{"id":1048,"date":"2012-10-11T14:04:57","date_gmt":"2012-10-11T21:04:57","guid":{"rendered":"http:\/\/norwitz.net\/blog\/?p=1048"},"modified":"2014-01-01T10:32:53","modified_gmt":"2014-01-01T18:32:53","slug":"mtdna-raw-data","status":"publish","type":"post","link":"http:\/\/norwitz.net\/blog\/2012\/10\/11\/mtdna-raw-data\/","title":{"rendered":"mtDNA: Using Raw Data to Fill Out Your Subtree"},"content":{"rendered":"

I’ve been heavily into genealogy for the last year, fleshing out both my and my husband’s family trees.\u00a0 Recently, I decided to delve into DNA.\u00a0 I chose 23andme<\/a> and have been thrilled with the results (this link gives me a small referral fee, thanks if you use it).<\/p>\n

One of the things they tested me for was my mitochondrial DNA (mtDNA).\u00a0 This is special DNA (not within the chromosomes) that everyone has but you only get it from your mother (it’s in egg cells but not sperm cells).\u00a0 In theory, I have the same mtDNA as my mother, her mother, her mother, and so on back to the beginning of human history.\u00a0 In practice, DNA copying isn’t perfect.\u00a0 Mutations (think of them as typos) sneak in.\u00a0 We can use the mutations to track maternal history across the generations, by when (and where) the splits happened.\u00a0 Each set of mutations is labeled with what is called a Haplogroup.<\/p>\n

My mtDNA Haplogroup, as calculated by 23andme, is U6a7.\u00a0 About 45,000 years ago, a group of humans left Africa for Europe.\u00a0 According to the mutation history, those who stayed in Europe had the Haplogroup U5 and those who turned back into northern Africa were U6.\u00a0 About 35,000 years ago, U6a spread around northern Africa.\u00a0 FamilyTreeDNA<\/a> puts U6 at 36,200 years ago and U6a at 26,900 years ago.\u00a0 But close enough.<\/p>\n

23andme tells me my subclave is a7 but only gives information about U6 when saying this means my maternal line is from “North Africa, the Near East, Iberian Peninsula, Canary Islands” and that the population I best match are the Berbers.\u00a0 Is my maternal line Muslim?\u00a0 Or Sephardic Jewish?\u00a0 I don’t know.\u00a0 All I know is that I’m Ashkenazi Jewish on all sides and my maternal grandmother and her mother are from Kosice, Slovakia. I haven’t been able to go any further back.<\/p>\n

The FamilyTreeDNA page on U6<\/a> gives far more subgroups: U6a7a, U6a7a1, U6a7a1a, U6a7a1b, U6a7a1c, U6a7a2, and U6a7b. Which one am I?\u00a0 I wrote 23andme for help and they did take a lot of time to explain things, but none of it got me that far.\u00a0 If you have a 23andme account, log in and go to Ancestry Labs, then choose Haplogroup Tree Mutation Mapper<\/a> and submit your Haplogroup.\u00a0 You’ll see a long list that looks like this:<\/p>\n\n\n\n\n\n\n\n
U6a7 defining mutations<\/td>\n<\/tr>\n
variant<\/td>\ncall<\/td>\nrCRS<\/td>\nanc<\/td>\n<\/tr>\n
rs28357684<\/a><\/td>\nA<\/a><\/td>\n15043<\/td>\nG<\/td>\n<\/tr>\n
i3001344<\/td>\n<\/td>\n15043<\/td>\nG<\/td>\n<\/tr>\n
i5049907<\/td>\n<\/td>\n15043<\/td>\nG<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

The variant is the SNP, the piece of the gene where the mutation in question is.\u00a0 The rCRS (also called position) is a number more commonly used but specific to a gene or, in this case, the mtDNA.\u00a0 Anc means the ancestral, regular, non-mutation form and the call is the result, or the genotype, of the person tested.\u00a0 This mutation defines U6a7 (and has three variants).\u00a0 Since my call (A) is different from the ancestry (G), I have the mutation and therefore am U6a7.<\/p>\n

