Thursday, September 27, 2012

Family Tree DNA 72 Hour Weekend Sale Starts Now

Family Tree DNA just announced a short 72 hour sale starting now through Sunday night 11:59pm (CDT).

Here is the text of the email I received:

It seems every time we run a flash sale a few people e-mail us days later that they were traveling, sick or just had not looked at their e-mails in time, so for all of you who want to entice a friend, neighbor or reluctant relative to get involved in Genetic Genealogy here's one more opportunity, but it will last for only 72 hours.
We are gearing this sale for newcomers and upgrades by promoting the Family Finder and the Full Mitochondria Sequence (FMS). This sale starts Friday, September 28, at 12:00am and ends Sunday, September 30, at 11:59PM.
New Kits Current Price SALE PRICE
Family Finder $289 $199
mtFullSequence $299 $199
Family Finder + mtFullSequence $559 $398
Upgrades Current Price SALE PRICE
Family Finder $289 $199
HVR1 to mtFullSequence $269 $199
HVR2 to mtFullSequence $239 $199
mtFullSequence $289 $199
As with all promotions, orders need to be placed by the end of the sale and payment must be made by the end of this sale. Learn More

Thursday, September 20, 2012

Let's All Start Using Terminal SNP Labels Instead of Y Haplogroup Subclade Names, Okay?

Is it just me or have the subclade names for Y-DNA just gotten out of control? I work with DNA all day long and I can't even keep up with all of the changes, so I have decided to start using the Terminal SNP labels exclusively. May I gently suggest that you do so also?

I frequently receive emails from otherwise well-informed people asking what their Y-DNA haplogroup subclade means, and it isn't their fault they are confused. You see, if they try to Google it, they are often unable to find information. If they try to locate academic papers on it, they are usually unsuccessful. Why is this? Well, the subclade name that they are given by their testing company may not be the same name that another testing company uses, or even the same as it was when they were first assigned it...and, quite likely, it isn't the same as the one on the most up-to-date tree at the International Society of Genetic Genealogy.

I have to admit that when R1b1b2 was changed to R1b1a2, I just started saying "R1b...whatever" when referring to it. Isn't it easier to just remember the defining SNP name R-M269?

For example, if you are R-L21+, then according to Family Tree DNA's Haplotree, you are R1b1a2a1a1b4, the ISOGG 2011 Haplogroup Tree's name for it. At 23andMe, you are R1b1b2a1a2f in agreement with the 2010 ISOGG Haplogroup Tree. If you tested in 2008, you might still think you are R1b1b2a1b6.  On ISOGG's 2011 Haplogroup Tree , L21+ was R1b1a2a1a1b4, but on ISOGG's 2012 Haplotree, you are R1b1a2a1a1b3. Apparently, R1b1a2a1a1b4 is now referring to L238/S182! I mean, really, how can anyone keep track? (Ah, for the days of the simple little R tree.) I don't know how our ISOGG Haplogroup Tree Committee* does it anymore! Apparently, the academics are getting tired of it too and it's just going to get worse when results from Geno 2.0 start rolling in with LOTS of new SNPs and subclades being defined.

Take look at the history of R-M222, the "Ui Niall Subclade", on just the ISOGG SNP Tree:
2007 = R1b1c7
2008 = R1b1b2a1b6b
2009 = R1b1b2a1a2f2
2010 = R1b1b2a1a2f2
2011 = R1b1a2a1a1b4b
2012 = R1b1a2a1a1b3a1a1

Reportedly, Geno 2.0 will define at least three new subclades beneath M222, but I hear it may be more. Do you think those subclade names might get even longer?

The R Haplogroup Tree is definitely the worst, but the problem is starting to affect other haplogroups too. At FTDNA, my dad is I2b1. Same at 23andMe. Sounds simple, right? Not anymore! The subclade name was recently changed to I2a2a on the ISOGG 2012 tree. I am so confused! This was one subclade name that I felt very comfortable with. I think I will just learn to call it I-M223 from now on. (I'll just ignore that his brother recently tested Z2062+, which isn't even on any of the trees yet!)

