What do the results of a Deep SNP test mean?

Often, at least at the current stage of genetic genealogy, DNA sequencing does not reveal enough information to identify a person’s particular Y chromosome or mtDNA haplogroup. The example I will be using in this post is Haplogroup E. Haplogroup E split into E1, E2, and E3 about 28,000 years ago. Current tests offered by many sequencing companies are able to place a person in the general “E” Haplogroup, but might be unable to determine exactly which subclade of E a person descends from. In such a situation, a “Deep SNP” test can be used to fill in that information.

A SNP is single nucleotide polymorphism, or a change in the DNA sequence at a single nucleotide. For instance, the switch of a C for G, a cytosine for a guanine. You can see a chart of some of the most common SNPs tested for genetic genealogy here or here. The Deep SNP test (which can go by other names) analyzes a person’s DNA, such as the Y chromosome, for the presence or lack of these mutation(s).

Each SNP is detected either by sequencing or by cutting the DNA with enzymes – the presence of a certain mutation will cause the enzyme to cut the DNA differently, either stopping it from cutting or allowing it to cut. The scientists can then analyze the results and determine whether or not the person has that particular mutation. Certain marker results will lead the person to be group in the haplogroup containing other people who have similar results.

Haplogroup E, for instance, is characterized by the mutation M96. If a person has this mutation, they would be M96+, it is extremely likely that they are directly descended from the founder of Haplogroup E. If they do not have the mutation, they are M96-, and they belong to another haplogroup. It is  helpful to follow along on the ISOGG Haplogroup E Tree.

Haplogroup E split into E1, E2, and E3 about 28,000 years ago. E3 is characterized by the SNP mutation P2, meaning that people who test positive for P2 (i.e. P2+), then it is extremely likely that they are directly descended from the founder of Haplogroup E3.

E3 split into E3a and E3b about 26,000 years ago. E3b is characterized by the SNP mutation M35. From Wikipedia: “E3b is believed to have first appeared in the Horn of Africa approximately 26,000 years ago and dispersed to the Middle East during the Upper Paleolithic and Mesolithic periods. From there, it traveled west with the expansion of Neolithic agriculturalists.”

So, therefore, if you belonged to subclade E3b, your Deep SNP test results would be (M96+, P2+, M35+). And E3b splits into even more subclades, meaning that you would have more SNP results.

Anytime you get Deep SNP results and aren’t sure how to interpret them, use the ISOGG Haplogroup Trees. The identifying SNP for each branch of the tree is listed right next to the branch. ISOGG updates the Haplogroup Tree yearly, and even includes source information! It’s a great resource for genetic genealogists.

By the way, this post came about after a great email conversation with Tim at Genealogy Reviews Online. Thanks Tim!

12 Responses

  1. Victor 17 December 2007 / 5:51 pm

    For the purposes of explaining SNP tests it’s Ok to simplify things a bit, but the examples employed can lead to a wrong idea.

    I wouldn’t exactly say that haplogroup E “split” into E1, E2 and E3. A SNP is a mutation that happens randomly in a single individual and subsequently passes to all his descendants. But these three mutations of haplogroup E didn’t happen in a single “split” event. Thousands of years could have elapsed between the appearance of one mutation and the next. And all the while the “derived” lineages (with the new SNPs) can coexist with the “ancestral” lineage up to our days.

    The same applies to the “split” of E3 into E3a and E3b. Coincidentally, the E3b branch is several thousand years older than the E3a branch.

    Best Wishes!

  2. Blaine Bettinger 18 December 2007 / 1:03 pm


    Those are some great points, thank you for adding to the conversation. I’ll use the term “branched off” rather than “split” in future references.

  3. Do Follow Proxy Directory 22 October 2008 / 4:27 pm

    Wow, sorry I had to look up some of them words, :), science is a interesting thing. I have a question for my science teacher. Give him a hard time because I learned something about science that he didn’t. Great post 🙂

    Regards, Lamonte

  4. Cindy Anderson 19 August 2009 / 4:31 pm

    Hello! I was wanting to have a deep snp test done showing my ethnicity,tribal information,medical tendencies,etc.,etc. Can you help me?

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