Unfortunately, there’s nothing that goes beyond U6a7.\u00a0 23andme doesn’t have a system to pay extra for a more detailed test.\u00a0 But maybe the answer was already there.\u00a0 I didn’t want to pay FamilyTreeDNA or another company for a test if I didn’t have to.\u00a0 23andme also told me it was possible I simply didn’t have markers to identify subgroups, so another test might not give me a better answer.<\/p>\n

So on to the raw data.\u00a0 What could it tell me?<\/p>\n

The Mutation Mapper page at 23andme shows you a circle with a lot of the raw data, but it is incomplete.\u00a0 The better option is to to click on “Account” on the top of the page then choose “Browse Raw Data” and click on “MT.”<\/a>\u00a0 It’s faster if you download it all into a text file, but you can also look online.\u00a0 (Of course, you can use raw data from any company.)<\/p>\n

The data will look like this online:<\/p>\n\n\n\n\n\n\n\n\n
<\/th>\nGene<\/th>\nPosition<\/th>\nSNP<\/th>\nVersions<\/th>\nMy Genotype<\/th>\n<\/tr>\n<\/thead>\n
\"\"<\/td>\nintergenic<\/em><\/td>\n3<\/td>\ni4001200<\/a><\/td>\nC or T<\/td>\nT<\/td>\n<\/tr>\n
\"\"<\/td>\nintergenic<\/em><\/td>\n7<\/td>\ni4001110<\/a><\/td>\nA or G<\/td>\nA<\/td>\n<\/tr>\n
\"\"<\/td>\nintergenic<\/em><\/td>\n9<\/td>\ni4001358<\/a><\/td>\nA or G<\/td>\nG<\/td>\n<\/tr>\n
\"\"<\/td>\nintergenic<\/em><\/td>\n26<\/td>\ni4000553<\/a><\/td>\nC or T<\/td>\nC<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

The downloaded version (the text file) looks a bit different:<\/p>\n\n\n\n\n\n\n\n\n
rsid<\/th>\nchromosome<\/th>\nposition<\/th>\ngenotype<\/th>\n<\/tr>\n<\/thead>\n
i4001200<\/td>\nMT<\/em><\/td>\n3<\/td>\nT<\/td>\n<\/tr>\n
i4001110<\/td>\nMT<\/em><\/td>\n7<\/td>\nA<\/td>\n<\/tr>\n
i4001358<\/td>\nMT<\/em><\/td>\n9<\/td>\nG<\/td>\n<\/tr>\n
i4000553<\/td>\nMT<\/em><\/td>\n26<\/td>\nC<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

The name of the gene (mtDNA has 37) and the SNP (or rsid) isn’t useful here, just look at the position (the rCRS).\u00a0 This is how you’ll match up results with known mutations.\u00a0 The versions are what’s possible and then it gives the test results, my genotype.\u00a0 Note that it doesn’t say which result is a mutation and which is ancestral.\u00a0 Nor do I know which positions have relevant mutations.\u00a0 Time for more research.<\/p>\n

The FamilyTreeDNA page on U6<\/a> does list all the mutations for each subgroup but not what the genotype is supposed to be.\u00a0 I needed to keep looking.<\/p>\n

I found this amazing resource:<\/p>\n

http:\/\/www.phylotree.org\/tree\/subtree_U.htm<\/a>
\n(they have other trees here: http:\/\/www.phylotree.org\/tree\/main.htm<\/a> )<\/p>\n

I paged down to U6a7 and saw that there were mutation lists for three variants: U6a7a, U6a7b, and U6a7c<\/p>\n

Each mutation is in the form: letter-number-letter (plus some optional markers).\u00a0 For example: T1193C.\u00a0 This means rCRS 1193 has two genotypes, T and C.\u00a0 The first letter is the “normal” or ancestral expression of that SNP.\u00a0 The second letter is the mutation.<\/p>\n

Another example: U6a7 is defined by: G15043A.\u00a0 If this position is an A for you, then you have the mutation and are U6a7 (perhaps with some other precursors established).\u00a0 If you have a G instead, then you do not have the mutation and are not U6a7.<\/p>\n

Using Phylotree, this is what I did next:<\/p>\n