Actually, there is some rhyme or reason to these discrepancies, so let me share it for those of you who have no idea what I am writing about. FTDNA last updated their Y haplogroup tree in 2010 and 23andMe in 2011.*  So, they are going by the subclade names that were recognized at those times. In contrast, the ISOGG Haplogroup Tree has been updated over 60 times JUST THIS YEAR! Every time a new SNP is discovered that is upstream of a known SNP (which is happening faster and faster all the time), it has to be inserted into the tree, thus changing the subclade naming pattern. This is why it is so much simpler to just learn the Terminal SNP label.

The ISOGG Haplogroup Tree is a tremendous resource that anyone who is doing Y-DNA research should be utilizing. It helps to keep things straight by giving the various names of the SNPs that are being used by different companies and labs. When two or more SNPs are identical, meaning that they are on the same place on the Y-haplogroup tree with the same mutation, ISOGG shows the names in a series punctuated by "/". For example, let's look at M173/P241/Page29. M173 comes from Peter Underhill's lab at Stanford; P241 comes from Michael Hammer's lab at the University of Arizona and Page29 comes from the Page, Whitehead Institute for Biomedical Research. They appear in academic publications with these names and ISOGG lets you know that they are identical SNPs. That way, if you are Googling or looking for academic papers about your SNP, you know to try those ones too.

Going back to my first example of R-L21+; Wikipedia states, "R1b1a2a1a1b4 (R-L21) is defined by the presence of the marker L21, also referred to as M529 and S145." The label L21 comes from Thomas Krahn's FTDNA lab in Houston, M529 comes from Peter Underhill's lab at Stanford and S145 comes from Jim Wilson's lab at University of Edinburgh. ISOGG shows the SNP as L21/M529/S145. The bottom line is that if you test L21, M529 or S145 at any company, your assignment is in an identical place on the Y-DNA tree, so the subclade name is not the significant factor, the SNP name is.

Of course, with so many new SNPs being discovered and assigned to the tree, there will likely be a certain amount of continuing confusion among those of us doing Y-DNA research for the time being, but I hope you will all consider joining me in taking the next step forward in the evolution of Y-DNA research in genetic genealogy and stop trying to remember those mind-bending sublcade names! And, while we're at it, let's give our ISOGG Y-Haplotree Committee a well-deserved virtual pat on the back too!

The Y Chromosome Consortium (YCC) is a cooperative association of geneticists, led by Dr. Michael Hammer, who first published the paper in 2002, "A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups", introducing the modern haplogroup nomenclature of Y-DNA. The tree was subsequently revised in 2003 by Mark A. Jobling and Chris Tyler-Smith in another paper, "The human Y chromosome: an evolutionary marker comes of age". Next, Family Tree DNA created the 2005 Y-Chromosome Phylogenetic Tree, which was the first online tree and only available to their customers. Soon thereafter, ISOGG created the first public online tree in 2006.  Tatiana Karafet of Dr. Hammer's lab (and others) published a paper further refining the Y chromosome tree in 2008, "New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree". As a result, both FTDNA and ISOGG updated their trees at that time. Then in 2010, FTDNA came out with a YCC-sanctioned tree which was distributed at the FTDNA conference and, as a result, ISOGG promptly did a major update to stay in alignment with the YCC.  Since then, no updates have come from the YCC. Undaunted, the ISOGG Y Haplogroup Tree Committee has continued to add information as it becomes available from various sources and is now the most up-to-date source of this information.  In November 2011 at the FTDNA Project Administrator's Conference, Spencer Wells of National Geographic, Michael Hammer of the University of Arizona, Thomas Krahn and Bennett Greenspan of FTDNA and Alice Fairhurst of ISOGG, reportedly agreed to all stay in alignment with the most current Y-DNA nomenclature to the best of their abilities. As always, there is new research that has not yet become public. As it is released, ISOGG will again align its tree with the most current information and will continue to add updates as they become available. With the upcoming launch of Geno 2.0, the ISOGG Committee will have their work cut out for them! Current ISOGG members who work with the tree and deserve our great appreciation are: Coordinator: Alice Fairhurst. Design team: Tanmoy Bhattacharya, Tom Hutchison, Richard Kenyon, Doug McDonald. Content experts: Abdulaziz Ali, Whit Athey, Ray H. Banks, Katherine Hope Borges, Aaron R. Brown, Phil Goff, Gareth Henson, Tim Janzen, Bob May, Eugene Matyushonok, Lawrence Mayka, Charles Moore, Ana Oquendo Pabon, Marja Pirttivaara, David Reynolds, Bonnie Schrack, Vince Tilroe, Aaron Salles Torres, Steve Trangsrud, Ann Turner and David Wilson.

