Concepts – Imputation

Until recently, the word imputation wasn’t a part of the vocabulary of genetic genealogy, but earlier this year, it became a factor and will become even more important in coming months.

Illumina, the company that provides chips to companies that test autosomal DNA for genetic genealogy has obsoleted their OmniExpress chip previously in use, forcing companies to utilize their new Global Screening Array (GSA) chip when their current chip supply runs out.

Only about 20% of the DNA locations previously tested by genetic genealogy companies are tested on this new platform. Illumina has encouraged vendors to utilize the process called imputation to infer DNA results for their customers that are common in populations, but has not been directly tested in customer’s DNA, in order for vendors to achieve backwards compatibility with people previously tested on the OmniExpress chip. You can read the technical details of imputation in a document produced by Illumina here.

LivingDNA, who was developing and launching a new product during the transition time between chips was the first vendor out the gate with a GSA product. Illumina represented imputation to be “very accurate” to LivingDNA, which is consequently how they represented the results to a group of genetic genealogists on a conference call in early 2017. LivingDNA was the lucky company to have the opportunity to “work the bugs out” with Illumina – said with tongue firmly in cheek. LivingDNA provides a list of papers describing their methods here.

Another company, MyHeritage also uses imputation, for an entirely different reason. My Heritage uses imputation to “add” to the DNA results of people who upload results from different vendors. They are the first company to attempt DNA matching between people using imputation, and they initially had and continue to have matching issues. In their initial release blog in September 2016, they state that imputation matching “is accomplished with very high accuracy.” In their Q&A blog in November 2016, they state that “imputation may introduce errors so we are in the process of fine-tuning it.” They have made changes since matching was originally introduced, but they still struggle with matching accuracy, most recently discussed by Leah Larkin in her article, MyHeritage Matching.

DNA.LAND does not perform testing, but is a nonprofit in the health care industry who  utilizes imputation for health-related research – imputing approximately 38.3 million locations in addition to the 700,000 locations in customers’ uploaded files. In order to encourage people to upload their test results, DNA.LAND performs matching and ethnicity reporting. Like MyHeritage, their matching results are problematic. DNA.LAND explains about imputation and summarizes by stating that “any reported value should never be taken as-is without further careful analysis.” I will be publishing an article shortly about DNA.LAND.

23andMe, on August 9, 2017, released their V5 product utilizing the new GSA chip. They have not said how they are addressing the imputation challenge and backward compatibility. Several issues have been reported.

As you can see, the genetic genealogy landscape is changing and like it or not, imputation is a part of the new scenery.

What, Exactly, is Imputation?

Imputation is the process whereby your DNA is tested and then the results “expanded” by inferring results for additional locations, meaning locations that haven’t been tested, by using information from results you do have. In other words, the DNA is adjacent locations is predicted, or imputed, by their association with their traveling companions.  In DNA, traveling companions are often known to travel together, but not always.

Imputation is built upon two premises:

1 – that DNA locations are usually inherited together in groups in a process known as linkage disequilibrium.

2 – that people from common populations share a significant amount of the same DNA

An example that DNA.LAND provides is the following sentence.

I saw a blue ca_ on your head.

There are several letters that are more likely that others to be found in the blank and some words would be more likely to be found in this sentence than others.

A less intuitive sentence might be:

I saw a blue ca_ yesterday.

DNA.LAND also says very clearly that imputed values can be incorrect. They also state that the values inferred are the common values, not rare mutations, and imputed results are most accurate in Caucasian populations and least accurate in African populations whose DNA is the most variant of any continental group. They caution against using these results for medical diagnosis.

SNPedia (Promethease) cautions against using imputed results as well and suggests that files utilizing only tested results, without imputed results, are more accurate.

Why Imputation?

Looking at this Autosomal SNP Comparison Chart, provided by the ISOGG Wiki, you can see the difference in the number of actual common locations tested by the various vendors.

This means that companies that allow uploads from different vendors utilizing widely divergent chip results have to do something in order to successfully compare the disparate files against each other for matching. Using  23andMe as an example, even though they don’t allow uploads from other companies, they have to do something to accommodate matching between the new GSA V5 chip and their earlier V3 and V4 chips.

Imputation Example

Let’s take a look at how imputation is used to “equalize” files uploaded from various vendors that only contain marginal amounts of overlap.

I’m using MyHeritage as an example. Imputation, in this case, is utilized in an attempt to make marginally compatible files more compatible.

The files from the Ancestry V2 kit and the Family Tree DNA kit have only about 382,000 locations in common, meaning about 300,000 locations are not in common. In order to attempt to equalize these and other kits, MyHeritage attempts to use imputation to deduce the DNA that a tester would/should/might have in the missing segments, based on various statistical factors that include the tester’s population and existing DNA.

Please note that for purposes of concept illustration, I have shown all of the common locations, in blue, as contiguous. The common locations are not contiguous, but are scattered across the entire range that each vendor tests.

You can see that the number of imputed locations for matching between two people, shown in tan, is larger than the number of actual matching locations shown in blue. The amount of actual common data being compared is roughly 382,000 of 1,100,000 total locations, or 35%.

Stay tuned for an upcoming series of articles about imputation and results in various scenarios.

Which Ethnicity Test is Best?

While this question is very straightforward, the answer is not.

