Showing posts with label BGA. Show all posts
Showing posts with label BGA. Show all posts

Thursday, December 6, 2012

23andMe's New Ancestry Painting - First Look!

23andMe's long awaited Ancestry Painting 2 (now called Ancestry Composition) is finally here. I am extremely pleased with my results and those of my family.

The results are presented as a ring chart with settings for different confidence levels and regional detail. The easiest way to figure out how it works is to just click around, trying the different options.

To inspect more closely, click on any of my images to enlarge.

This is my Standard Painting with no regional detail (still 100% Booooring!):















After clicking on the rings or on the + sign, I get this:














 Clicking some more, I get this:














Then, changing from Standard setting to Speculative, I get this:
















I vastly prefer the "Speculative" setting since it seems to fit very well with what I know of my ancestral origins.

The pie chart below reflects my known ancestry. It was created from an Excel spreadsheet made by John Tierney and available on his blog.

Ancestral breakdown based on my family tree


Compare to my new AP2 percentages:



My Finnish and Scandinavian percentages seem a bit low, but in my sisters' paintings, they look about right:
















 My mother's also appears to fit with what I know of her heritage:















My dad's siblings have an interesting surprise in that we finally got some different colors:

















It appears that perhaps I do have some African ancestors after all (in a relatively recent time frame)!

My brother-in-law's ancestry becomes even clearer with the new Ancestry Painting. The small amount of Asian disappeared and was replaced with an increased African component. From what I've seen during beta testing, this appears to be the case with many of those with African American ancestry.

Compare to his old Ancestry Painting:



Another person who is half Indian got this interesting result:

  Compare that to his old Ancestry Painting:













Much improved, right?


 Look at this chart:


Beautiful, huh?


CHROMOSOME PAINTING

I am happy to report that, although we did not get a chance to beta test this portion of the new feature, the chromosome painting, including the X chromosome, is now live.

My painting:


With my Finnish ancestry highlighted:



This is what it looks like with one Finnish parent:


*Note that the paternal and maternal chromosome orientation is not always consistent in placement (top versus bottom) in this chart.
 
This man has one Indian parent:


Pretty clear, isn't it?

And this a beautiful painting:






Don't you agree?


PHASING AND SPLIT VIEW

23andMe uses their own customized version of a phasing engine called BEAGLE to separate out the genetic components inherited from each of our parents, even without actually testing them.  However, if you have a parent or child in the 23andMe database, then your phasing will be improved. This will lead to more accurate assignments as well as more detail contained in your ancestral breakdown (i.e. Italian versus Unspecified Southern European). Therefore, if you are fortunate enough to have tested one of these close family members, you need to let 23andMe know about this by connecting their profiles to your Family Tree.

If you have at least one of your parents in the 23andMe database (and connected to your tree), then you get a third view called "Split View". This view will automatically show you which parent contributed which portions of your ancestry. 





REFERENCE POPULATIONS
                                         
23andme is currently using 22 populations. They can all be seen on my breakdown here:




In order to get more information on the origin of the reference populations, you can click on their labels and it opens up to this:


For some populations, 23andMe has a lot to go on:



                                      
and for some, not so much (as expected):


















Obviously, we would all like to see more detail and variety in the African reference populations. For now, this is all there is:




















The new Ancestry Composition is expected to continue to change and improve as 23andMe builds their database. As you can see, this is especially important for African Americans. In the announcement on the forum, 23andMe geneticist and Product Manager Mike Macpherson acknowledges, "But there’s still more to do. One important example of this is that the system is designed to be able to update the reference populations. As it is now, Ancestry Composition can dive into European ancestry, but it offers limited resolution into East Asia and Africa. We’re working now on an update that will split up the Eastern Asian and Sub-Saharan African populations."

The 23andMe white paper explaining how this new feature works tells us just how far they have come, "We compiled a set of 7,868 people with known ancestry, from within 23andMe and from public sources. That’s over 15,000 chromosomes, since every individual contributes a chromosome from both their mother and their father. This a big jump over the 210 individuals that powered our original Ancestry Painting feature." The paper further tells us that the public reference datasets that make up the "Public" numbers that you see above, include the Human Genome Diversity Project, HapMap, and the 1000 Genomes Project. It goes on to explain, "Populations may be inherently difficult to distinguish because of historical mixing, or we might not have had enough data to tell them apart. As we obtain more data, populations will become easier to distinguish."

