The First Ever Independent Genetic Genealogy Conference was a Smashing Success!

It has been a week now since our history-making  SCGS/ISOGG Genetic Genealogy Conference in Burbank. It was a smashing success in every way. I wanted to take a moment to thank all of the speakers who generously came, often from all the way across the country, to share their knowledge and expertise with us. I was thrilled and honored by the enthusiastic response from all of the speakers to my invitations to participate.

Professor Henry Louis Gates, Jr. and Dr. Spencer Wells were our headliner speakers and they definitely lived up to their reputations (and more). We would have been extremely lucky to have even one of them attend. For me, having both accept my invitation to speak was nothing short of incredible!

Dr. Wells of National Geographic did a wonderful job encouraging all of us citizen scientists and recognizing our efforts. I had seen him speak before and always love how he makes the science so interesting and approachable, even for the beginners in the audience. Dr. Wells spent the day at the conference, attending presentations and interacting with the community. He even joined us for dinner and socialized with a group of genetic genealogists late into the night. He is definitely one of us!

The packed house for Spencer Wells' wonderful opening presentation

Professor Gates spoke at our luncheon and he was absolutely hilarious! I had no idea he would have us rolling in the aisles with laughter the way he did. If he ever decides that he wants a new career, stand-up comedy should be first on his list! He regaled us with tales of his own family history and his early ventures into television. The Professor was a fitting participant in our history-making day since his PBS shows were the first to introduce genetic genealogy into American homes. He also stuck around most of the day, attending presentations and socializing with the attendees. (I have to tell you that giving a presentation while looking out on the audience of Dr. Wells, Professor Gates, Dr. Mountain and many of my colleagues was quite intimidating!)

Professor Gates entertaining us

With these two celebrities, it might seem easy to forget our other speakers, except that they were all so outstanding in their own right! We had wonderful representation from the companies that our community depends on - Bennett Greenspan from Family Tree DNA, Dr. Joanna Mountain from 23andMe and Dr. Ken Chahine from AncestryDNA all gave presentations packed full of valuable information for genetic genealogists. Their speeches were standing room only. This was a very important part of the event to me. From the beginning of the planning process, one of my goals for the conference was to gather management from all of these companies in one place with the common purpose of promoting the education of the community. This was the very first time that this has happened and it will not be the last time.

Dr. Mountain explaining the finer points

Many of our leading genetic genealogists also generously gave of their time to ensure that our first conference would be a success. The informative presentations from Dr. Tim Janzen, Blaine Bettinger, Judy Russell, Dick Hill, Debbie Parker-Wayne, Alice Fairhurst, David Reynolds, Emily Aulicino and Katherine Borges were essential to this groundbreaking event. Many of these presentations were livestreamed and/or recorded so more people could benefit from these outstanding speeches. Dr. Kathy Johnston and Bonny Cook were also integral to the event and helped it to run as smoothly as it did. Additionally, all of the roundtable discussion leaders and the general volunteer efforts were very much appreciated by us all.

Blaine Bettinger sharing his knowledge

We had a total of 352 attendees, including speakers, which is a very good turnout for the first conference of this kind in the history of our field. We even had attendees from China, Australia and the UK, making this an international event! Thank you all for the tremendous support! The success of this inaugural event ensures that we can hold similar conferences in the future. This has proven that the time had indeed come for genetic genealogy to have its own annual conference. Thanks to SCGS for giving us this trial run, Paula Hinkel for her expertise in conference planning, which ensured a perfectly executed day, and Vicki Hilb for taking such good care of the speakers.

Next year we plan to hold the event on the East Coast, so those who could not make the long trip this year can participate in our second annual conference. I hope to again entice our wonderful Dr. Wells and Professor Gates to join us (they say they will!). We intend to hold a two day event next time in order to allow attendees to see more of the speakers and presentations. I will update everyone once we have dates and a location nailed down. I hope it will be as much fun as this one was!

Unfortunately, I didn't get pictures of everyone since it was such a whirlwind day, but thanks to Tim Janzen, I have quite a few to share with you all.  (His are the clear ones. :-))

 CeCe and Professor Gates

Tim Janzen Presenting

 

Dick Hill telling his tale...

The Gates Luncheon

 

Confirming My Pedigree with DNA

What the Livestreaming looked like from our end

 

Does DNA Testing Work?

Socializing was fun with Blaine...

...and Debbie Parker-Wayne (with Cyndi Howells of "Cyndi's List" in the background)

I couldn't have asked for a better group of people with whom to share the day! There were so many familiar faces and friendly people that it was impossible to have the time to speak to everyone I wanted to. It was wonderful to be among people who share the same passion for genetic genealogy. Thank you to everyone who made the event so successful. It really was a dream come true!

Update: I received some great new photos from Katherine Borges which I have added, two below and one above in the section about Dr. Well's speech.

Adam, Spencer Wells, me, Lennart, Leo and Alice's infamous gold hat

At the Jamboree ISOGG booth, Back Row: Emily, Bonny, me, Kathy
Front Row: Linda and Katherine

A Sneak Peek at the UPDATED AncestryDNA Search Filter

AncestryDNA has been hard at work perfecting the new search filter these last few weeks. Not surprisingly, it has undergone some changes since I last shared it with my readers.

