Monday 8 August 2016

The new GPS Origins test from DNA Diagnostics Center – caveat emptor

We've had a few questions in our ISOGG Facebook group about a new GPS Origins test  so I thought I'd take a look at it. I'm not aware of anyone who has tested with the company and received results. At present the test is only available in the US and Canada during the initial launch period but there are plans to make it available in other countries in 2017.

You can either order a new test from scratch for an introductory price of US $149 or you can transfer your raw data from AncestryDNA, Family Tree DNA or 23andMe to order a GPS Origins report for $59. The transfer is not currently active and is advertised as "coming soon".

Here is a description of the test from the home page of the company website:
The GPS Origins™ (Geographic Population Structure) ancestry test uses the latest genetic research and a new ancestral tracking technique to pinpoint much more precisely where your DNA was formed. The GPS Origins™ test indicates the town or village where groups of your ancestors from different cultures met - building a rich picture of the migration journeys that formed your deep genealogical heritage.
There is further information in the How it Works section of the website:
The GPS Origins™ test then traces the migration route of your DNA back to where it originated from and dated the age of your DNA signature. It does that for both your maternal and paternal lineages indicating where your DNA began. Your results are detailed in a report that reveals your ancestral origins. 
Your personalized report identifies your top three Ancestral Origins (the Gene Pools or ancestral communities that contributed significant portions of your genetic makeup) and shows the percentages of DNA you inherited from each. The report is much more detailed than an estimate of ‘ethnicity’.

Your story starts with the shared origin of all humankind, and then builds into a vibrant picture of where and how your ancestors lived, and the conditions that led them to migrate. Your report contains maps illustrating the two most important migration journeys and describes how your ancestors’ circumstances changed as they crossed continents to find better lives. The report concludes with a summary page of helpful links to discover additional information to reveal your ancestral origins...
The GPS Origins™ test is a revolutionary ancestry test that enables you to trace where your DNA was formed over 1,000 years ago, along with its migration routes, down to the nearest village or town.

Current ancestry DNA tests locate where your DNA formed within countries or continents. Typically you find that some of your ancestries come from Western Europe, Africa or South Asia, and given broad estimates of your ethnicity. These tests generally cannot identify your origins to particular countries or locations.
It would be very exciting to have a DNA test which could provide this level of accuracy but unfortunately the reality is probably not going to live up to the hype. The GPS Origins test appears to be an updated version of a test originally offered by a company called Prosapia Genetics. The Prosapia test was based on algorithms described in a paper by Elhaik et al Geographic population structure analysis of worldwide human populations infers their biogeographical origins (Nature Communications, 2014). Customers were given a co-ordinate indicating their supposed place of origin 1000 years ago. There were a lot of complaints from customers, many of whom discovered that they had an aquatic origin in the middle of an ocean or river! See my blog post Driving in the wrong direction with a dodgy DNA satnav. Although the Prosapia Genetics website is still live there has not been any activity on their Facebook page or Twitter account for a long time, and it is not clear if the test is still on sale.

The new GPS Origins test has been developed by Dr Eran Elhaik, the lead author of the 2014 Nature Communications paper, and is using the same algorithms. The company claim in their FAQs that "The accuracy of GPS was demonstrated by identifying the DNA signature of ancient Ashkenazic Jews and their formation approximately 1500-2000 years ago." They are referring to a recent study by Das et al in Genome Biology and Evolution on Localizing Ashkenazic Jews to primeval villages in the ancient Iranian lands of Ashkenaz. Eran Elhaik was one of the co-authors of this paper. Both of these papers are highlighted on the GPS Origins website in a section on Research behind the GPS Origins™ test.

Unfortunately the company has failed to mention that the Das et al paper has been heavily criticised and that the original research on which the GPS test is based has been called into question. See the paper by Flegontov et al in Genome Biology and Evolution (2016) on the Pitfalls of the geographic population structure (GPS) approach applied to human genetic history: a case study of Ashkenazi Jews.