I have tested with or uploaded my DNA file to the following vendors to obtain ethnicity results:

The links above provide product reviews of recently released or updated results.

Guess what? None of the vendors’ results are the same. Some aren’t even close to each other, let alone to my known and proven genealogy.

In the article, Concepts – Calculating Ethnicity Percentages, I explained how to calculate your expected ethnicity percentages from your genealogy. As each vendor has introduced ethnicity results, or updated previous results, I’ve added to a cumulative chart.

It bears repeating before we look at that chart that ethnicity testing is relatively accurate on a continental level, meaning:

  • Africa
  • Europe
  • Asia
  • Native American
  • Jewish

Intra-continent or sub-continent, meaning within continents, it’s extremely difficult to tease out differences between countries, like France, Germany and Switzerland. Looking at the size of these regions, and the movement of populations, we can certainly understand why. In many ways, it’s like trying to discern the difference between Indiana and Illinois.

What Does “Best” Mean?

While the question of which test is best seems like it would be easy to answer, it isn’t.

“Best” is a subjective term, and often, people interpret best to mean that the test reflects a portion of what they think they know about their ethnicity. Without a rather robust and proven tree, some testers have little subjective data on which to base their perceptions.  In fact, many people, encouraged by advertising, take these tests with the hope that the test will in fact provide them with the answer to the question, “Who am I?” or to confirm a specific ancestor or ancestral heritage rumor.

For example, people often test to find their Native American ancestry and are disappointed when the results don’t reveal Native ancestry. This can be because:

  • There is no Native ancestor.
  • The Native ancestor thought to be 100% was already highly admixed.
  • The Native ancestor is too far back in the tester’s tree and the ancestor’s DNA “washed out” in subsequent generations.
  • The testing company failed to pick up what might be arguably a trace amount.

Genealogy Compared to All Vendors’ Results

In some cases, discrepancies arise due to how the different companies group their results and what the groupings mean, as you can see in the table below comparing all vendors’ results to my known genealogy.

In the table below, I’ve highlighted in yellow the “best” company result by region, as compared to my known genealogy shown in the column titled “Genealogy %”.

British Isles – The British Isles is fairly easy to define, because they are islands, and the results for each vendor, other than The Genographic Project, are easy to group into that category as well. Family Tree DNA comes the closest to my known genealogy in this category, so would be the “best” in this category. However, every region, shown in pink, does not have the same “best” vendor.

Scandinavian – I have no actual Scandinavian heritage in my genealogy, but I’m betting I have a number of Vikings, or that my German/Dutch is closely related to the Scandinavians. So while LivingDNA is the lowest, meaning the closest to my zero, it’s very difficult to discern the “true” amount of Scandinavian heritage admixed into the other populations. It’s also possible that Scandinavian is not reflecting (entirely) the Vikings, but Dutch and German as a result of migrations of entire peoples. My German and Dutch ancestry cumulatively adds to 39%.

Eastern European – I don’t have any known Eastern European, but some of my German might fall into that category, historically. I simply don’t know, so I’m not ranking that group.

Northwestern Europe – For the balance of Northwestern Europe, 23andMe comes the closest with 43% of my 45.24% from my known genealogy.

Mediterranean and Southern European – For the Mediterranean, Greece, Italy and Southern Europe, I have no known genealogy there, and not even anyplace close, so I’m counting as accurate all three vendors who reported zero, being Living DNA, Family Tree DNA and MyHeritage.

Unknown – The next grouping is my unknown percentage. It’s very difficult to ascribe a right or wrong to this grouping, so I’ve put vendor results here that might fall into that unknown group. In my case, I suspect that some of the unknown is actually Native on my father’s side. I haven’t assigned accuracy in this section. It’s more of a catch all, for now.

Native and Asian – The next section is Native and Asian, which can in some circumstances can be attributed to Native ancestry. In this case, I know of about 1% proven Native heritage, as the Native on my mother’s line is proven utilizing both Y and mitochondrial DNA tests on descendants. I suspect there is more Native to be revealed, both on her side and because I can’t positively attribute some of my father’s lineage that is mixed race and reported to be Native, but is as yet unproven. By proof, I mean either Y DNA, mitochondrial DNA or concrete documentation.

I have counted any vendor who found a region above zero and smaller than my unknown percentage of 3.9% as accurate, those vendors being Family Tree DNA, Ancestry, 23andMe and MyHeritage.

Southwest Asia – I have no heritage from Southwest Asia, which typically means the Indian subcontinent. National Geographic reports this region, but their categories are much broader than the other companies, as reflected by the grey bands utilized to attempt to summarize the other vendor’s data in a way that can be compared to the Genographic Project information. While I’m pleased to contribute to the National Geographic Society through the Genographic Project, the results are the least connected to my known genealogy, although their results may represent deeper migratory ancestry.

Summary

As you can see, the best vendor is almost impossible to pinpoint and every person that tests at multiple vendors will likely have a different opinion of what is “best” and the reasons why. In some ways, best depends on what you are looking for and how much genealogy work you’ve already invested to be able to reliably evaluate the different vendor results. In my case, the best vendor, judged by the highest total percentage of “most accurate” categories would be Family Tree DNA.

While DNA testing for ethnicity really doesn’t provide the level of specificity that people hope to gain, testers can generally get a good view of their ancestry at the continental level. Vendors also provide updates as the reference groups and technology improves.  This is a learning experience for all involved!