Stephen Baloglu, Ancestry.com's Director of Product Marketing, described what appears to be the version that will go live in the next few weeks:

The search includes looking within your DNA matches for surnames and birth locations in their family tree that they have linked to their DNA results. It does not currently include searching for username, but we may update that in the future. The top request was surnames/birth locations, so we started there. Also, we expect people to more likely know surnames they're looking for much more often than ancestry username.

He also shared these screen shots and accompanying descriptions with me on June 6th. Click to enlarge them for a closer look.

 

In a YouTube video on Ancestry.com's account (dated June 3, 2013), this slide is shown describing the AncestryDNA search filters.

Notice that the username search was, apparently, still expected at that time. Ancestry.com employees Anna Swayne and Crista Cowan discuss it on the video from about 15:30 to 16:00.  Crista clarifies that the username filter will be "an ability to search by the name of somebody who is a DNA match" and Anna says that it "will be coming soon". However when I asked Ken Chahine, General Manager of AncestryDNA, about the username filter at the recent DNA conference on June 6th, he explained that Ancestry.com does not currently have the option to search by username built into their system, which is limiting AncestryDNA's ability to provide it. [Update: I have asked for clarification on this point.]

Although this additional filter would be convenient, in my opinion, it isn't essential. For example,  I would like to search my mother's account to determine which of my matches with a surname of interest also appear in her account, but I can do so almost as easily by searching on that surname. Further, to search your account to see if your research partners appear as matches, you can also filter by your shared surname(s). I would really like to see an "In Common With" filter to determine which of my matches are from my mother's side, but, fortunately, I can already use Jeff Snavely's tool for that purpose.

With these upcoming filters, Jeff's terrific tool and Family Tree DNA's recent announcement that they are accepting raw data uploads from AncestryDNA (for only $49!), this test is becoming much more useful for genetic genealogists. (Now, if only we could get that chromosome browser onsite!)

Stephen tells me that there still isn't a confirmed date for the new search filter's arrival, but I expect it to appear sometime this summer.

AncestryDNA, Raw Data and RootsTech

Tim Janzen and I discussing the AncestryDNA features at RootsTech with AncestryDNA staff

Since RootsTech there has been lots of discussion regarding the features that AncestryDNA is and is not planning to offer their customers. I will address the many questions that I have received about the meetings in which I participated at the show, but first let's review:

Raw Data Downloads
On Thursday, AncestryDNA fulfilled their promise to allow customers to download their raw data. As Dr. Ken Chahine had assured me back in November, the file is not encrypted and is compatible with third party tools.

I sent my file to a number of third party providers:

1. After working with it a bit, John Olson announced on the site that he expects that Gedmatch will be accepting AncestryDNA uploads in about two weeks. 
2. David Pike told me that he has updated his tools to work with the AncestryDNA files.
3. Leon Kull has reportedly updated his HIR search site to work with them as well.  
4. Dr. Ann Turner has created an Excel macro to convert the AncestryDNA files to 23andMe format. 

At the "Ask the Expert" Genetic Genealogy panel that I moderated at RootsTech on Saturday:

1. Bennett Greenspan told the audience that Family Tree DNA will be accepting AncestryDNA transfers into Family Finder starting on May 1st.
2. Dr. Catherine Ball confirmed that the raw data file is not phased and that they are delivering it as they receive it from the chip manufacturer Illumina.  She also confirmed what Dr. Ann Turner had already discovered - the data labeled as "Chromosome 25" is from the PAR region. Further, the "Chromosome 23" label refers to the X chromosome data and "Chromosome 24" refers to the Y chromosome.

Additional notes:

1. Unlike Family Tree DNA, AncestryDNA is not removing any SNPs from the data - medically relevant or not. 
2. The overlap between AncestryDNA's raw data file and 23andMe's should be around 690,000  SNPs due to the fact that they are both using the same Illumina OmniExpress Plus base chip. The ~10,000 SNP difference can be accounted for due to a different set of poorly preforming probes and test SNPs. Family Tree DNA's should have a similar overlap for the same reasons.
3. There is no mitochondrial DNA included in the raw data file because it is not included on the Illumina chip that they are using. (23andMe adds the mtDNA SNPs).

Search Function
As I expected from earlier conversations with AncestryDNA, a search function is next on the list. Kenny Freestone, Product Manager for AncestryDNA, discussed it in his presentation under the heading "What's Next". Although it is already in the works, Kenny could not provide a firm timeline for its availability when I asked.

We will be able to filter our list of matches by surname, location and username. As anyone who has worked with their AncestryDNA matches knows, this is sorely needed. There is no doubt that the many requests from customers pushed this up their list of priorities.

Genetic Ethnicity Update
Later this year, AncestryDNA will be updating their Genetic Ethnicity feature. They will provide more granularity in Europe and West Africa. We can also expect more accurate breakdowns. A number of AncestryDNA personnel acknowledged to me over the weekend that certain "ethnicities" (i.e. - Scandinavian) are overestimated for many customers. However, they also emphasized that much of the perceived problem with their admixture analysis stems from the question of "where and when". What they mean by this is that it is very difficult (and sometimes impossible) to pinpoint where specific DNA signatures were at an exact time in history.

As I always remind my readers, this portion of the science has a long way to go and will improve with more data and time. On the "more data" front, during her speech at the AncestryDNA luncheon on Friday, Dr. Ball was reportedly requesting that genealogists who know that all eight of their great grandparents were born in the same place share this information with AncestryDNA. This seems to imply that, like 23andMe has successfully done, AncestryDNA plans to use customer data to improve their predictions. They are also starting to work on incorporating the coveted SMGF collection into their admixture analysis, which should improve it greatly.

