DNA Lesson Series: The mtDNA and its role in Ancestry
mtDNA Part I - mtDNA 101
mtDNA Part II - Facts about mtDNA
mtDNA Part III - mtDNA Structure
mtDNA Part IV - Ancestral Markers
mtDNA Part V - Detecting Mutations in the mtDNA
mtDNA Part VI - mtDNA Ancestral Markers
mtDNA Part VII - The Cambridge Reference Sequence
mtDNA Part VIII - mtDNA Test Types  <<– you are here
mtDNA Part IX - mtDNA Haplogroup Determination
mtDNA Part X - mtDNA Subclades
mtDNA Part XI - mtDNA Haplogroup H
mtDNA Part XII - Subclades of mtDNA Haplogroup H
mtDNA Part XIII - Distribution of Subclades of H
mtDNA Part XIV - Descendents of Maria-Theresa
mtDNA Part XV - Luke the Evangelist
mtDNA Part XVI - Empress Feodorovna
mtDNA Part XVII - James “Earthquake McGoon” McGovern

In this blog, we will provide a broad overview of the different types of mtDNA tests available, and in the next blog, we go over some case studies to help you understand when they are used, and what each one will tell you about your ancestry.

DNA Testing 101:  There are 4 main types of mtDNA tests:

1. HVR1 Test
2. HVR2 Test
3. SNP Haplogroup Backbone Test
4. SNP Subclade Test

Let’s take a look at the main differences between these test types:

Test Type #1:  HVR1 Test

Overview:  The HVR1 Test is the most informative mtDNA test, and it is always the first test that is performed when you start tracing your maternal ancestry (the Maternal mtDNA test). The HVR1 test uses “DNA sequencing” technology to read all of the nucleotides from locations 16,000 to 16,400 of your mtDNA.  This is the entire HVR1 region, located in the D-Loop of the mtDNA.

Highlights of the HVR1 Test:  The HVR1 region is considered the most informative region of the mtDNA for ancestral studies for a number of reasons:

1. The HVR1 region contains an abundance of markers.  The HVR1 region is located in the D-Loop, so it contains an extremely high concentration of mutations (ancestral markers).  Thus, this region is highly informative.
2. The HVR1 region is easy to test.  The entire HVR1 region can be easily tested using sequencing technology.  All 400 nucleotides in the entire HVR1 region can be read from a single test.
3. The HVR1 region is well studied.  The HVR1 region is the most well studied region of the mtDNA due to its high concentration of mutations and ease of testing.  Most scientific studies to date, including indigenous data and other anthropological studies, have focused mainly on the HVR1 region.  Thus, there is more scientific data available for markers in the HVR1 region than any other region of the mtDNA, making the HVR1 region by far the most informative region of the mtDNA.

Prerequisite:  There is no prerequisite for taking the HVR1 test.  The HVR1 test is aways the first and most fundamental test that is performed when using mtDNA to trace ancestry.  The HVR1 test can be used “stand-alone” for User search and comparisons and haplogroup predictions.  All of the other test types serve to supplement the results of the HVR1 test.  There are usually enough markers and hypervariablity within the HVR1 region alone to differentiate between different individuals who are not part of the same haplogroup or family line.  Also, due to the large number of highly informative markers found in the HVR1 region, your haplogroup can often be predicted from examing just the markers in your HVR1 region. 

Test Type #2:  HVR2 Test

Overview:  Like HVR1 testing, the HVR2 test also uses “DNA sequencing” technology.  This test focuses on reading all of the nucleotides from locations 1 to 400 of the mtDNA.  This is the entire HVR2 region, the second most important region in the D-loop of the mtDNA. 

Highlights of the HVR2 Test:  Like HVR1, the HVR2 region is also located in the D-Loop of the mtDNA so it contains many ancestral markers.  The HVR2 region is always tested in conjunction with or subsequent to HVR1 Testing.  The HVR2 test will supplement the HVR1 results in the following ways:

1. Strengthen the results of User searches and comparisons.  The more regions of the mtDNA that are used for comparison, the more stringent and precise the results of the comparison.  For example, in cases where people are matching exactly at the HVR1 region, further comparison of the HVR2 region will provide greater resolution, and further confirm or refute the matches found in the HVR1 region. 
2. Assist in haplogroup prediction.  The HVR2 region contains quite a few markers which are important for haplogroup determination, and when used in conjunction with HVR1, will provide a stronger haplogroup prediction (we will examine a case study in the next blog).

Prerequisite:  The HVR1 test is a prerequisite for taking the HVR2 test.  The HVR2 region is rich in ancestral markers and HVR2 testing is an excellent way to supplement the results of the HVR1 Test.

Test Type #3:  SNP Haplogroup Backbone Test

Overview:  While the markers in the HVR1 and HVR2 Regions can be easily detected by sequencing, the Coding Region is extremely large, making sequencing impractical.  The SNP Haplogroup Backbone Test is a special panel of approximately 20 markers in the Coding Region which are specific for haplogroup determination.  By testing just the HVR1 or HVR2, you will only receive part of the “picture” of your mtDNA.  The SNP Haplogroup Backbone Test will allow you to view markers in the Coding Region of your mtDNA.

The following table illustrates all of the SNPs that are examined in the SNP Haplogroup Backbone Test:

Prerequisite:  The HVR1 and HVR2 tests are prerequisites for the SNP Haplogroup Backbone Test.  The SNP Haplogroup Backbone test examines markers in the Coding Region of the mtDNA and together with results of the HVR1 and HVR2 test, will allow you to confirm your haplogroup.   

Test Type #4:  SNP Subclade Test

Overview:  The SNP Subclade Test examines a special panel of markers in the Coding Region of the mtDNA which allows you to determine which “sub-clade” you belong to once your Haplogroup has been determined.

Prerequisite:  The HVR1, HVR2, and SNP Backbone Tests are prerequisites for the SNP Subclade Test.  Your Haplogroup must be confirmed before you can proceed with SNP Subclade testing.  At the moment, SNP Subclade Tests are available for the following mtDNA Haplogroups:

• R
• M
• H

If a subclade test is not available for your haplogroup, please check back often as new sub-clade tests are added occasionally.  Whenever a subclade test for your haplogroup becomes available, you will be able to access it from your control panel. 

The four types of mtDNA Tests are summarized in the following table:

The main goal of mtDNA testing is to gain a complete understanding of all of the important SNP mutations in your mtDNA.  The HVR1 test focuses on markers in the HVR1 region, the HVR2 test focuses on markers in the HVR2 region, and the SNP Test Panels focus on relevant markers in the Coding Region.  In the next blog, we will go over a case study to allow you to understand how these tests work together to uncover your ancestry.