I hope that seeing the differences between the various vendors will encourage people to test at multiple vendors, or transfer their results to additional vendors to gain “a second set of eyes” about their ethnicity. Several transfers are free. You can read about which vendors accept results from other vendors, in the article, Autosomal DNA Transfers – Which Companies Accept Which Tests?

I also hope that ethnicity results encourage people to pursue their genealogy to find their ancestors. Ethnicity results are fun, but they aren’t gospel, and shouldn’t be interpreted as “the answer.” Just enjoy your results and allow them to peak your curiosity to discover who your ancestors really were through genealogy research! There are bound to be some fun surprises just waiting to be discovered.

If you are interested in why your results may vary from what you expected, please read “Ethnicity Testing – A Conundrum.”

If you’re interested in taking a DNA test, you might want to read “Which DNA Test is Best?” which discusses and compares what you need to know about each vendor and the different tests available in the genetic genealogy market today.

______________________________________________________________________

Standard Disclosure

This standard disclosure will now appear at the bottom of every article in compliance with the FTC Guidelines.

Hot links are provided to Family Tree DNA, where appropriate. If you wish to purchase one of their products, and you click through one of the links in an article to Family Tree DNA, or on the sidebar of this blog, I receive a small contribution if you make a purchase. Clicking through the link does not affect the price you pay. This affiliate relationship helps to keep this publication, with more than 850 articles about all aspects of genetic genealogy, free for everyone.

I do not accept sponsorship for this blog, nor do I write paid articles, nor do I accept contributions of any type from any vendor in order to review any product, etc. In fact, I pay a premium price to prevent ads from appearing on this blog.

When reviewing products, in most cases, I pay the same price and order in the same way as any other consumer. If not, I state very clearly in the article any special consideration received. In other words, you are reading my opinions as a long-time consumer and consultant in the genetic genealogy field.

I will never link to a product about which I have reservations or qualms, either about the product or about the company offering the product. I only recommend products that I use myself and bring value to the genetic genealogy community. If you wonder why there aren’t more links, that’s why and that’s my commitment to you.

Thank you for your readership, your ongoing support and for purchasing through the affiliate link if you are interested in making a purchase at Family Tree DNA.

LivingDNA Replaces Download Terms

Great news, and fast on the part of LivingDNA.

Yesterday, I wrote about indemnity language required when downloading your raw data file from LivingDNA.

LivingDNA said last night that the verbiage did not really reflect their intentions.

Today, they have modified their terms going forward and retroactively, according to David Nicholson, Managing Director of LivingDNA, and have simplified the content.

Below is the new download verbiage, as provided by David.

I am greatly relieved. The indemnification language is gone and is replaced by you agreeing to, in essence, be responsible for yourself and release LivingDNA from anything bad that happens resulting from your download. (Caveat – I am not a lawyer. This is only my personal opinion.)

As always, please read all language and be sure you understand the verbiage and ramifications to your own situation, with LivingDNA and all vendors. Seek legal advice if you have questions or concerns with any legal document.

Thanks, LivingDNA, for listening to the community and addressing our concerns so quickly.

Beware – LivingDNA Requires Customer to Indemnify Company to Download Raw Data

Update:  Please note that LivingDNA has replaced the Indemnity language referred to below.  You can read the update here.

Say what?

Yep, you read that right.

I discovered that LivingDNA now provides a raw data download for their customers, with a huge, and I mean HUGE, caveat – indemnification of the company (LivingDNA) if they are sued as a result of your download of your DNA data.

Yes, seriously! This is not April 1st.

While this may sound like a trivial complication, it’s not, given that one of the reasons genealogists purchase ethnicity tests is to download the data and transfer the results to other companies or services for additional ethnicity results or matches to other testers, a feature not provided by LivingDNA.

Let’s walk through the download steps and take a look.

At LivingDNA, your raw data is now available on the left hand side of your page. Click on “Download Raw Data” to view.

You will then see the following screen, captured in two graphics, below. Please note that you can click to enlarge any graphic.

Do NOT do anything else until you READ and understand the entire contents of the Download Raw Data page.

LivingDNA provides what I would consider typical verbiage and also some appropriate cautions about how you may or may not match people you expect to match, and you may match people you don’t expect to match. In other words, they are gracefully trying to say you may encounter a misattributed parentage, either in your line or the line of someone you expect to match. Given that LivingDNA doesn’t provide matching services, this is especially important for their customers to understand.

But then comes the (thankfully) bolded bombshell. Bolding is theirs, not mine, although I would also add the color red.

By choosing to download your data you agree to indemnify (which broadly means to reimburse) Living DNA and its related companies and their directors and employees for any losses, damages or costs they incur as a result of any claims being made against them which relate to you downloading your data and the use by you of your data, or as a result of you having shared your data with any third party.

Holy cow.

Not only are you indemnifying LivingDNA,  you’re also indemnifying their directors and employees and related companies.  Furthermore, “claims” could mean that someone doesn’t even need to file a lawsuit.  As I said, I’m not an attorney, but I’m a savvy enough consumer to know this isn’t good for me.

You must click the “consent” box in order to proceed.

The consent says very clearly that by downloading, you agree to provide indemnity to LivingDNA. Bolding and red, both mine, below.