The good news is that AncestryDNA customers don't have to wait for this update to gain more insight into their ancestral origins. Now that AncestryDNA has made the raw data available, customers will be able to upload their raw data file to the various third party sites to try out the admixture calculators and/or send it to Dr. McDonald for his very highly regarded analysis.

Matching
AncestryDNA are currently working on an algorithm to improve matching for endogamous populations, specifically Ashkenazi Jews.

As I reported in November, the minimum threshold for matching is 5 megabase pairs. This was reconfirmed in a conversation I had with Dr. Ball on Friday. I also learned that there is no minimum SNP requirement. We discussed the possibility of AncestryDNA switching to centiMorgan measurements in the future.

Price
The test is now $99 for everyone - subscribers and non-subscribers. This was likely in response to 23andMe's recent price drop. Having attracted well over 120,000 customers in less than a year in business, AncestryDNA is proving to be an important player in this field. This new policy to attract subscribers and non-subscribers alike will only improve their market share.

International Customers
It does not appear that AncestryDNA has plans to offer their test to international customers in the near future, instead choosing to focus on the U.S. market for now.

Matching Segment Data and Chromosome Browser
On Friday at RootsTech, Dr. Tim Janzen and I sat down for a meeting with AncestryDNA management. Among others, we were joined by Dr. Ken Chahine, Senior Vice President and General Manager of DNA, and Dr. Catherine Ball, Vice President of Genomics and BioInformatics. (Dave Dowell also attended a portion of the meeting.)  I found them to be very receptive to hearing our requests and the reasons behind them. At no time did they state that they had decided not to build a chromosome browser or release matching segment data to their customers in the future. Dr. Ball did express some privacy concerns, but was open to hearing ideas of how this could be addressed.

Tim Janzen explains his feelings while Ken Chahine looks on

During the meeting, Tim very emphatically explained his feelings on the need for matching segment data (above) and I resorted to begging (below)... {hehe}

Catherine Ball, Ken Chahine, Tim Janzen, me, Dave Dowell and Steve Baloglu

On Saturday, after attending Kenny Freestone's presentation, four advanced genetic genealogists approached him to discuss the chromosome browser issue. In addition to myself, Tim Janzen, Angie Bush, and Nathan Machula were present for the conversation. Kenny didn't have much to say and mostly listened to the arguments that we presented covering why we feel that it is essential that AncestryDNA offer the matching segment data behind their relative predictions. At no time did he state that AncestryDNA would not offer a chromosome browser or that the delay in doing so was because AncestryDNA didn't think that their customers could understand it.  He did, however, confirm that it was not a top priority at this time. He also said that he personally reads all of the requests sent through the feedback button, so if you want them to reassess their priorities, then be sure and let them know.

Tim emphasized that both 23andMe and Family Tree DNA included a chromosome browser feature at the launch of their autosomal DNA product and wondered aloud why AncestryDNA had not done so as well.  I explained to Kenny (as well as in my meeting with management) that, as genealogists, we expect conclusions to be evidence based. It is not in line with this principle to simply be told that a certain common ancestor is responsible for a DNA match and be expected to take AncestryDNA's word for it. Where is the proof?  Since Kenny had shown a chart during his presentation of his ancestral lines that he claimed were genetically confirmed by AncestryDNA matches, I also pointed out the fact that those lines that he had shaded in weren't really confirmed without the actual genetic data to support that claim. To illustrate, I laid out my experience as follows:

On my AncestryDNA account, I was happy to find a shaky leaf hint a few weeks ago.

Upon reviewing the match, I noted that the common ancestor was through my mother's side. I was initially excited to see that I had inherited DNA from my 7th great grandparents on paper, Joseph Denison and Prudence Miner.

The only problem is that this match doesn't appear anywhere on my mother's 47 pages of matches. Do you know what this means? It means that I must have inherited the DNA responsible for the match through my father's side. Since all DNA inherited through my mother's line must come through her, AncestryDNA has identified the wrong common ancestor as the source of the DNA shared between LGB and me. A fluke of the algorithms...? Perhaps. Let's look at some more of my matches.

Once again, as you can see, the common ancestor identified by AncestryDNA is on my mother's side. A thorough search of my mother's matches shows that, once again, this person is not reported as a match to my mother. From this, we can only reach the conclusion that the DNA responsible for this match comes through my father's side - not my mother's. The common ancestor that I share with "Baerion" must be beyond a brick wall in her family tree or on my paternal side. In general, I have had more success filling in the branches of the maternal side of my family tree than the paternal side, so this is certainly possible.

Just to demonstrate that this isn't an isolated occurence, here is another one:

This match doesn't appear on my mother's match list either! So, out of my ten matches that have shaky leaves attached,  three of them apparently have common ancestors wrongly identified as the source of our matching DNA. Do you see the problem here? Does AncestryDNA?  If this match were, instead, at 23andMe or Family Tree DNA, I could check the DNA segment that we share and compare it to my other matches and/or my chromosome map. This would provide additional information and/or evidence to help me determine through which of my ancestral lines this segment of DNA was inherited. Might there be other explanations for these discrepancies? It is certainly possible, but without the underlying genetic data, it is impossible to say.

