Showing posts with label U5b1b2. Show all posts
Showing posts with label U5b1b2. Show all posts

Wednesday, December 12, 2012

My Geno 2.0 Results: Step-by-Step

As much fun as I have had posting and reading about other people's Geno 2.0 results in the last couple of weeks, I have to admit, there's nothing quite like getting my own (finally)!

OVER THIRTY-FIVE THOUSAND SOLD
According to the "infographic" below, I am one of 559,515 Genographic Project participants. (You can access this individualized image through the yellow "Share" button on the top right of the "Your Story" page.)


There were 524,384 participants from Geno 1.0, so judging from this, there are now 35,131 new Geno 2.0 participants. That is certainly a lot and we don't even know if that is the number of kits sold to date or just the number of results being returned now. This means at least 35,131 kits have sold since Geno 2.0's introduction in July of this year. (Pretty awesome!)

MY STORY




















MY MATERNAL LINE
My Geno 2.0 mitochondrial DNA haplogroup is U5b1b2 which is consistent with 23andMe's and mtDNA Community's label for me, while my full mitochondrial sequence at Family Tree DNA designates me as mtDNA Haplogroup U5b1.

If you click on the arrows on your map, you will be walked step by step through the migration pattern of your direct maternal line ancestors, ending with a heatmap of the frequency of your subclade (if available). Of course, being female, I don't have a Y-chromosome to explore, but as part of their results, males also receive their Y-DNA haplogroup subclade (terminal SNP), direct paternal line's migration route and heatmap.

















The next step that is recommended by National Geographic is to "Complete Your Profile" and "Contribute Your Story". These can be accessed through the Profile tab and the Our Story tab respectively, but for the first to be accessible, you need to opt into research participation under Profile > Account Settings. The default is "You are currently not participating", but if you check the box below and click on save...

 
...it changes to this:


Then, under Profile, go to "About Me", "About My Family" and "About My Ethnicity" and fill in the pertinent details.


Next, go to the Our Story tab at the top and you will see this:


If you scroll down below this, you will find this window, where you should enter information about your direct maternal ancestral line. This story should only include information on your mother's mother's mother's (etc...) line. Here's mine:


To see your story and the others that have been contributed, click on the "Read Stories" button on the opposite window under "Browse All Stories".


These are the other participants whose mtDNA haplogroup is U5b and have contributed their stories so far. There aren't very many people tested with mtDNA like mine yet as you can see from the "Universe" graphic above (the big blue circle with the red-orange center). The five dots are people whose mtDNA is most similar to mine.

Just for fun, here is peek at a few of the public Y-DNA stories. See anything interesting?



WHO AM I: AUTOSOMAL DNA AND ADMIXTURE
Next, let's take a look at my autosomal admixture results.


According to this, my admixture includes:
45% Northern European
35% Mediterranean
15% Southwest Asian
2% Northeast Asian

Which places me closest to...


Pretty cool since I am 25% Finnish, which as far as I know, is my biggest chunk of ancestry from any single area. My percentages don't match up exactly by any means. My Mediterranean component is significantly higher and my Northeast Asian component is lower than the typical Finn. The description for this latter component notes "... it is also found at a frequency of 5-10% in the Finns, likely introduced by the migrations of the Saami people from Siberia into Finland over the past 5,000 years." Since only one quarter of my ancestry comes from Finland, this discrepancy makes sense.

But, wait, hold on...


Iberian?! I don't have any known Iberian ancestry. Anyway, it doesn't look to me like I match it all that closely anyway.  (For details on how they reach these conclusions, read my earlier post.)

I'm not sure that this method of trying to match all of a person's ancestry to one population label works well for very admixed individuals like me. My individual components may appear to fit best with these two populations when taken as a whole, but this doesn't account for the mixed ancestry I have from multiple regions.

HOMINID DNA
This part of the test is definitely intriguing although I don't really know what to make of it.


The Neanderthal percentage is very close to my 23andMe Neanderthal result of 2.5%. The Denisovan seems on the higher end compared to other results I have seen, but investigating that will have to wait for another day.

EXPERT OPTIONS: TRANSFERRING AND DOWNLOADING
There seems to be much confusion regarding downloading the raw data file and transferring the results to Family Tree DNA, so I thought I would review the Expert Options section.

To transfer your results to Family Tree DNA, go to the Profile tab and then Expert Options:


Click on "Transfer to FTDNA":


Check the option for Geno 2.0 and enter your NatGeo Kit Number (found on your box and/or Profile> Account Settings> Geno 2.0 ID Code, where you have previously entered it to register). Then, check the box if you have a Family Tree DNA kit and enter your kit number and password as above. Click on "Next". On the next screen, you will be prompted to enter your address and it will look like you are going to be charged, but choose "Invoice" (instead of Credit Card) and keep going. Then, you will receive a screen to review that will show a cost of $0. Place the order and, if successful, you should get this:


and this:


 If you aren't sure if it worked, check your home page for this:


So far my account results don't show anything different, but I already have the mtDNA full sequence, so I'm not sure what would be imported anyway.  Many of the men importing their results are getting an extensive list of Y-SNPs on their Haplotree page like this:


Although importing Geno 2.0 results doesn't delete the results from the SNP testing that was previously performed at FTDNA, it will override what appears on the project pages.