I have read the information provided about gaining access to my genetic data, and in particular I understand that my use of my data is my responsibility and that by downloading my data, I am providing an indemnity to Living DNA.

Merriam-Webster says this about indemnify:

I’m not a lawyer, but let me explain one thing further about indemnification. It includes the costs of defense – meaning the lawyers, and the lawyers travel, etc. Lawyer fees alone can run into tens of thousands of dollars, and more. Currently intellectual property attorneys bill at the rate of $450 per hour, or did last year, and defense preparations take hundreds of hours. If this makes you shake in your shoes, it should!

So let me say this in plain English. If you upload your LivingDNA file to any third party site and you match someone who is angry that your match revealed (or helped to reveal) that their father is not their father (for example), but is instead your father, or uncle, or cousin, etc., and they decide to sue LivingDNA for running your test – you have to pay for LivingDNA to defend themselves against the lawsuit – no matter how frivolous and no matter the outcome. I would think this would also extend to someone utilizing numerous matches to discover a link to unknown parentage if someone is unhappy about the outcome. In essence, if anyone sues LivingDNA or make a claim over anything having to do with your test, you have agreed to pay for LivingDNA to defend themselves, affiliated companies, employees and directors, even if the suing party loses. And if the suing party wins, you get to pay for that too.

The bottom line is that you have to agree that you are responsible for whatever after downloading your DNA. “Whatever” means anything that you can think of, and probably several things you can’t. The example above is by no means a comprehensive list of what could go wrong and cause you a massive legal headache. If anything goes wrong after you download your DNA, you’re responsible.

Period.

Consider yourself warned.

There is absolutely no upside or benefit in this verbiage to you. None. Nada.

So what am I going to do with my LivingDNA results? Not one single solitary thing. The ante is just too large. Thankfully, I’ve already tested with the other vendors so I don’t need to upload my results from LivingDNA anyplace.

That’s exactly what I recommend you do too – nothing. Don’t even download. Personally, I would simply test elsewhere, all things considered.

You cannot control how your matches utilize the fact that you match and what they do with that information. It will be interesting to see if LivingDNA will require their customers to indemnify them against the results of matches at their own company if they add the matching feature as they have stated they plan to do.

Given that I’m not an attorney, if you are considering downloading your LivingDNA data and uploading elsewhere, I strongly, STRONGLY, recommend that you contact an attorney and obtain a professional opinion.

Today, as I write this, I know that Family Tree DNA and GedMatch don’t accept LivingDNA files as a standard upload because the chip LivingDNA uses is different than any other vendor.

Even if everyone accepted LivingDNA files, in my opinion, given the LivingDNA indemnity language, if you want to upload your results to any site, you would be far safer to test a second time with one of the three major vendors and avoid the potential indemnity headache.

Click here to read my LivingDNA Product Review that was written a month ago, before the data download become available.

You can see which vendors accept whose transfer files in the article, Autosomal DNA Transfers – Which Companies Accept Which Tests?

Within the next few days, I’ll be publishing an article titled, “Which Ethnicity Test is Best?,” so stay tuned.

______________________________________________________________________

Standard Disclosure

This standard disclosure will now appear at the bottom of every article in compliance with the FTC Guidelines.

Hot links are provided to Family Tree DNA, where appropriate. If you wish to purchase one of their products, and you click through one of the links in an article to Family Tree DNA, or on the sidebar of this blog, I receive a small contribution if you make a purchase. Clicking through the link does not affect the price you pay. This affiliate relationship helps to keep this publication, with more than 850 articles about all aspects of genetic genealogy, free for everyone.

I do not accept sponsorship for this blog, nor do I write paid articles, nor do I accept contributions of any type from any vendor in order to review any product, etc. In fact, I pay a premium price to prevent ads from appearing on this blog.

When reviewing products, in most cases, I pay the same price and order in the same way as any other consumer. If not, I state very clearly in the article any special consideration received. In other words, you are reading my opinions as a long-time consumer and consultant in the genetic genealogy field.

I will never link to a product about which I have reservations or qualms, either about the product or about the company offering the product. I only recommend products that I use myself and bring value to the genetic genealogy community. If you wonder why there aren’t more links, that’s why and that’s my commitment to you.

Thank you for your readership, your ongoing support and for purchasing through the affiliate link if you are interested in making a purchase at Family Tree DNA.

LivingDNA Product Review

Living DNA entered the landscape for ethnicity testing in the summer/fall of 2016. Hands down, they win the contest for “cool logo.”

Ordering and Waiting

I ordered my test, and the results were frustratingly slow in arriving – more than 3 months after submission. Their website currently says “within 10-12 weeks our results will be ready to explore.” Speedy is not their middle name. At first I thought the delivery time of 12 weeks was a startup snafu, but apparently it’s their standard delivery window.

Sometimes vendors offer free tests with the hope of a good review. I typically order tests like any other customer from a vendor, because it’s not a fair review if the vendor knows they are testing someone who will likely review their product. In other words, I don’t want special treatment. However, in this case, I did complain to the Marketing Director and received my results shortly thereafter. I don’t know how long those results would have taken otherwise.

Price

LivingDNA is a British company, registered in England and Wales. Their price in US dollars is normally $159 with an additional $9.95 for standard delivery (5-7 working days) or $39.95 for premium delivery (2-3 working days). At the time I ordered, US purchasers were required to purchase premium delivery, making the price of an ethnicity test effectively $199.