I am in the fortunate position to have tested my mother at AncestryDNA in addition to myself, so I can clearly see there is an issue. What about all of those people who have not tested a parent and are blindly accepting AncestryDNA's shared ancestor hints because they don't know otherwise? Isn't that kind of like copying someone's tree and just taking their word for it that it is correct with no sources or evidence attached? For now, those of us who do understand the finer points of autosomal DNA matching will have to do our best to convince our matches to upload to Gedmatch so they can see for themselves what they are missing.

As much as I, too, am disappointed that AncestryDNA has not yet provided the matching segment data, it is clear to me that the reasons behind this decision are far more complex than what others may claim is an attempt to dumb down the product because Ancestry.com thinks its customers are stupid. From my many conversations with Ken Chahine and others from AncestryDNA over the past year, I have come to appreciate that working within the framework of this 1.6 billion dollar corporation comes with its own set of challenges.

The Future
Tim Sullivan, CEO, has made it clear that Ancestry.com is committed to the DNA business and Ken Chahine has always been upfront with me and come through with his promises. So, I am going to give them the benefit of the doubt. From our very first conversation, I have advocated for the genetic genealogy community and looked out for our best interests and I won't stop doing so. I believe that they will do the right thing for their customers and the genetic genealogy community eventually. It may not happen as quickly as we would all like (yesterday!), but they are not the big bad wolf and I think it does us all a disservice to continually paint their intentions in a negative light. We are in early days yet. Let's give them a break.

Ken Chahine Answers My Questions and Reveals Behind-the-Scenes Information about AncestryDNA

I recently had a long and enlightening conversation with Dr. Ken Chahine, General Manager of AncestryDNA. Due to the lack of information from reliable sources regarding the details of what is going on behind the scenes at AncestryDNA, there has been considerable speculation among those interested in the product. As it turns out, much of this has been incorrect.

AncestryDNA's Matching Threshold
First, mostly due to the large number of matches, it has been widely speculated that AncestryDNA is allowing for a much lower threshold than either 23andMe or Family Tree DNA, reporting matches based on as little as two cM. In reality, Ken tells me that AncestryDNA has been using a 5 Mb cutoff [Mb = mega base pairs = 1,000,000 base pairs] for reporting matches in their lowest category - "very low confidence". He explains how they came to this decision and what AncestryDNA sees as the benefits to their customers:

AncestryDNA, we believe, is the only service that phases the genotyping data and has validated the matching algorithm with large pedigrees.  That leads to two important differences.  First, it allowed us to test various segment cutoffs from 5-10 Mb* with and without a proprietary filter that preferentially removes incorrect matches. We've initially selected the 5 Mb cutoff with the filter as providing the best balance between false negative (true matches that we fail to call a match) and false positives (false matches that we call true matches). Second, it allowed us to make a better cousinship prediction.  For example, our data suggest that most relationships that are theoretically predicted to be third cousins are really fourth cousins or deeper.  Therefore, a fourth cousin match at AncestryDNA, we believe, is a third cousin match at other services.

Ken's assertion that AncestryDNA is using a more conservative prediction calculation does appear to be in agreement with what I and many of my colleagues have observed. Time will tell if it is indeed more accurate. The filter aimed at reducing the number of IBS (Identical By State) matches sounds like a promising addition. When we have the ability to examine the raw data we should be able to reach conclusions about how effective the filter is at fulfilling its purpose.

Mb vs cM - What does it mean to us?
As you may know, the centimorgan rather than mega base pairs is used by Family Tree DNA's Family Finder and also primarily by 23andMe as the length of measurement for matching autosomal DNA segments. So, how does this 5 Mb threshold compare to the 5.5 cM* threshold used by Family Tree DNA (*edited from 7.7 cM after I was sent this) and the 7 cM threshold used by 23andMe in their Relative Finder feature? The National Institutes of Health website tells us that in human genetics, "one centimorgan is equivalent, on average, to one million base pairs" or 1 Mb.  Genome.gov agrees, "Generally, one centimorgan equals about 1 million base pairs." However, in reviewing my Ancestry Finder download at 23andMe, which lists the length of segments both in Mb and in cM, I came to the conclusion that, unfortunately, it isn't that simple - at least for our purposes. In some cases, the numerical value in Mb was larger than in cM for the same segment, but in other cases it was smaller. I copied portions of my Ancestry Finder download to demonstrate examples. If you have tested at 23andMe, take a look at your own file to get a feel for the comparison.

The first chart shows the respective values when the Mb value was 11 and the second when the cM value was 11:

                 

Notice the wide range of values in both directions. It appears to be impossible to find a direct correlation between segment lengths measured in Mb and cM. In some cases, the two values weren't even close:

            
The reason the number of base pairs that a centimorgan corresponds to varies so widely is because when the distance along a chromosome is measured in mega base pairs (Mb), the value strictly reflects how many millions of base pairs there are in a matching segment, but when using centimorgans (cM) to express the distance along the chromosome, the frequency or chance of recombination expected within that segment is being measured. Some portions of the genome are expected to recombine more often than others, therefore sometimes a segment of 1 Mb has a relatively good chance of remaining intact and sometimes it does not.

Different Predictions and More Matches
This difference between AncestryDNA's way of calculating the length of segments and that of the other two companies may explain, in part, the reason that some of us are seeing the same matches at AncestryDNA as we have at the other two companies, with very different predictions. The fact that AncestryDNA is using a phasing engine before running the matching algorithms will also account for some of the reported discrepancies. When asked why AncestryDNA is, on average, returning more matches than the other two companies, Ken offered one possible explanation. He said that it may be a result of the AncestryDNA database containing primarily customers with deep roots in the United States and, in many cases, descending from large Colonial New England families.