At least for me, this is a very good start! In fact, I think this just might be the best admixture tool I have tried so far. What do you think?

Tuesday, September 18, 2012

LivingSocial's AncestrybyDNA Offer is NOT the AncestryDNA Test!

It has come to my attention that many people interested in genetic genealogy may be purchasing the AncestrybyDNA test thinking it is the AncestryDNA test offered through Ancestry.com. This week LivingSocial has been promoting a $97 "deal" for AncestrybyDNA that reads "AncestryDNA" in the headline (which is trademarked, by the way).

LivingSocial offer on 9/14/12 (price is actually $97 - I have $40 credit in my account)

I was worried when I first saw it that some people may mistake this for the AncestryDNA test due to the headline. Exactly as I feared, I starting seeing messages on mailing lists from people that were under the impression that this was a way of purchasing one of the "invitation only" AncestryDNA tests. (The AncestryDNA test is now out of Beta and you can order here.) I mentioned this to Ken Chahine, General Manager at AncestryDNA, because I was afraid that some people might be tricked into buying this test due to of the misleading way it was presented and then stay away from genetic genealogy after a bad experience.

Today, I noticed that the offer looks different.

LivingSocial offer on 9/18/12

I'm not sure when they changed it, but I am bothered by the fact that upwards of 443 AncestrybyDNA tests have been purchased in the interim. When they offered the same deal in July of this year, you can see that there were significantly less takers (only 81).

LivingSocial offer on 7/28/12

Is this increase due to the heightened visibility and popularity of the AncestryDNA test during this time? It wouldn't surprise me a bit if that is the case.

AncestrybyDNA is a test that has been around for a long time. It is an autosomal DNA test, but not by any means the same as the new autosomal AncestryDNA test. It is a biogeographical ancestry analysis which is based on only 176 markers, while in stark contrast, the AncestryDNA test is based on 700,000 markers. Further, the AncestrybyDNA test does not have any relative finder capabilities, which, in my opinion, is currently the strongest aspect of the AncestryDNA test.

The FAQs on the AncestrybyDNA website states, "The AncestrybyDNA™ test provides your ancestral proportions based on years of collaborative research of populations representing 4 ancestral groups. This research identified 176 informative markers in our DNA, called Ancestry Informative Markers (AIMs)." The FAQs on the AncestryDNA site explain, "The AncestryDNA test uses microarray-based autosomal DNA testing, which surveys a person’s entire genome at over 700,000 locations, all with a simple saliva sample. Additionally, the new online interface integrates state-of-the art tools for you to utilize your DNA results for family history research."

The description on the LivingSocial ad is as follows:
Everyone has a story, even if we don't know exactly how it begins. Uncover the early chapters of your past with today's deal from AncestrybyDNA.com: Pay $97 (regularly $195) for an AncestrybyDNA test, with results available online. Swab the inside of your cheek and send it in for analysis -- your DNA sample will be tested for your complete ancestral makeup based on your chromosomes, giving you results of your full ancestry, instead of just simple information based on your direct maternal and paternal lines. Your ancestral origins will be quantified in percentages across four population groups: Indigenous American, European, East Asian, and African. With a personalized ancestry test certificate and a detailed manual to explain and interpret your results available online, you will have a clearer picture of where you come from -- and possibly be able to close the book on some family mysteries. 

I think this description is also a bit misleading. The AncestrybyDNA test is based on old technology by today's standards and is not useful for genealogical purposes. While possibly of entertainment value, to say that it will test "your complete ancestral makeup" and give you results on "your full ancestry" is really stretching it.

I have nothing against AncestrybyDNA and I'm a fan and customer of LivingSocial, but if you bought this offer thinking you were getting an AncestryDNA test from Ancestry.com, I would write to LivingSocial and ask for a refund. Fair is fair.


**Update - 1/21/13 - This offer is back again. After receiving a lot of very negative feedback about this test and the disappointment caused by it, I would like to suggest that if you are considering purchasing it, please do your research and review these four other geographic origin DNA tests that I recommend instead. (Personally, I like 23andMe and at $99 it is only $2 more than the AncestrybyDNA Living Social offer. You will get MUCH more detailed, useful results from that test.)

**Update- as of 9/26/12, almost 4000 tests have been sold through this promotion.
LivingSocial offer on 9/26/2012