The LivingDNA ethnicity test costs substantially more than Ancestry or 23andMe at $99 or Family Tree DNA at $79, plus shipping. The other vendors products include ethnicity results plus matching to other testers and varying comparison tools. LivingDNA hopes to offer matching between testers in the future.

Terms and Conditions

Thankfully, Judy Russell recently provided a great overview and digestion of Living DNA’s terms and conditions. Please read Judy’s First look: Living DNA terms of use.

Vendors can and do modify their terms and conditions, so always read what any vendor provides, including any fine print.

LivingDNA’s Claims

The page that greets customers provides the following verbiage.

LivingDNA claims twice the detail of other ancestry tests. Detail, which means reference populations and regions in this case, does not necessarily equate to accuracy, but we’ll see how they fare in that department.

LivingDNA is the only company, to date, that offers ethnicity breakdown by regions within the British Isles, based on the POBI (People of the British Isles) project results funded by the Wellcome Trust.

Living DNA claims to have a 3-in-1 ancestry test, meaning ethnicity, mitochondrial and Y DNA, which isn’t exactly true, but it’s not entirely false either. It’s a matter of perception.

LivingDNA is a scan test that scans specified locations in your genome. Haplogroups, both Y and mitochondrial, are defined by specific locations that carry mutations. LivingDNA scans for Y and mitochondrial haplogroup mutations at some level, but they do not offer anything more for Y and mitochondrial DNA than the haplogroup designation. In other words, no detail and no matching. The LivingDNA results are in the same ballpark as 23andMe or the Genographic project, but much less detailed than Family Tree DNA. Ancestry doesn’t offer any Y or mtDNA results, haplogroup or otherwise. To see a detailed comparison of Y and mtDNA testing and who provides what, please refer to Which DNA Test is Best?

LivingDNA does not offer DNA matching, nor do they currently provide a download raw data file so that you can upload your results elsewhere. They indicated in a February Rootstech conference call that they want to move towards both of these goals.

All major vendors (with the exception of Genographic) provide free updates to existing customers when they update their data base, so it’s good that LivingDNA does too.

As for the LivingDNA claim to “view your ancestry through history,” let’s take a look and see what they deliver.

Navigation

Notice on the left hand side of the page that I have two options under Ancestry:

  • Family Ancestry – your ethnicity results
  • Motherline – your mitochondrial DNA results

If I were a male, I would also have Fatherline.

Where ever you are on the site, additional options are always shown on the upper left hand side of the page.

Mother Line – Mitochondrial DNA

First, let ‘s look at my mitochondrial DNA results. Your Motherline options are shown on the bar to the left of your page.

The “Download Results” function has not yet been implemented.

The first Motherline page provides an overview.

I know already that my full haplogroup through full sequence testing at Family Tree DNA is J1c2f. Let’s see what LivingDNA tells me.

Living DNA shows my haplogroup as J1c, which isn’t incorrect as far as it goes, but isn’t complete either.

Living DNA gives me an option to ‘take a tour” of my results, so I did. The heat map, below, shows the locations of my “mother line haplogroup.” Heat maps are hotter, or darker, meaning more intense, where the frequency is greater.

Please note that you can click on any image to enlarge.

I’m not clear whether LivingDNA is displaying a map for haplogroup J1c, or core haplogroup J, given the “hottest” region shown is, surprisingly, Yemen. J1c is typically considered to be European, so surely this map must be referring to haplogroup J plus all subgroups.

The LivingDNA heat map is significantly different than the spatial frequency map for haplogroup J, shown below, published in the academic paper, Genetic Stratigraphy of Key Demographic Events in Arabia published in PLoS ONE in March 2015 by Fernandes et al.

Next, Living DNA discusses the genetic migration for haplogroup J.

Followed by a migration map.

Haplogroup J is shown in Europe here. What happened to Yemen? From this map, it looks like J was born near the Black Sea and traveled directly to Europe, which certainly doesn’t track with the heat map or the PLoS ONE article.

Last, the phylogenetic tree showing the path from Mitochondrial Eve, the first known woman to have offspring that lived to today, to me. I notice in this tree that the migration map above omits haplogroup JT between R and J.

Fatherline – Y DNA

Clearly, being a female, I don’t carry a Y chromosome, but the Y DNA section holds the same pages of information as the mitochondrial DNA section, above, which you also receive if you are a male.

Family Ancestry

The Family Ancestry section is where you will find your autosomal ethnicity results.

You have four options, shown on the left bar.

The first page you will see offers you the option to take a tour and then provides basic information.

In the “What Makes You” section, my results show that I’m 93.4% European and 6.6% unassigned in the rest of the world.

Well, that’s pretty boring, but there’s more.

Click on the “+” to the right of the word “Global” which shows regional results, shown below.

Clicking on the “+” again shows the full breakdown, including the British Isles detail. They could certainly make finding this information more intuitive than “+” and “-“. I suspect a lot of people miss this detail, and if you’re testing for ethnicity, which is all LivingDNA offers today, this IS the important part of the test.

You can click on each region to show history about that region, but I surely wish they had shown a map of the British Isles with the sub-region highlighted instead of the image of the body. It’s impossible to discern which present day counties are included in which LivingDNA regions.