Adding International Customers to the Database
This discussion prompted me to inquire as to when AncestryDNA plans to offer the test to international customers. Ken said that it is certainly "on the radar", but they do not have an estimate of when this will happen yet. He explained some of the reasons for this:

1. Demand is still high within the United States and they are "processing samples as fast as we can right now".
2. The privacy laws in Europe are, in some cases, different than the US. Therefore, this will take additional time to address.
3. They will need to work out logistical issues.

He emphasized that Ancestry.com is a large company, which necessitates significant forethought and planning before taking action.

Uploadable Raw Data
During our conversation, Ken also addressed the questions surrounding the format the raw data will be presented in as well as the much-hoped-for matching segment data.

"We will be providing raw data download in early 2013.  We have not made any formal decision on segment data.  We understand that it is important to some of our customers and are taking it into serious consideration." 

When I asked him whether the raw data would be formatted in such a way that will be compatible with uploading to third party sites such as Gedmatch.com, he assured me that it would. Fortunately, this puts to rest all of our speculation that the "related security enhancements" Ken referred to in his keynote address at the Consumer Genetics Conference last month would interfere with the data's usability. When I inquired further about the future availability of segment data, he said that he cannot promise anything in that regard, but was open to discussing what presentation formats of that data might be acceptable to genetic genealogists.

Admixture and Reasonable Assumptions
Some have also interpreted Ken's statement (reported by Esquire) that some customers are using their own knowledge to make reasonable assumptions that are leading to incorrect conclusions, to mean that AncestryDNA is using an altogether different method of determining our matches than the other two companies offering autosomal DNA tests for genealogy.  He explained to me that what he was actually referring to was that many customers are assuming that because autosomal DNA matching is only applicable to relatively recent ancestry, that the admixture results also reflect that time period and should match what we know of our ancestral origins from our family trees. He emphasized that AncestryDNA's "Genetic Ethnicity" feature (like any admixture tool) is not looking at the large segments used for relative matching, but rather is examining much smaller blocks and single markers that are ancestrally informative. Therefore, some of this admixture is very old - offering a glimpse much further back in time than our known family trees. He offered reassurance to those who feel that this portion of the test is not yet as accurate as it should be (me included):

AncestryDNA is data-driven.  Our team of scientists are constantly analyzing the data looking for ways to improve the ethnicity and matching prediction algorithms. The science, and hence the customer experience, is only going to improve with time.

At some point, the Sorenson data will likely be incorporated into the AncestryDNA test, which should improve the admixture predictions tremendously.

Even the CEO is working with his matches!
In closing, it was very nice to hear that "everyone from the CEO down is working with their matches" at Ancestry.com. This should lead to a management team that is educated about what we as genetic genealogists are trying to accomplish and how best to do it. As a result, I look forward to improved tools and results at AncestryDNA in the future.

I want to thank Ken Chahine and Stephen Baloglu for their recent efforts to shed some light on aspects of the AncestryDNA test and clear up some of the confusion. As I told both of them, the more transparency that AncestryDNA can offer to the genetic genealogy community, the more satisfied we will all be with the product. According to Ken, it is likely that more details will be revealed soon. That is a very good thing because as I was writing this, I thought of many more questions for him!

AncestryDNA Launch and Other Related News

AncestryDNA's Wide Release

AncestryDNA is now available to all without an invitation. The new price is $129 for subscribers.

For non-subscribers the price is $199, however if you order a package deal with the 6 month Ancestry.com US Discovery membership, the price drops to $189. The package deal with 6 months of the Ancestry.com World Explorer membership is $249. Obviously, this is a loss leader with the intent of acquiring and retaining subscribers. (You can order here.)

There is a chart provided to compare the options. I have reproduced the relevant portion below:

Based on the information provided in the chart, it appears that even non-subscribers will receive new matches and be able to contact them, however it is unclear if they will be able to access their matches' trees (see line 4 in the graphic). I called the AncestryDNA customer service, but the rep wasn't sure of the answer, although he said that he thought they would be accessible since "that is an important part of the service". [*10/26/12 Update - I spoke with another customer service rep today named Jeremy. He told me that "Connect with your DNA matches" from the chart above does NOT mean that you will be able to contact them unless they contact you first. It only means that you will be able to see the match and review their family tree.  So, non-subscribers WILL be able to see their matches' family trees, but they will NOT be able to initiate contact with them. 10/31/12 Update - The information contained in the last update was inaccurate. Please see the official clarification here.]

In other AncestryDNA News... 
Earlier this month, Dr. Ken Chahine announced a significant addition to the AncestryDNA service in his keynote presentation at the Consumer Genetics Conference in Boston. Crista Cowan reported the news from the conference on the Ancestry.com blog:

AncestryDNA believes that our customers have the right to their own genetic data. It is your DNA, after all. So we’re working to provide access to your raw DNA data in early 2013, which includes related security enhancements to ensure its safety during every step of the process. Moving forward, we plan to add even more tools and improvements for our customers, and any new features will be available to all AncestryDNA members.

