During my webinars this week for APG, someone asked a question about mitochondrial DNA and I told them I would follow up on my blog. I thought I knew the answer, but I needed to be sure.
When I displayed the slide of my full sequence in the RSRS format, they noticed some of the letters were lower case. Truthfully, since client comparisons are still in the CRS format, I hadn’t paid a lot of attention to my RSRS values except for an initial look-see when the corresponding paper came out (“A ‘Copernican’ Reassessment of the Human Mitochondrial DNA Tree from its Root”) and the RSRS results were added to our personal page information. I know, my bad.
In my blogs titled Citizen Science, the CRS and the RSRS and What Happened to My Mitochondrial DNA?, I explained about the CRS and the RSRS. In a nutshell, the RSRS, the Reconstructed Sapiens Reference Sequence is the new way of interpreting mitochondrial results, comparing them to a “reconstructed” Eve instead of someone who tested in Cambridge in 1981. That 1981 person set the standard for the CRS, or Cambridge Reference Sequence.
But soon, we will be using the RSRS. My understanding is that the Geno 2.0 results, although only providing the haplogroup defining mutations, will be given in RSRS format.
So let’s take a look at what this person saw that caused a question.
In the last mutation in the coding region, all the way at the end, you see that a mutation is noted as C15452a.
Now let’s take a look at the CRS version.
You see the same mutation, but it’s noted differently, as 15452A.
What is the difference, or maybe better asked, why the difference?
On the CRS page, the mutations are shown, as above, but there is also a second part of that page, shown below.
On this second part of the results, the normal value in the CRS, and the value carried by the person with the mutation in 1981, is shown. So this is a translation table for your results. You can see that it shows that the CRS value for location 15452 is normally C and my value is an A.
What are those Cs and As? Or for that matter the other two letters, T and G? Well, referring to Tuesday’s introduction class, these are the 4 base nucleotides that make up the “rungs” in the DNA double helix ladder.
T, A, C and G are short for Adenine, Cytosine, Thymine and Guanine. You can see these nucleotides as they each make up half of the connection between opposite sides of the double helix as it uncoils. Normally, a T is paired with a C and the A is paired with the G. However, not always. When a mutation happens, sometimes the pairing is inverted and a C gets paired with an A or a T gets paired with a G.
When a typical mutation happens, meaning T/C and A/G, it’s called a transition. When a more unusual mutation happens, meaning C/A, A/C, G/T and T/G, it’s called a transversion. I think this is what I said the other night, but given how often I use these terms, which is almost never, it would have been easy to get them switched.
I know, by now you’re VERY sorry you asked aren’t you:)
But we’re not quite to the answer yet, so please, bear with me and read on. Remember, this could qualify you to win the new Genetic Genealogy Trivial Pursuit game whenever that version emerges. We are almost to the punch line….
In order to make life easier and to eliminate the need for a translation table, the new RSRS refers to mutations a little differently. You’ve guessed by now, haven’t you. Yep, you’re right, my mutation shown as C15452a has its own translation table built right in. The mutation location is 15452. The normal value, meaning the one Eve had (RSRS), as well as the CRS, was a C. However, my value is an A, but since it’s a little a, we know that this is a transversion, not a transition. You can see another transversion at my location 825.
Why is this important in genetic genealogy? It’s not, really, because it’s already taken care of for you. If someone else has a value there of C15452T, they simply won’t be shown as a match to me with my value of C15424a. So you don’t have to figure this out, it’s taken care of for you in the matching routine. But hey, you wanted to know, and now you do. Good eye for the catch!
You can read more about the RSRS in the paper by Dr. Behar et al, “A ‘Copernican’ Reassessment of the Human Mitochondrial DNA Tree from its Root” or by visiting the website mtDNA Community launched in conjunction with the paper. And if you’re really a glutton for punishment, check page 677 in the paper for more about different notations and what they mean for mitochondrial DNA. There is more than just T, A, C and G for inquiring minds that want to know!
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