My English ancestors whose locations I know are from Lancashire and Kent, and I can’t tell which of the English regions referenced by LivingDNA would include the locations my ancestors are from.

Ireland, on the other hand, is pretty self-explanatory, but is also a pretty large area.

The Family Ancestry Map shows the locations where your ancestors were found.

Clicking “explore in full” and then the “+” button shows me the following, as does the “Through History” selection.

I’m 72.5% Great Britain and Ireland and 12% North and West European and 6.2% unassigned European which is reflected on the map below, with the darker area having the higher frequency. However, please note that the legend and map are reversed.  On the legend, the Europe unassigned at 6.2% is shown as the darkest shade of green, where on the map, the Great Britain and Ireland shown at 75.2% is shown as the darkest, which is accurate if you are using heat maps.

Click on the “+” sign once again moved to subregions showing the detail of where your ethnicity is found.

Clicking on the region at left shows the associated region on the map.

Please note that some of the features both above and below did not display correctly, or at all, using a PC with either Edge or Internet Explorer browsers.  MACs did better.

Another really easy to miss feature is the “click here” just above the word “standard” which allows you to view your family ancestry at different points through history, beginning with 500 years ago. I really like this video type feature as it shows you the movement of your ancestors with time.

Expanding back in time.

At the bottom of each time period is some history to go along with the time period you’re viewing.

Clicking on the Chart option, shows the following.

How Accurate is Living DNA’s Ethnicity?

I wrote the article “Calculating Ethnicity Percentages” to explain how to determine, based on your known genealogy, what to anticipate in your ethnicity percentages, and to compare the various vendors’ accuracy, although Family Tree DNA has since released an update since that article was published.

For purposes of comparison, I calculated all of my 64 GGGG-grandparent’s ethnicity percentages – each individual accounting for approximately 1.56% of my DNA today.

The following chart shows how LivingDNA compared with my known genealogy.

LivingDNA significantly overestimated my total British Isles. My known and inferred British Isles, based on surnames and colonial American records, is no more than 50.7%, while Living DNA shows it at half again as much, at 75.2%. That’s simply not possible, given the immigration records of my ancestors and the proven locations of their origins in Germany, the Netherlands and France.

I can’t align the known locations of my British or Scottish ancestors with the British Isles regions shown, so I really don’t know if the subregion breakdown within the British Isles is accurate or not. That’s not a problem with the LivingDNA analysis, but is due to the fact that my British Isles ancestry with proven locations is scant.

LivingDNA shows Scandinavian that I don’t show in my genealogy, but they aren’t alone, as we’ll see in a minute when we look at how they stack up to the other vendors.

LivingDNA badly missed the mark for my German which is proven at 25% and my Dutch proven at 14%, although clearly that unassigned European probably comes from that grouping. Living DNA shows Germanic at 9%.

LivingDNA clearly struggled with DNA outside of Europe, as they could not identify any DNA anyplace else in the world. Other vendors have identified Middle Eastern, North African and Native American. Of those, only the Native American is solidly proven.

Altogether, with unassigned Europe and unassigned in the rest of the world, 12.8% of my DNA is unassigned.

Compared to Other Vendors

I’ve updated the chart below to include the LivingDNA results along with the new Family Tree DNA update that occurred in April 2017. The only vendor results which are not the results provided by vendors with a current test is the Genographic project, whose ethnicity results changed in November 2016 when they switched their testing vendor to Helix. I have not retested at Genographic. I have included Genographic in the chart, but excluded them in the comparison because their categories are so broad as to not be functionally comparable to the major vendors and the results are obsolete at this point.

Compared to the other three major vendors, Living DNA was the worst at determining my British Isles ethnicity percent as compared to other regions. Family Tree DNA was the best.

All vendors showed Scandinavian, which is not reflected in my genealogy. The school of thought most prevalent is that Scandinavian is possibly reflective of Viking ancestry that was so ingrained into the population as to remain a constant today. That may be true, at least to some extent. LivingDNA shows less Scandinavian than anyone else, making them the most accurate in this category given that I have no known Scandinavian genealogy.

LivingDNA was second worst in determining my Dutch/French/German heritage if you presume that all of the 6.2% European unassigned fell into that group. If you don’t make that presumption, then LivingDNA was the worst. 23andMe was the best.

LivingDNA had the highest amount of unassigned at 6.6% of any vendor while Family Tree DNA and Ancestry assigned all of my DNA and 23andMe only has .1% unassigned.

LivingDNA missed my Native altogether, while all three other vendors found it, even though it is a small percentage.

Summary

LivingDNA did not perform well in any category relative to ethnicity as compared to the other major vendors with the exception of Scandinavian. Surprisingly, they placed last in the British Isles category which is their area of expertise.

Some of my British Isles heritage is inferred, which could theoretically have raised my genealogical percentage of DNA if I am incorrect in my inference. In other words, in reality, my British Isles heritage % could be even lower than the 50.7% shown on the chart. It’s also possible that amount is slightly low, but my British Isles can’t be much higher because more than 45% of my genealogy is unquestionably proven elsewhere with relatively recent German and Dutch immigrants. So, at most, my British Isles can’t be more than 55%.

If LivingDNA had shown less British Isles than my genealogy, I would have been accepting of that information, given that their specialty is supposed to be British Isles ethnicity and some of my British Isles is inferred. However, LivingDNA was 50% higher than my own calculations, showing 75.2%.