Apparently, there is a delay for some accounts receiving the raw data download option and so far, mine hasn't appeared yet. When it does, it will be located under the "Expert Options" tab, just above the "Transfer Data to Family Tree DNA" option and look like this:


It is downloaded into a CSV file after clicking on the Download button.

I was hoping to be able to check my raw data file to see how my mtDNA heteroplasmy was reported, but apparently that will have to wait for another time. 

LOTS MORE TO COME...
Obviously, I don't have my own Y-DNA results to review, but I have been reading all of the reports from our citizen scientists who are already immersed in investigating those newly released results. I will be sure to report on their findings since this will, undoubtedly, be the area of the most groundbreaking discoveries.

In my next post, I will compare and review my admixture results from all four companies.

[Disclosure: I received a complimentary Geno 2.0 kit from National Geographic for review purposes. This has not affected my opinions or analysis.]

Tuesday, January 25, 2011

A comparison of my 23andMe mtDNA v3 and v2 results

There are 13 false positive SNPs that are being found in practically everyone's v3 mtDNA results. No doubt, 23andMe will soon remove them as they are aware of the problem. This post will ignore those since they are clearly in error.

As I mentioned yesterday, my reported mtDNA subclade did not changed in my v3 results and is correct - U5b1b2. According to an analysis done by Dr. Ann Turner of my mtDNA data, there are 795 new SNPs in my v3 results, of which 99 are no-calls for me. I had 28 no-calls out of 2133 SNPs in v2 of the chip. 21 of those had calls in v3. The higher rate of no calls on the v3 versus the v2 is because many of the news SNPs are experimental. If it becomes evident that people are getting no-calls for the same SNPs, the list may be pruned by 23andMe to eliminate them.

All SNPs where calls were made in both chips gave identical results.

I have one miscall 16192C, where I have a mutation 16192T. This also occurred in v2 of the chip (and also in my cousin).  According to Dr. Turner, "It is probably due to the fact that it is very close to the poly-C region surrounding 16189. The probes just don't work well in repetitive regions like that. (Side note: 16189C is a very common mutation, so Mother Nature has a bit of a problem there, too!)."

Here is a list of my CRS values:

16184 C
16185 C
16186 C
16187 C
16188 C
16189 T
16190 C
16191 C
16192 C
16193 C

Thank you to Dr. Turner for her generous time and efforts to help all of us to better understand our mtDNA and 23andMe results.

To read more about my mtDNA tests, you can see my post about my Full Mitochondrial Sequence (FMS) test from FTDNA here.

Monday, January 24, 2011

Update: 23andMe's New v3 Chip Results Are In

Today there is a lot of excitement in the personal genomics community because 23andMe's eagerly awaited v3 results are finally coming in. The customers receiving their results today are ones who bought their kits near the beginning of the last holiday sale. Making it even more exciting is that, according to 23andMe, they are loading thousands of data sets today in this first round. Apparently, they had a very good response to the last sale. This is very good news for customers who are interested in the ancestry aspects of their genetic scans. Judging from this, over the next month, the number of potential "cousins" should jump substantially from the approximately 60,000 records already in their database.

So far, my health results, Ancestry Painting and U5b1b2 mtDNA haplogroup assignment look identical to my v2 results. I am still waiting for my Relative Finder and Ancestry Finder to load. However, I am hearing that some customers have revised and, apparently, improved Ancestry Paintings as well as updated haplogroup assignments.

Giving a little insight into what changes we can expect, Michelle K from 23andMe posted this in the 23andMe Forums on January 19th:

"The first batch of v3 results will become available by the end of this week. Please note that v2 data will not be overwritten by v3 data, rather the two will be merged into one data file. Here are some changes you can expect to see:

RelFinder and Family Inheritance: The Relative Finder algorithm has been updated. Customers who upgrade to v3 may notice small changes to their percentages DNA shared or segment locations in Family Inheritance. Existing, not-yet-upgraded customers may also see small changes to their results as their relatives upgrade.

Ancestry Painting: The Ancestry Painting algorithm has been updated. Upgrading customers may notice small changes to their percentages. Existing, not-yet-upgraded customers will not be affected.

Haplogroups: Upgraded v3 customers may see a slight change in their haplogroup due to updated haplogroup trees and v3 compatibility. The change, if any, should be very minor -- only affecting resolution and not affecting major group assignments. All other existing customers will have their haplogroups recomputed on the new trees later this year. This means, for example, if a child is analyzed on v3 and their parent is on v2, they may have different haplogroup assignments.
Raw data: Upgraded v3 customers may have data for v2 SNPs they previously had no-calls for, if the SNP is on v3 and it yielded data. A complete list of v3 SNPs is expected to be available in the Mendel example profiles by mid-February."

