Saturday, April 21, 2012

Full Sequence mtDNA Analysis In Process

This article on mtDNA tests provides some useful information for analyzing mtDNA ancestral motherline test results:

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. 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 analyzed in a Full Sequence test.
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.

The mtDNA test which placed me into motherline haplogroup U5b analyzed HVR1 and HVR2 of the control region. I've ordered a Full Sequence mtDNA test from a second testing company which will confirm my haplogroup placement with 100% certainty (since my entire mtDNA sequence will be elucidated), plus it will open up my access to another large genetic database for finding additional genetic matches. It offers another level of detail and confirmation of my motherline. The first test assigned me with good certainty to haplogroup U5b. The Full Sequence test can confirm my U5b placement, tell me if I belong to one of the many subclades of U5b, provide me with an additional set of mtDNA genetic markers from the coding region, and possibly link me up to new genetic matches as well. As a former scientist myself, I am more comfortable with independently confirmed results anyway.

It could be up to six weeks or more before I get results back, as I just ordered this test today. Soon, soon, soon I will know even more about my motherline.

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