My mitochondrial haplogroup at Living DNA was not incorrect, but it was incomplete, showing only 2 of 4 branches of haplogroup J, as proven by full mitochondrial sequencing. By comparison, the two other vendors who provide the same type of scan tests for mitochondrial and Y DNA, 23andMe shows me as J1c2 and the Genographic Project 2.0 test shows me as J1c2f. Family Tree DNA shows me as J1c2f as well, but their mitochondrial DNA test is more comprehensive and is a separate test altogether, not included in their Family Finder autosomal test.

I can’t correlate my known English genealogy to specific regions as reported by LivingDNA because my only ancestors whose British Isles locations are specifically known came from London, a melting pot from all over the rest of England, Kent and Lancashire, so I can’t pass any judgement as to the relative accuracy of LivingDNA’s British Isles breakdown except to say my known Irish appears to be accurate.

What I can say is that for anyone who doesn’t have primarily British Isles DNA, or entirely British Isles DNA, I would not recommend this test given the issues noted above. Additionally, LivingDNA is substantially more expensive at $149 than the competing products at $99 (23andMe and Ancestry) and $79 (Family Tree DNA,) all of whom also include matching.

For this test to be useful, the tester would need to be nearly or entirely British and have their genealogy proven to specific regions within the British Isles in fairly recent generations to ascertain accuracy. For me, with a high level of American colonial DNA mixed with relative recent ancestors from western Europe, the test fared poorly.

I would be very interested in knowing the accuracy from the standpoint of multiple testers whose ancestors are entirely from the British Isles and have proven an extensive genealogy back through their 64 GGGG-grandparents. In other words, are the regions within the British Isles accurate?

Keep in mind that all ethnicity tests are really estimates and vary based on the reference panels used by the vendor and the algorithms the vendor uses internally to assign your DNA to specific ethnicities.  LivingDNA points out on their website that inheritance is not a constant at 50% per generation (of ancestral DNA being passed to the next generation) and ethnicity testing is not an exact science – and they are right, on both counts.

In other words, your mileage will vary – a lot.

Autosomal DNA Transfers – Which Companies Accept Which Tests?

Somehow, I missed the announcement that Family Tree DNA now accepts uploads from MyHeritage.

Other people may have missed a few announcements too, or don’t understand the options, so I’ve created a quick and easy reference that shows which testing vendors’ files can be uploaded to which other vendors.

Why Transfer?

Just so that everyone is on the same page, if you test your autosomal DNA at one vendor, Vendor A, some other vendors allow you to download your raw data file from Vendor A and transfer your results to their company, Vendor B.  The transfer to Vendor B is either free or lower cost than testing from scratch.  One site, GedMatch, is not a testing vendor, but is a contribution/subscription comparison site.

Vendor B then processes your DNA file that you imported from Vendor A, and your results are then included in the database of Vendor B, which means that you can obtain your matches to other people in Vendor B’s data base who tested there originally and others who have also transferred.  You can also avail yourself of any other tools that Vendor B provides to their customers.  Tools vary widely between companies.  For example, Family Tree DNA, GedMatch and 23andMe provide chromosome browsers, while Ancestry does not.  All 3 major vendors (Family Tree DNA, Ancestry and 23andMe) have developed unique offerings (of varying quality) to help their customers understand the messages that their unique DNA carries.

Ok, Who Loves Whom?

The vendors in the left column are the vendors performing the autosomal DNA tests. The vendor row (plus GedMatch) across the top indicates who accepts upload transfers from whom, and which file versions. Please consider the notes below the chart.

(Chart updated September 28, 2017)

Please note that on August 9, 2017, 23and Me began processing on the Illumina GSA chip which is not compatible with earlier versions.  As of late September 2017, only GedMatch accepts their upload and only in their Genesis sandbox area, not the normal production matching area.  This is due to the small overlap area with existing chips.  You can read more about the GSA chip and its ramifications here

  • Family Tree DNA accepts uploads from both other major vendors (Ancestry and 23andMe) but the versions that are compatible with the chip used by FTDNA will have more matches at Family Tree DNA. 23andMe V3, Ancestry V1 and MyHeritage results utilize the same chip and format as FTDNA. 23andMe V4 and Ancestry V2 utilize different formats utilizing only about half of the common locations. Family Tree DNA still allows free transfers and comparisons with other testers, but since there are only about half of the same DNA locations in common with the FTDNA chip, matches will be fewer. Additional functions can be unlocked for a one time $19 fee.
  • Neither Ancestry, 23andMe nor Genographic accept transfer data from any other vendors.
  • MyHeritage does accept transfers, although that option is not easy to find. I checked with a MyHeritage representative and they provided me with the following information:  “You can upload an autosomal DNA file from your profile page on MyHeritage. To access your profile page, login to your MyHeritage account, then click on your name which is displayed towards the top right corner of the screen. Click on “My profile”. On the profile page you’ll see a DNA tab, click on the tab and you’ll see a link to upload a file.”  MyHeritage has also indicated that they will be making ethnicity results available to individuals who transfer results into their system in May, 2017.
  • LivingDNA has just released an ethnicity product and does not have DNA matching capability to other testers.  Living DNA imputes DNA locations that they don’t test, but the initial download only includes the DNA locations actually tested.
  • WeGene’s website is in Chinese and they are not a significant player, but I did include them because GedMatch accepts their files. WeGene’s website indicates that they accept 23andme uploads, but I am unable to determine which version or versions. Given that their terms and conditions and privacy and security information are not in English, I would be extremely hesitant before engaging in business. I would not be comfortable in trusting on online translation for this type of document. SNPedia reports that WeGene has data quality issues.
  • GedMatch is not a testing vendor, so has no entry in the left column, but does provide tools and accepts all versions of files from each vendor that provides files, to date, with the exception of the Genographic Project.  GedMatch is free (contribution based) for many features, but does have more advanced functions available for a $10 monthly subscription. The GedMatch Genesis platform is a sandbox area for files from vendors that cannot be put into production today due to matching and compatibility issues.
  • The Genographic Project tested their participants at the Family Tree DNA lab until November 2016, when they moved to the Helix platform, which performs an exome test using a different chip.
  • The Ancestry V2 chip began processing in May 2016.
  • The 23andMe V3 chip began processing in December 2010. The 23andMe V4 chip began processing in November 2013. Their V5 chip August 9, 2017.