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 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 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, 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

Sunday, September 16, 2012

Adoptee Finds Birth Family at AncestryDNA

After my posts criticizing AncestryDNA for their handling of "Chris and Pat's" matching, it is only fair to report the terrific news that the second adoptee mentioned in my original story (let's call her Jenny) has confirmed that her close match is, indeed, authentic. A few weeks ago "Jenny" reported that she received a match with a predicted first cousin at AncestryDNA. Today we received the news that Jenny has actually found her biological paternal aunt!

At first I thought there was a discrepancy between the prediction and the actual relationship, but after seeing screen grabs from Jenny's account, I realized that Ancestry has two different categories that each include first cousin; one is "Close Family - First Cousin" and the other is "First Cousin - Second Cousin".  Given this opportunity, let's take a look at Ancestry's "First Cousin" categories.

I happen to have a known first cousin in my mother's AncestryDNA account, so I can compare the two categories here. Vi is predicted to be a First Cousin to my mother with a range of 1st Cousin to 2nd Cousin:

My mother's first cousin at AncestryDNA

With this explanation:

Click to Enlarge

Since I have this same cousin available for comparison at 23andMe, I can tell you that she shares 14.5% of my mother which is a bit higher than average. So, AncestryDNA got this right even though Vi and my mom share more than would be expected for a first cousin relationship.

My mother's first cousin at 23andMe
I share a first cousin once-removed relationship with Vi and 7.44% of my DNA, and she correctly falls into the same First to Second Cousin Category for me at AncestryDNA.

There is another category at AncestryDNA that is labeled as Close Family to First Cousin. It looks like this:

With this explanation:

Click to Enlarge

This is the category that the Jenny's match was placed, so in this case AncestryDNA's prediction was also correct.

AncestryDNA has not released their category guidelines, but from this I can deduce approximately what the percentage cut-off must be between the two categories (if they are using the traditional matching process that we are familiar with from 23andMe and Family Tree DNA's Family Finder). An aunt would share approximately 25% of her DNA with her niece, first cousins share approximately 12.5% of their DNA, first cousins once-removed share approximately 6.25% of their DNA and second cousins share approximately 3.125% of their DNA. These are variable numbers which are only an average, so some individuals, like my mom and her cousin Vi, will share more and some will share less than expected. AncestryDNA has apparently taken this into consideration since they correctly placed my mom's first cousin Vi in the lower First Cousin - Second Cousin category instead of the Close Family - First Cousin category. Without more comparisons, it is impossible to accurately guess AncestryDNA's upper end cut-off for this category, but at 23andMe my highest aunt/uncle relationship comparison is 27.88%, while my lowest is 21.14%, so they probably include at least 28% in this category and possibly much higher since the next closest genetic relationship level shares about 50% of their DNA - full siblings. AncestryDNA likely takes additional information into account in their predictions such as longest segment length and how many shared segments, but for general guidelines, the categories possibly look something like this:

Close Family - First Cousin Category        28% - 15% in common
First Cousin - Second Cousin Category     15% -  5% in common

If this is close to their actual thresholds, then the Close Family Category could include half-siblings, grandparents, aunts and uncles (as we have seen in Jenny's case) and possibly great grandparents/first cousins who are on the high end of expected shared DNA.

With all of this analysis, I don't want to get sidetracked from the joy of this story. Jenny is absolutely thrilled to find her paternal birth family and they seem to be thrilled to find her! She is very appreciative of AncestryDNA's part in her discovery and, thanks to that aunt who is a member of, Jenny already has an extensive genealogy for half for her biological family!