I will be posting all week with updates about the new v3 results, so stay tuned...

Friday, December 31, 2010

My Full Mitochondrial Sequence, Heteroplasmy and Comparing mtDNA designations at FTDNA and 23andMe

I received my Full Mitochondrial Sequence (FMS) results from FTDNA last week. FTDNA lists my mtDNA haplogroup as U5b1, while 23andMe reports it as U5b1b2. I am fortunate in that I have four exact matches in the FTDNA database, including a close relative of Dave Dowell of Dr D Digs Up Ancestors.
Often mtDNA testing is not especially meaningful genealogically, but in my case it is more so because this subclade does seem to be predominantly Finnish, which matches my paper trail perfectly. My matrilineal great grandmother Mathilda Huhtala (1878-1950)  immigrated to the United States from the South Ostrobothnia area of Finland in 1902. Thanks to my wonderful Finnish friends, including one of my early high resolution mtDNA matches, I have a pretty solid paper trail back to Margaretta Mattsdotter Kauppi Storstraka Taipale born 21 July 1712 in Härmä, Lansi-Suomen Laani, Finland. Margaretta is my sixth great grandmother and from the same area of Finland as Mathilda.
I have ten High Resolution (HRV1 + HRV2) mtDNA matches. Eight of these are Finnish and two suspect Finnish ancestry. Eight of the ten have done the FMS test and, of those, I match four. I'd say that I got pretty lucky since so many people have no matches to their FMS in the database so far. There seems to be quite a lot of interest in DNA testing among my subclade. Perhaps this is because Finns have an unusually high participation rate in DNA testing overall compared to other countries outside of the US.

I asked Dr. Ann Turner to review my results. She was especially interested in comparing the mtDNA sequences recorded by FTDNA to my 23andMe raw data. She found 34 no-calls in my 23andMe mtDNA data, including one at 6260 where, according to FTDNA, I have a heteroplasmy (notated by a "R"). She checked my mother's 23andMe data and discovered that she also showed a no-call there. Dr. Turner noted that no-calls are usually not significant, but in this case, she theorized that my mother may also have a heteroplasmy at that location, resulting in the shared no-call.

(Note on heteroplasmy- Funny how a concept becomes so much clearer when you learn that it affects you personally.)

From my custom report prepared by Dr. Turner:
You have the mutations that define superhaplogroup UK (11467G, 12308G, and 12372A)...U5 splits off with 3197C, 9477A, and 13617. U5 in turn is divided into smaller groups, with 7768G and 14182C defining U5b, 5656G defining U5b1, and 12618A defining U5b1b. Somewhat unusually, a mutation in HVR2, 217C, defines the deepest level, U5b1b2.
...the most recent mutations (are) the ones that have not been observed often enough to be formally recognized as a subhaplogroup. Population geneticists sometimes call these “private” mutations, using the word in the sense of “confined to particular persons or groups.” Private mutations may in fact be very recent or quite old, but regardless of their absolute age, they are the ones that narrow down the pool of matrilineal relatives to your closest cousins. Not everyone will even have a private mutation. Your private mutation is 6260R.

Interestingly at 23andMe where I have tested ten close matrilineal relatives so far, one of my first cousin's mtDNA haplogroup is designated as U5b, while the rest of us are U5b1b2. Dr. Turner investigated this difference by checking my cousin's raw data for no-calls. As she suspected, my cousin has a no-call at a defining SNP, thus causing the different designation. She also noted that this cousin does not share my heteroplasmy at 6260, adding, "That's a good illustration of how heteroplasmy levels can vary within a family."

Since Dr. Turner confirmed that there are no known medical implications to my mtDNA results, I am sharing them here for anyone who is interested:
 
HVR1 differences from CRS
16189C, 16192T, 16270T

HVR2 differences from CRS
73G, 150T, 217C, 263G, 309.1C, 315.1C, 573.1C, 573.2C

CR differences from CRS
750G, 1438G, 2706G, 3197C, 4769G, 5656G, 6260R, 7028T, 7768G, 8860G, 9477A, 11467G, 11719A, 12308G, 12372A, 12618A, 13617C, 14182C, 14766T, 15326G

I am in the process of submitting my results to GenBank. It is a bit complicated, so I am including links and helpful instructions I received from Ian below.

If you are looking for your FASTA file to submit to Ian Logan for GenBank, it has been moved. Here is what you do:
Login to your FTDNA account. https://www.familytreedna.com/login.aspx
Go to the mtDNA -> Print Certificate/Report/Data page.
Look for where it says:
mtDNA Results
FASTA File - FASTA
Click on the FASTA File link to download your FASTA file. Further submission instructions are here.

[Disclosure - My company StudioINTV has an existing production agreement with FTDNA that has no bearing on the opinions I express. I receive no other compensation in relation to any of the companies or products referenced in my blog.]