Here is the abstract from the paper:
In a recent interdisciplinary study, Das and co-authors have attempted to trace the homeland of Ashkenazi Jews and of their historical language, Yiddish (Das et al. 2016. Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz. Genome Biology and Evolution). Das and co-authors applied the geographic population structure (GPS) method to autosomal genotyping data and inferred geographic coordinates of populations supposedly ancestral to Ashkenazi Jews, placing them in Eastern Turkey. They argued that this unexpected genetic result goes against the widely accepted notion of Ashkenazi origin in the Levant, and speculated that Yiddish was originally a Slavic language strongly influenced by Iranian and Turkic languages, and later remodeled completely under Germanic influence. In our view, there are major conceptual problems with both the genetic and linguistic parts of the work. We argue that GPS is a provenancing tool suited to inferring the geographic region where a modern and recently unadmixed genome is most likely to arise, but is hardly suitable for admixed populations and for tracing ancestry up to 1000 years before present, as its authors have previously claimed. Moreover, all methods of historical linguistics concur that Yiddish is a Germanic language, with no reliable evidence for Slavic, Iranian, or Turkic substrata.
The Das et al paper was also criticised from a linguistic perspective by Marion Aptroot in a paper in Genome Biology and Evolution (2016) entitled Yiddish language and Ashkenazic Jews: a perspective from culture, language, and literature

Here is the abstract from her paper:
The typology of Yiddish and the name Ashkenaz cannot serve as arguments to support the theory put forward by Das et al. (2016). (Localizing Ashkenazic Jews to primeval villages in the ancient Iranian lands of Ashkenaz. Genome Biol Evol. 8:1132–1149.) that the origin of Ashkenazic Jews can be located in ancient Iran. Yiddish is a Germanic, not a Slavic language. The history of the use of the term Ashkenaz from the Middle Ages onward is well documented. Ashkenazic Jewry is named for the Hebrew and Yiddish designation for Germany, originally a Biblical term.
The new GPS Origins test is therefore based on an unproven methodology, which can't be replicated and which does not produce the village-level or even country-level accuracy that has been claimed. It is merely giving you geographical co-ordinates which represent an average of your closest matches in a reference database of modern populations. The whole concept of the test is fatally flawed because it is simply not possible to use the DNA of living people to identify at an individual level where your DNA originated 1000 or more years ago. Similarly we cannot trace the individual migration journeys of our ancestors from modern DNA. Ancient DNA is providing interesting new insights about past populations but these inferences apply to everyone's ancestors and are not unique to an individual.

The new test does seem to have some "improvements" compared to the old Prosapia test. Rather than providing one co-ordinate to represent the origins of your ancestors it would appear that the new test will provide a place of origin for both parents. Presumably this opens up the possibility of customers having origins in two rivers or oceans instead of just one!

If anyone does get results from this test I would be interested to hear from you and to see a sample report.

Further controversies
It should be noted that Eran Elhaik has been at the centre of a number of controversies in recent years.

In 2013 Elhaik published a paper in Genome Biology and Evolution on The missing link of Jewish European ancestry: contrasting the Rhineland and the Khazarian hypotheses. His findings were refuted by a leading team of Jewish researchers in a paper entitled No evidence from genome-wide data of a Khazar origin for the Ashkenazi Jews (Behar et al, Human Biology, 2013).

In 2014 Elhaik was the lead author of a letter in the European Journal of Human Genetics on The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome. This letter was a critique of  a paper by Mendez et al entitled An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree (American Journal of Human Genetics, 2013). Elhaik even published a mocking video on YouTube explaining where he thought the authors had made mistakes:

Mendez et al published a robust rebuttal Reply to 'The extremely ancient' chromosome that isn't' by Elhaik et al (European Journal of Human Genetics, 2013) pointing out that the authors' criticisms resulted from "a misunderstanding of population genetic theory, as well as a misrepresentation of the methodology of Mendez et al". They also discussed the "technical and conceptual flaws" that undermined the claims.