Jenny shared her thoughts with me:

I need to give AncestryDNA some credit, they were 100 percent right on this one. Although I still stand by my opinion that their system needs changes, because there still is no way to know if there are errors...They need to release the raw data, not everyone is going to be as lucky as I was, but I also don't want to discourage people from submitting their DNA.  The more DNA they receive, the better the results I would presume.  They have a great system for the most part, but with no way to interpret it, we have to just have blind faith in Ancestry that our results are correct.

Personally, I am very happy to be able to report this positive flip side to my earlier story because I do not want to discourage anyone from participating in DNA testing. Although not my first choice, with a database that has exceeded 65,000 (judging from recent ID numbers), AncestryDNA is a viable place to search for relatives whether it be for adoption reunification or genealogical purposes. You can bet that we, as a community, will keep badgering the folks at AncestryDNA for our raw data and access to more detailed genetic information, but some will enjoy success with their matching system even as it currently is. In fact, because of their outstanding automated matching combined with their vast collection of already existing family trees, a number of individuals have already reported confirming many common ancestors with their matches at AncestryDNA and, in some cases, broken through decades-old brick walls. These successes could greatly aid in, perhaps, the loftiest dream of our community - to build a universal genetic family tree by "assigning" DNA segments to specific ancestors, but only if AncestryDNA decides to release the genetic data to their customers. Let's keep our fingers crossed that they will soon listen to us, because what a wondrous thing this could be!

[10/26/12: This test is now out of Beta, so you can order it here.]

Saturday, September 15, 2012

23andMe Reports "No Match" for Adoptee's Predicted Parent/Child at AncestryDNA

Since so many of you have expressed an interest in the outcome of this situation, here is the promised follow-up on "Chris and Pat's" predicted parent/child match at AncestryDNA

Both parties received their results from 23andMe this week and, unfortunately, it was determined that they are not a match after all. This means that it is not possible for them to be more closely related than third cousins and, most likely, they share no genealogical relationship at all. Not surprisingly, Chris (the adoptee) is extremely disappointed and, understandably, discouraged. 

Dr. Joanna Mountain, Senior Director of Research at 23andMe, volunteered to review the results with Chris in order to assist in discovering any enlightening new information pertinent to Chris' heritage. Although Chris did not have any matches close enough to come to any definite conclusions at this time, Dr. Mountain was able provide some direction and helpful insights of which Chris was very appreciative. 

I requested statements from both companies in regard to these results: 

“We already acknowledged a laboratory error a few weeks ago that affected a small number of customers’ DNA results that showed incorrect matches. We immediately took action to communicate directly with our customers in order to correct their results, which in some cases required a retest of their DNA. In an effort to solve the issue as quickly as possible, we expedited processing and are already delivering updated results as they become available. Overall, feedback from our customers was positive and most were pleased that we followed up with them personally and took the necessary efforts to correct this in a timely manner. 
We apologize for this error as we continue to fine-tune this new service and have implemented additional measures as an ongoing effort to ensure the quality of our new DNA product.” 

[AncestryDNA's earlier acknowledgement]

"We hope that becoming part of the 23andMe community proves rewarding for everyone involved. 
We believe the clarity we were able to provide in this instance along with the ancestry and health features we offer will serve to move their search forward and wish them the best of luck in their continued efforts." 

The good news is that new matches will continue to come in as the database grows and we now have the raw data to work with, so this will not be the end of Chris' story. Since Chris' family is very proactive and two search angels and I will continue to assist them in their efforts, I am confident that there will be better news to report in the future.

Thursday, September 6, 2012

Flash Sale on 23andMe kits

It was just posted on the 23andMe forum that the promotions site Gilt City (think GroupOn) is offering a discount on 23andMe kits. You can purchase one kit for $225 (savings of $74) or three kits for $600 (savings of $99 each). The site says that the offer is good until Thursday, September 13th, but they may sell out before then. You have until December 6, 2012 to redeem it. (Makes a great holiday gift!)

Find the sale here.

**Great news - This sale has been extended through Oct 1st.