I'm very glad to hear that AncestryDNA is listening to its customers (well, the really vocal ones at least). Back in March when I was first introduced to the product, I cited the lack of raw data as one of the major drawbacks to their offering and have continued to beat (and beat) on that drum since then. So, in addition, to the other bloggers and customers who have repeatedly asked for this feature, I feel like this is a victory for genetic genealogy. (Now, we just need to keep pushing for the matching segment data!) I was concerned that the raw data would not be released in a downloadable format due to the wording in the announcement "access to your raw DNA data...which includes security related enhancements", especially after reading Dr. Chahine's comments to the Presidential Commission for the Study of Bioethical Issues in Washington D.C in August. So, I was happy to be informed by Stephen Baloglu, Ancestry.com Director of Product Marketing, during a recent AncestryDNA webinar in which I participated, that the raw data would be in a "downloadable format". Hopefully, that format will also be uploadable to third party sites like Gedmatch.com so, in the absence of AncestryDNA providing it, we can access the matching segment data that genetic genealogists require for their research.

Stephen Baloglu also provided some insight into AncestryDNA's matching system when he responded to a inquiry from Shannon Christmas, "We use total amount of DNA shared and contiguous shared length of segments to calculate how closely you match someone else." I know this doesn't seem like earth-shattering news since it sounds pretty much like what their competitors are doing, but with so little of the scientific method behind AncestryDNA's algorithms public knowledge, every little bit is noteworthy to some of us.

Crista also reports:
We plan to continue to be a part of the genetics landscape moving forward and will be at more events, including the American Society of Human Genetics in San Francisco, where we will present some amazing new discoveries that our scientists have been working on.

I will be keeping my eyes and ears open to hear what that might be!

And, last but not least, I'm sure everyone has already heard about Ancestry.com's impending sale to Permira and might be wondering what this will mean for the DNA portion of the business. I am told that there should not be any major changes and we can see from the press release that DNA appears to be an area they expect to expand in the future, "Ancestry.com's focus will continue to be on investing in content, technology and its user experience, expanding its product offerings in areas like DNA, and building the Ancestry.com brand and the family history category, all on a global basis." Although according to the website, the "AncestryDNA test is not yet available for purchase outside of the United States", this sounds like they intend to promote the DNA tests beyond the United States in the future which would be a positive development for those seeking their genetic connections overseas. 

As always, I will continue to follow the developments of all genetic genealogy related news and make sure my readers are updated. 

[While I was writing this post, I glanced at my new AncestryDNA matches and found a confirmed 5th cousin on my Roderick/Long line with a predicted range of 4th -6th cousins and a 96% confidence level. Yay! I sure do wish I could see our matching segments though! In that vein, Tim Janzen reports that he called today and asked if Ancestry.com would be releasing the matching segment data as well, "The representative said that Ancestry.com might not do that, but that they might  create an 'opt in' option that would allow people to share the matching segment data if they are interested in doing so."]

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

Follow Up: Lab Error Responsible for Adoptee's Confusing Match at AncestryDNA

This morning I received a call from John Pereira, VP of Business Development at Ancestry.com, to discuss my post regarding the recent issue involving the confusion surrounding the adoptee's parent/child DNA match. He informed me that it was caused by a lab error. He declined to tell me the exact nature of the error and, of course, couldn't discuss "Chris and Pat's" specific case with me, but emphasized that it wasn't a problem with AncestryDNA's algorithms or underlying science. He shared with me that the error affected a small number of people and AncestryDNA is doing all they can to remedy the situation, including implementing new policies to ensure this doesn't happen again. Those affected are being retested with fresh samples as an extra precaution. Without addressing any specific customer(s), he explained that those affected were "matched to some people who they shouldn't have been". He assured me that they were rushing out new kits (this was confirmed by the adoptee in my post, "Chris") and would process them as quickly as possible as soon as the new samples are returned. He couldn't give an exact time frame, but assured me that it would not take nearly as long as had been earlier quoted to "Chris" by Ancestry.com's representative.

In this case, it doesn't sound like having access to the underlying genetic data would have completely solved the problem since it would also have been incorrect. However, I still stand by my opinion that, with it, this situation would have been much more easily resolved. (In fact, a good example of this was the 2010 sample mix-up that affected 23andMe customers. Thanks to our active community and 23andMe's data transparency, the problem was quickly discovered and rectified.) Upon seeing an inheritance pattern that was clearly parent/child and reviewing the details of the corresponding match, it would have been undeniable in my mind that there was a lab error since these two people absolutely could not have shared that relationship. We wouldn't have wasted any time trying to fit a square peg into a round hole or on a "wild goose chase" as one of those affected termed it. There would have been no hours spent researching, speculating or, most likely, even blogging about it.

Let's face it, lab errors do occasionally happen. It is just very unfortunate for everyone involved that one of the small number of people affected was an adoptee and that an immediate family member prediction was the result of this error. It is heart wrenching to witness someone who has been denied their right to know "who they are" go through this experience on top of everything else they have been forced to endure in their search for their biological roots. By definition, we as genealogists understand the value of learning about our heritage and our ancestors. As a result, I cannot apologize for my passionate response to this situation. As a blogger, while striving to be unbiased about the various DNA testing companies, I do write from my own perspective. As an active participant in the genetic genealogy and adoptionDNA communities, I am not a completely detached observer. I have strong opinions and, sometimes, I unequivocally share them.

