical purposes, the FMS test is usually necessary.

Prices at Family Tree DNA (edited):
* HVR1 "mtDNA": not offered after May 2013
* HVR1 + HVR2 "mtDNA Plus": $49
* FMS ("Mega") - the Full Sequence of the mitochondria: $299 or lower, check the price list

Results: What do they mean?
Please study Family Tree DNA’s FAQ page on mtDNA results:
"The answers to questions about mitochondrial DNA (mtDNA) test results. What do your mitochondrial DNA (mtDNA) results mean? What should you do next? How recently are you related to your matches? Should you upgrade?"

mtDNA Haplogroups
There are many mt-haplogroups (not to be mixed up with Y-DNA haplogroups), and for people with European ancestry there are about ten different ones that are common. One of these, H, includes about half of all people with European ancestry.

The different haplogroup definitions can be found in the phylotree, which is updated regularly with new research.

mtDNA and Ethnic Ancestry
Your mitochondrial DNA is only a tiny part of your genetic make-up. Typically our mtDNA haplogroup reveals our ancestry in the direct maternal line some 5000-50 000 years back. If you look at your full ancestry tree, this is just the thin line at the very end of the ancestral fan, following the mothers only. Imagine how tiny a portion of your ancestry this is 5000 years ago.

Thus an mtDNA-test can only tell you something about this tiny, narrow line.

If you wish to have an estimate of your ethnic origin, try the extensive autosomal tests like Family Finder (FTDNA) or Relative Finder (23andMe), which test some 700 000 – 1 000 000 SNPs across your autosomes.

Your mtDNA pages at FTDNA
If you have tested with Family Tree DNA, check out the MyFTDNA User Guide:

There is a lot of information to be found on your pages.

What can my mtDNA test not tell me?
Eye, hair and skin colour, what food you can eat and not, how tall you are, your blood type: all these traits are decided by several genes on your autosomes, and not your mitochondrial DNA.

Comparing to other testers: mitosearch
Independent of your testing company, it is recommended that your results are uploaded or entered to mitosearch, a free and open database for everyone who has tested mtDNA.

You can enter your HVR1 results (note that the 16- is not entered, only the last three digits) and your HVR2 results. If you also wish to share your Coding Region this can be entered in the Additional information section.

A few notes:
* If you tested with FTDNA your results can be automatically uploaded when you are logged in - but note that HVR2-mutations will normally have to be entered manually
* If you tested with 23andMe, you did not test the complete HVR1 and HVR2, so it is difficult to enter results, however you may find some of the numbers in your mtDNA raw data file - study the comparison table between 23andMe (Yoruba Reference Sequence) and other companies (Cambridge Reference Sequence), from SNPedia.

Contribute to Research
If you have done a Full Sequence test (FMS) you can donate your sequence to GenBank to contribute to research. This will help define further subclades of your haplogroup. It is especially important if you have few or no matches, and if you have many mutations that are not yet defining a subclade of your haplogroup. Ian Logan has created a how to on his web page.

If you have completed the FMS at FTDNA you will probably be asked to fill in a "New Survey" about your maternal line and be asked to release the sequence to FTDNA's researchers. 

"Fast Mutators"
There are a few SNPs that are considered to mutate frequently, and it can be useful to disregard these when comparing results. The list is found on phylotree, above the actual tree structure.

The SNPs disregarded in phylogeny are:
* 309.1C(C)
* 315.1C
* 523-524d (aka 522-523d)
* 16182
* 16183C
* 16193.1C(C)
* 16519

Prices and Recommendations

EDIT: FTDNA has changed its pricing policy from May 2013, and HVR1 only is not offered any longer, HVR1+2 (formerly mtDNAplus) is now $49. 

The Full Sequence test is expensive, but there are sales a few times a year, and it is a good idea to take advantage of these. Family Tree DNA is far cheaper than Genebase.

In general a Full Sequence test is necessary to use mtDNA for genealogical purposes. A "simple test", HVR normally only gives you your haplogroup and the "long lines".

Normally it is cheaper to buy the full test at once than to purchase the test in three steps:

Three steps:
mtDNA (HVR1): $99
mtDNA plus upgrade "mtDNA refine" (HVR2): $85
mtDNA "Mega" upgrade (FMS) from HVR2: $239
Total for FMS: $423

Two steps:
mtDNA (HVR1): $99
mtDNA "Mega" upgrade from HVR1: $265
Total for FMS:  $364

Two steps:
mtDNA plus (HVR1+2): $159
mtDNA "Mega" upgrade from HVR2: $239
Total: $ 398

One step:
mtDNA Full Sequence:
$289 (for existing customers with other tests)
$299 (for new customers)
$199-$219 (various sale prices)

So you see why it is recommended to get the full test at once, and to look for sales!

1 comment:

  1. Hej
    Jag har lagt ut en länk till din blogg på http://slaktforskning.blogspot.com under fliken Länkar.
    Jan Granath