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  <<– you are here
mtDNA Part VI - mtDNA Ancestral Markers
mtDNA Part VII - The Cambridge Reference Sequence
mtDNA Part VIII - mtDNA Test Types
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 discuss the technology used to detect mutations in your mtDNA.  A basic understanding of DNA testing techniques will help you to understand the science behind DNA ancestry testing.  

DNA Testing 101

The two most common methods used to detect mutations in mtDNA are 1) DNA Sequencing, and 2) SNP Testing.  Let’s talk about each one and how they work.

1.  DNA sequencing. 

DNA sequencing is a special process which is used to read the chain of nucleotides in a specific segment of your DNA, much like reading a book. 

This technology allows the lab read the entire genetic code of a whole section of your mtDNA.  The following report is an example of the results of a sequencing test in the HVR1 region of an individual’s mtDNA. 

As you can see, all of the nucleotides in HVR1 region (locations 16001 to 16520) have been decoded.  All mutations detected in the sequence are indicated in pink.  

The benefit of DNA Sequencing technology is that it can accurately read entire lengths of your DNA.  The limitation of DNA Sequencing technology is that only approximately 400 to 500 nucleotides can be read at a time (in one test). 

This technology is used for testing the HVR1 and testing the HVR2 (D-Loop) region of your mtDNA.  The HVR1 region is approximately 500 nucleotides in length (spans location 16000 to 16569).  The HVR2 region is approximately 400 nucleotides in length (spans locations 1 to 400). 

DNA Sequencing technology is the best test method to detect mutations in the HVR1 and HVR2 regions (D-Loop):

1. A single sequencing test can detect all of the markers in the HVR1 region (called the HVR1 test), and another sequencing test can detect all of the markers in the HVR2 region (called the HVR2 test). 
2. Most of the mutations found in the mtDNA are located in HVR1 and HVR2 (high concentration of mutations compared to the coding region)
3. The HVR1 region is the most widely studied region of the mtDNA for ancestral studies and provides the most ancestral information. 

However, DNA Sequencing is not the best method for examining mutations in the Coding Region of your mtDNA because the Coding Region is extremely long, over 15,000 nucleotides in length. 

Since each sequencing reaction can only test approximately 500 nucleotides at a time, a lot of reactions would be required in order to sequence the entire coding region, making it impractical and costly.  Also, as discussed in previous blogs, there are very few mutations in the coding region, making it unnecesary to sequencing every single nucleotide in the coding region.  Thus, DNA Sequencing is not the best way to look for mutations in the coding region.

2.  SNP Test Panels

The second method to detect mutations in the mtDNA is called “SNP” testing.  Unlike DNA Sequencing, this technique does not read the entire length of DNA.  Instead, it targets specific nucleotides.  Only the nucleotides that provide useful information are tested, and all other nucleotides are ignored.  This is the best method for efficiently testing large regions of DNA. 

For example, if the presence of a mutation at location 16223 is an important indicator that someone does not belong to Haplogroup H, then the laboratory will pinpoint and specifically test location 16223 to see if a mutation exists in this location. 

This is like “sharp shooting”.  Instead of testing an entire region of the DNA, we are specifically targeting exact locations and nucleotides that are important for answering a specific question. 

SNP Test Panels are special handpicked panels of SNP markers which will answer a specific set of questions.  For example, a mtDNA Haplogroup Backbone SNP Test Panel will examine all markers which will tell us which mtDNA Haplogroup an individual belongs to.  We will talk more about specific SNP Test Panels in the further blogs. 

In Part VI, we will discuss how mutations in our mtDNA allow us to trace our maternal ancestry.