Visualize 23andMe haplogroup defining SNPs with Mitowheel!
Posted by attilacsordas on April 7, 2009
Last Friday 23andMe came up with Haplogroup Tree Mutation Mapper which is the first experimental feature that can be instantly tested by biogeek customers (a large portion of the company’s customer base) in its freshly launched technology sandbox 23andMe Labs that is much like Google Labs.
Haplogroup Tree Mutation Mapper “shows you which particular mutations in a person’s mitochondrial DNA (maternal ancestry) or Y chromosome (paternal ancestry) were used to determine their haplogroup assignment.”
Basically you are picking the Y chromosome or type the name of a maternal mitochondrial haplogroup (like T) into the search box and as a result you get a list back with the position and id-s of the defining mutations. With that information you can play different genetic genealogy games if you like.
But playing with a pure textual list of SNPs doesn’t sound too fascinating and the tool is not really a “Mapper” as there’s no visualization included. Wouldn’t it be nice if you can visualize all those haplogroup defining SNP positions at once and get extra biological information on them right away? Well, you cannot do that within the 23andMe website but you can do that with Mitowheel which is a graphical representation of the circular human mitochondrial genome (Disclaimer: I am part of developer team, see post and the Mitowheel blog).
For instance the SNPs on the left are parts of the T haplogroup defining mutations used by 23andMe. The rCRS is the revised Cambridge Reference Sequence, the rs<numbers> are the reference cluster IDs of SNPs. rCRS is a reconstruction of a single European individual’s mtDNA, the source was an unnamed placenta without further identity and it contains several rare alleles. I’ve also heard rumors that some blurry nucleotides were replaced by cow DNA. The rCRS nevertheless provides a uniform nucleotide numbering scheme (0-16569) even if the 3106 position is a phantom position (like chief evangelist) as there was an incorrect duplication of 3107C in the original sequence. So if you check the rCRS positions on the list, the one you should use in Mitowheel is +1 position away that you can see in parentheses if you click on the individual SNP rsids within the 23andMe site.
So here are all the positions 23andMe is using for T haplotyping and you can type them into the Mitowheel search box: 10463, 13368, 14905, 15607, 15928, 188, 4917, 709, 8697 and step through all of them by clicking the arrow in the search box and get a lot of extra information by checking the info popup box.
As a 23andMe customer you can instantly look for functional information on your particular SNPs with Mitowheel by adding the nucleotide letters of your specific mutation to the positions like in 8697A, so the following is the result of the search for all of my T defining SNPs: 10463C, 13368A, 14905A, 15607G, 15928A, 1888A, 4917G, 709A, 8697A
As Mitowheel incorporates data on fully sequenced human mitochondrial genomes that have been deposited in the GenBank database the allele frequencies of 23andMe customers can be checked at those positions and groups can be created based on Gábor Zsurka’s, Mitowheel founder, post. Each little gray bar above or below a nucleotide letter represents the number of individuals who carry a SNP at the given position as compared to the revised Cambridge reference sequence.
The group creating search looks like the following in case of my T defining SNPs (a plus sign is added to the search items above):
+10463C, +13368A, +14905A, +15607G, +15928A, +1888A, +4917G, +709A, +8697A
33 Responses to “Visualize 23andMe haplogroup defining SNPs with Mitowheel!”
Sorry, the comment form is closed at this time.