Update 26th August 2016
There is an ongoing thread on the Anthrogenica forum about the GPS Origins test. Some people have shared screenshots of their test results.

Update 30th November 2016
I have now tested with GPS Origins. See my blog post: A review of the GPS Origins test: four ethniticites and four reports.

Update 1st December 2016
I have discovered that the linguist Asya Pereltsvaig has published two critiques of Das et al 2016 on her blog:
I had the opportunity compare tests done on the GPS Origins chip compared with transfers from AncestryDNA and 23andMe. See my blog post The GPS origins test - the DREAM chip compared with AncestryDNA and 23andMe transfers.

© 2016 Debbie Kennett

Wednesday 3 August 2016

AncestryDNA partners with Quest Diagnostics to provide "wellness" offerings

It was announced today that AncestryDNA have partnered with a company called Quest Diagnostics. This new partnership will allow AncestryDNA to meet the growing consumer demand for their test both in the US and in other countries and will also allow them to expand their services by offering tests for "wellness and health traits".

AncestryDNA have already made their first steps into the health market by launching a new service called AncestryHealth which is currently in beta testing and is only available in the US.

It was revealed back in October 2015 that AncestryDNA were in talks with the FDA and were "seeking permission to use its DNA kit to tell people about everything from their disease risk and genetic carrier status, to how well their bodies might react to a specific drug".

In May this year AncestryDNA launched a new chip which "includes some markers associated with health". AncestryDNA said at the time "We continue to explore the possibility of developing health products in the future, and may do so with proper regulatory and legal approval."

The full press release provided by Quest Diagnostics is reproduced below.

Quest Diagnostics and AncestryDNA collaborate
to expand consumer DNA testing

World leaders in consumer genomics and diagnostic information services team up
Driven by rapidly growing global consumer demand for self-discovery through genomics

MADISON, N.J., and LEHI, Utah, Aug. 3, 2016 /PRNewswire/ -- Quest Diagnostics (NYSE: DGX), the world's leading provider of diagnostic information services, and AncestryDNA, the leader in family history and consumer genomics, are teaming up to help meet the rapidly growing consumer demand for genetic tests that provide insights into genetic ethnicity, origins and other factors. The new collaboration will allow AncestryDNA to scale its testing services and pave the way for new wellness offerings.

Quest Diagnostics Incorporated logo
Under a new multi-year global collaboration, Quest Diagnostics will provide genotyping test services on behalf of Ancestry's AncestryDNA, a service that today identifies and quantifies an individual's ethnic origins based on results of DNA testing. In just over four years, AncestryDNA has grown to become the world's largest consumer genomics provider, with more than two million consumer DNA samples in its database.

"We are very excited to be partnering with Quest Diagnostics to offer our consumer DNA test to more consumers around the world," said Tim Sullivan, Chief Executive Officer of Ancestry. "There's an inherent human need to learn more about who we are as individuals and how we connect to the world around us. As the success of AncestryDNA has already demonstrated, the stories and revelations contained within our DNA can have incredibly meaningful, life-altering effects that change how we think about ourselves and our world."

"People are very interested in their family history, and knowing one's family health history is very important in helping us manage our health," said Steve Rusckowski, Quest Diagnostics President and CEO. "Sharing our unique capabilities with Ancestry will help everyone learn more about themselves. We look forward to leveraging our tremendous expertise in genetic testing and information to offer a first-in-class experience to Ancestry and its customers."

"Quest stood out from all others through the breadth of their vision and their unwavering commitment to quality, as well as being well positioned to partner with us to provide wellness and health traits," said Ken Chahine, EVP and GM of AncestryDNA. "Adding a second diagnostic partner is a critical step forward as we work to continue to meet the consumer demand we're seeing for our DNA tests in the U.S. and markets around the world. We'll also now be able to move toward an East-West logistical approach, testing kits closer to where our consumers live and, ideally, reducing the time they need to wait to receive their results."