Incompatible Files

Please be aware that vendors that accept different versions of other vendors files can only work with the tested locations that are in the files generated by the testing vendors unless they use a technique called imputation.

For example, Family Tree DNA tests about 700,000 locations which are on the same chip as MyHeritage, 23andMe V3 and Ancestry V1. In the later 23andMe V4 test, the earlier 23andMe V2 and the Ancestry V2 tests, only a portion of the same locations are tested.  The 23andMe V4 and Ancestry V2 chips only test about half of the file locations of the vendors who utilize the Illumina OmniExpress chip, but not the same locations as each other since both the Ancestry V2 and 23andMe V4 chips are custom. 23andMe and Ancestry both changed their chips from the OmniExpress version and replaced genealogically relevant locations with medically relevant locations, creating a custom chip.

Update:  In August 2017, 23andMe introduced their V5 chip which has only about 20% overlap with previous chips.

I know this is confusing, so I’ve created the following chart for chip and test compatibility comparison.

(Chart updated Sept. 28, 2017)

You can easily see why the FTDNA, Ancestry V1, 23andMe V3 and MyHeritage tests are compatible with each other.  They all tested utilizing the same chip.  However, each vendor then applies their own unique matching and ethnicity algorithms to customer results, so your results will vary with each vendor, even when comparing ethnicity predictions or matching the same two individuals to each other.

Apples to Apples to Imputation

It’s difficult for vendors to compare apples to apples with non-compatible files.

I wrote about imputation in the article about MyHeritage, here and also more generally, here. In a nutshell, imputation is a technique used to infer the DNA for locations a vendor doesn’t test (or doesn’t receive in a transfer file from another vendor) based on the location’s neighboring DNA and DNA that is “normally” passed together as a packet.

However, the imputed regions of DNA are not your DNA, and therefore don’t carry your mutations, if any.

I created the following diagram when writing the MyHeritage article to explain the concept of imputation when comparing multiple vendors’ files showing locations tested, overlap and imputed regions. You can click to enlarge the graphic.

Family Tree DNA has chosen not to utilize imputation for transfer files and only compares the actual DNA locations tested and uploaded in vendor files, while MyHeritage has chosen to impute locations for incompatible files. Family Tree DNA produces fewer, but accurate matches for incompatible transfer files.  MyHeritage continues to have matching issues.

MyHeritage may be using imputation for all transfer files to equalize the files to a maximum location count for all vendor files. This is speculation on my part, but is speculation based on the differences in matches from known compatible file versions to known matches at the original vendor and then at MyHeritage.

I compared matches to the same person at MyHeritage, GedMatch, Ancestry and Family Tree DNA. It appears that imputed matches do not consistently compare reliably. I’m not convinced imputation can ever work reliably for genetic genealogy, because we need our own DNA and mutations. Regardless, imputation is in its infancy today and due to the Illumina GSA chip replacing the OmniExpress chip, imputation will be widely used within the industry shortly for backwards compatibility.

To date, two vendors are utilizing imputation. LivingDNA is using imputation with the GSA chip for ethnicity, and MyHeritage for DNA matching.

Summary

Your best results are going to be to test on the platform that the vendor offers, because the vendor’s match and ethnicity algorithms are optimized for their own file formats and DNA locations tested.

That means that if you are transferring an Ancestry V1 file, a 23andMe V3 file or a MyHeritage file, for example, to Family Tree DNA, your matches at Family Tree DNA will be the same as if you tested on the FTDNA platform.  You do not need to retest at Family Tree DNA.

However, if you are transferring an Ancestry V2 file or 23andMe V4 file, you will receive some matches, someplace between one quarter and half as compared to a test run on the vendor’s own chip. For people who can’t be tested again, that’s certainly better than nothing, and cross-chip matching generally picks up the strongest matches because they tend to match in multiple locations. For people who can retest, testing at Family Tree DNA would garner more matches and better ethnicity results for those with 23andMe V2 and V4 tests as well as Ancestry V2 tests.

For absolutely best results, swim in all of the major DNA testing pools, test as many relatives as possible, and test on the vendor’s Native chip to obtain the most matches.  After all, without sharing and matching, there is no genetic genealogy!

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