As I told John, I believe it would go a long way in easing their customers' minds if AncestryDNA were to release a statement that explained specifically what went wrong. "Lab error" is a bit wide in scope and when someone is handling our genetic data, we want details. On that note, it won't come as a surprise to my readers that I re-emphasized to John the importance to the genetic genealogy community that AncestryDNA release our genetic data to us. I mentioned that my colleagues and I were happy to discover that Ken Chahine's statements to the Presidential Commission for the Study of Bioethical Issues in Washington D.C. on August 1st were in line with our belief that our genetic data belongs to us (video and transcript).  During the second session, Dr. Chahine stated that "the customer retains ownership of their DNA and data". However, we feel that AncestryDNA's policies do not currently reflect this. John reiterated what I have been told before, which is that they are genuinely considering the best way to deliver this data to us. In response to my persistence, John told me that they are aware that this is important to me, but that they have to take into consideration everyone's feedback, not just mine. As a result, giving us access to our genetic data is not at the top of their list of priorities. He explained that they read lots of feedback and do a significant number of surveys and focus groups in order to determine what is most important to their customers and, by that process, their priorities are dictated. The problem with that is that the vast majority of those people will be new to DNA and a person just venturing into the world of genetic genealogy doesn't even know what they should be asking for. I appreciate that AncestryDNA's goal is to reach well beyond our community (as it should be and is in our best interest), but if these customers are engaged by their results and want to know more, where do they go? I can tell you one thing they do, they write to me and/or join our community's mailing lists and forums and ask questions. In my experience, these people who wish to explore genetic genealogy further, without exception, are disappointed when they realize what they have been denied. So, all of you out there who care about this issue need to make your voices heard. Let them know it isn't just me.

For all of you who have commented here, sent me emails and weighed in on mailing lists and forums, thank you! I am so sorry that I have not been able to respond to each of you, but I am reading them and John confirmed that AncestryDNA is too (except my email, of course!). My inbox is overflowing, but I do want you to know that I appreciate your sharing your thoughts, ideas and opinions and will try to respond to you all as soon as possible. I will also keep everyone updated on the outcome of the situation regarding "Chris and Pat" as privacy permits. Let's keep our fingers crossed for them.

*Update - 23andMe finds no match for "Chris and Pat".

My Review of AncestryDNA's Admixture Tool and a Glimpse into the Future of Genetic Genealogy

I have waited to review my experience with my personal AncestryDNA Beta test until I got a good grasp of how the process is working.  So far, I can say that I think there is a lot of promise in AncestryDNA's approach to autosomal DNA analysis, but there are also things that have caused some confusion and concern among the community. I will address just one component of the test today and follow-up with another post to keep this review from becoming unwieldy.

Admixture and the "Scandinavian" Question 

I have been researching the apparent overestimation of the Scandinavian component in AncestryDNA's admixture tool for some time. Like Blaine Bettinger of The Genetic Genealogist, I have been contacted by many people who were surprised by a significant prediction of Scandinavian in their "Genetic Ethnicity" results that is in conflict with their known family history. I have also read the same confusion expressed on many blogs when the testers' results didn't reflect what they know of their family tree. My own results in this area were a bit surprising as well. There are too many examples of this to simply ignore it or to explain it away by non-paternity events (NPEs) or bad genealogies. Blaine Bettinger has already done a thorough job on his recent blog post (Problems with AncestryDNA's Genetic Ethnicity Prediction?) explaining why our admixture results legitimately may not align with our known genealogies, so I won't go too deeply into that at the moment. I highly suggest you read his post for background if you haven't already.

To understand the  perceived problem, let's look at my results as an example:

My "Genetic Ethnicity" Prediction - Click to enlarge

Although I know that approximately 12.5% of my DNA originated from Scandinavia courtesy of my Norwegian great grandmother Fredrikka Herstad, I did not expect the 57% Scandinavian admixture prediction. Of further concern,  I am 25% Finnish on paper and am only predicted as 7% Finnish by AncestryDNA's Genetic Ethnicity feature. For a person who doesn't know much about Finnish DNA, they may assume that my Finnish DNA is simply bleeding into the Scandinavian percentage, however Finnish DNA is quite unique and clusters distinctly separate from the Scandinavian countries (and all others). Although I may have a small amount of Swedish DNA from early migration to Finland, I am quite sure that it is not a significant amount based on my documented genealogy and, especially, my extensive research at both 23andMe and Family Tree DNA where I have myriads of Finnish "cousins" and very, very few Swedish ones. One could argue that these "ethnicity" predictions reach further back than autosomal DNA cousin matching, but I have seen how my Finnish DNA clusters using other admixture tools and am quite confident in my assessment.

Fortunately, there has already been some improvement in AncestryDNA's algorithm as to how it affects my personal admixture results. When I first received my beta results they revealed no British Isles component at all, which definitely gave me pause since my great grandfather George Allen was 100% British. Since then, my percentages have changed, as AncestryDNA warned us they might. My current 28% British Isles is much closer to what I would expect, without taking into account my substantial Colonial American ancestry. I expect their admixture algorithms will continue to improve.

My mother's case is even clearer. Below is her "Genetic Ethnicity" prediction.  Although she is a full 50% Finnish, she is only predicted to possess 23% Finnish DNA. The 62% Scandinavian is especially surprising since my mother has no known Scandinavian ancestry, but she does have significant Colonial American ancestry, predominantly originating from the British Isles, of which her results show none. The Central European component fits well with her known Pennsylvania Dutch great grandmother Ruth Stoalabarger. From this it appears that all of my mother's British Isles and about half of her Finnish is somehow being interpreted as "Scandinavian".