Ancestry selected Quest Diagnostics after considering several laboratory organizations through a formal request for proposal process. Quest Diagnostics will perform genetic testing on Ancestry customer samples at its state-of-the-art laboratory in Marlborough, Mass. Additional terms were not disclosed.

Quest's Marlborough facility uses next-generation sequencing and other technologies to provide testing in genetics, inherited cancers, neurological disorders and other complex diseases. Opened in 2014, the 200,000 square foot laboratory can accommodate expected growing demand for AncestryDNA. Quest expects to begin performing testing for Ancestry in the first quarter of 2017. Over time, the two companies intend to explore additional opportunities such as developing tools and applications to guide people on building and understanding their "family medical tree."

About Ancestry
Ancestry, the global leader in family history and consumer genomics, harnesses the information found in family trees, historical records, and DNA to help people gain a new level of understanding about their lives. Ancestry has more than 2.4 million paying subscribers across its core Ancestry websites and more than 2 million DNA samples in the AncestryDNA database. Since 1996, more than 18 billion records have been added, and users have created more than 80 million family trees on the Ancestry flagship site and its affiliated international websites. Ancestry offers a suite of family history products and services including AncestryDNA, Archives, ProGenealogists, and Fold3.

About Quest Diagnostics
Quest Diagnostics empowers people to take action to improve health outcomes. Derived from the world's largest database of clinical lab results, our diagnostic insights reveal new avenues to identify and treat disease, inspire healthy behaviors and improve health care management. Quest Diagnostics annually serves one in three adult Americans and half the physicians and hospitals in the United States, and our 44,000 employees understand that, in the right hands and with the right context, our diagnostic insights can inspire actions that transform lives.

Quest, Quest Diagnostics and all associated Quest Diagnostics registered or unregistered trademarks are the property of Quest Diagnostics.

Family Tree DNA's summer sale

Family Tree DNA are having a summer sale. The Family Finder is being offered at the lowest ever price of $69. Even with the currently weak pound that is still a bargain at just £52. If you've not already done a Family Finder test at FTDNA now is your chance. FTDNA have the advantage of a truly international database as well as providing a welcome range of additional tools such as a chromosome browser to let you get the best out of your results. You can also join all the relevant projects. Here is the relevant section of the e-mail I received from Family Tree DNA with the details of the tests that are included in the sale. I've included the sterling prices in red.

Dear Group Administrators,
Summer in Houston means relentless heat. Ruthless sunshine punctuated by the occasional thunderstorm. The hum of air conditioner compressors is the season’s soundtrack.
You know what else it means?
Yep. You got it. It means the Sizzlin’ Summer Sale is about to launch!
This summer the focus is on bundles that include Family Finder: Y37 + Family Finder, Y67 + Family Finder, FMS + Family Finder, and Comprehensive Genome (FF+Y67+FMS). The prices are in the chart below.
But wait - there’s more!
The heat must have gotten to Bennett because the only individual test he’s reduced pricing on is Family Finder, which will be $69. You read that right. $69 US DOLLARS!
(For those of you who are new and may not be aware, Bennett Greenspan is the founder and president of FTDNA.)
Not only has he set the Family Finder price ridiculously low, but he’s not giving us an end date for this sale. It could last a few days or a few weeks - we don’t know and he’s not telling!
So what we’re saying is, take advantage of these great prices while they’re hot!
Here’s the pricing: 
Retail Pricing
Sale Price
Group Price
Family Finder
$69     (£52)
Y37 + Family Finder
$218 (£164)
Y67 + Family Finder
$317 (£238)
Comprehensive Genome (FF+Y67+FMS)
$489 (£367)
FMS + Family Finder
$258 (£194)

**Please note - these bundles must remain bundles. If you buy at the sale price for future use, the entire bundle must be used on one tester. Canceling tests from the bundle will cause tests to revert to regular price.**