My mother's "Genetic Ethnicity" Prediction - Click to Enlarge

I spoke to Ken Chahine, General Manager for AncestryDNA, on Thursday to try to get an educated perspective on what might be happening rather than jumping to conclusions. Ken was aware of the controversy surrounding the admixture results, but told me that he feels more confident about their predictions since talking to Sir Walter Bodmer and Peter Donnelly of the "People of the British Isles" Wellcome Trust project at the University of Oxford.  He said that they shared information with the AncestryDNA team suggesting that they too are finding a much larger Scandinavian component in the British Isles than expected. Some of their findings can be seen in the recent article here. According to Ken, these discoveries support the notion that the British Isles was a true melting pot long before the United States earned that moniker and further suggests that there was lots of migration between the British Isles and Norway, Sweden and Denmark. Ken feels that these conclusions support AncestryDNA's findings of significant Scandinavian admixture in many who would expect a more substantial British Isles component, like myself. I still have to wonder though if the "Scandinavian" label is a bit of a misnomer. I guess the question is: If the DNA has been in the British Isles for thousands of years, is it still "Scandinavian"? It is impossible to fully address this issue without access to the underlying genetic data on which AncestryDNA's analysis is based.

Further addressing this issue, Ken wanted to remind all of us that our ancestors' DNA can be diluted pretty quickly. Genetic drift comes into play, so we cannot expect our Family Tree to exactly resemble our admixture results. A good explanation of this can be found in Blaine's blog post Everyone Has Two Family Trees - A Genealogical Tree and a Genetic Tree. This concept really only starts to come into play five or more generations deep in our family trees and shouldn't have a substantial effect until we reach deeper than the great great great grandparent level.

Throughout our discussion, Ken emphasized that the exact science of admixture prediction is a "very tough problem to solve". I think we can all agree with him on this point. Anyone who has worked with admixture predictions knows that all of these tools are still rough and will benefit greatly from the increasing availability of reference samples. Ken told me that AncestryDNA now has seven PhDs on staff working on this "problem" - all with computational and mathematics expertise. Especially intriguing is the AncestryDNA team's emphasis on identifying new Ancestry Informative Markers (AIMs) with the goal of ultimately identifying rare alleles (frequency of less than 1% of the population), rather than focusing on long stretches of DNA.

 "Finding these rare alleles will completely transform genetic genealogy." - Ken Chahine

I have to admit that Ken did make me feel a lot better about the direction that AncestryDNA is going with their new autosomal DNA test. He talked at great length about their goal to identify rare alleles from specific areas of the world. Ken's opinion is that the current Illumina chip in use by all three of the companies is not optimal for admixture analysis because the chosen SNPs are too common. According to Ken, for inclusion on the Illumina chips, SNPs are chosen that can be found in at least 5% of the population and are primarily geared toward health-related genes. In contrast, he explained that the real goal should be to find alleles that are RARE and not found in the general population (less than 1%), eventually enabling us to identify these alleles as originating in specific geographic areas and thus pinpointing the ancestral origins of those who possess this marker. (Obviously, full sequencing will provide the eventual solution.)  Ken said his team seeks to use alternative means of discovery (other than chip technology). I was impressed to hear that the AncestryDNA team researches "every single day" for these new AIMs.

Other Points of Note

1. Every day AncestryDNA is updating their algorithms. It is a "living" tool, ever-changing with new input daily. With more plentiful, unique samples and better techniques the admixture and IBD predictions will continually improve.

2. The AncestryDNA team is trying to discover how shared segments relate to where the common ancestor is on our family trees. (I have also wondered if there are any identifiable patterns imbedded in "random" autosomal DNA inheritance.)

3. They are only starting to utilize the Sorenson data now. Their current admixture tool is based on public data.

 4. All data is 100% phased before analysis. That is their first step at AncestryDNA. Ken said that it never occurred to him not to phase the data and that he was surprised that the other companies were not doing this as well. He explained that the computational requirements are enormous due to the phasing and that they looked at three or four different phasing engines - and found that all were roughly comparable.

The Future

There are still no answers regarding whether/when AncestryDNA will be providing the underlying genetic data to their customers, i.e. - specific matching segments or downloadable raw data, but Ken assured me that they are working on it. He said that they are still in the decision-making process and are currently evaluating the best way to deliver this data. He strongly dispelled the rumors that I had heard that AncestryDNA has decided that they will not provide the raw data to customers. It is indeed essential that this happens because blind faith has no place in a scientific environment such as this. Both Family Tree DNA and 23andMe release the genetic data, in line with their stated belief that all personal genetic information is the property of the individual, thus allowing for outside analysis and intellectual challenge. How can anyone disagree with this?

This conversation with Ken was an exhilarating one in regard to what is in store for us genetic genealogists. He possesses a promising vision for the future of genetic genealogy. The potential for strides in genetic genealogy is mind-blowing with a company pouring these kinds of resources into its advancement and working toward a well-defined, singular goal. This begs certain important questions: What will happen to the competitors if they are not able to match this level of financial commitment? Will AncestryDNA commit to an "open access" model that enables the citizen scientist to share in the new discoveries made, following in the footsteps of Family Tree DNA and 23andMe? Will the increased competition in this sector lead to leaps forward for all? Time will tell, but I can guarantee that the coming months will be very exciting ones in the world of genetic genealogy.

[10/26/12: This test is now out of Beta, so you can order it here.]
[5/19/13: I have noticed that many people who are looking for information about the AncestrybyDNA test are coming here. This is not the same company or test. For more on this, please read this post.]

Disclosure: I received both of the tests discussed above complimentary from AncestryDNA during their early beta testing phase.