The GPS origins test - the DREAM chip compared with AncestryDNA and 23andMe transfers

Last November I wrote a review the GPS Origins test in which I was able to compare reports for four people with very different ethnicities, all of whom received disappointing results. However, the reports were all based on transfers of data from 23andMe or AncestryDNA. The GPS Origins test was designed for use with a custom microarray chip known as the DREAM (Diversity of REcent and Ancient huMan). This chip has has over 800,000 markers compared with 700,000+ markers for the AncestryDNA v1 chip and 500,000+ markers for the 23andMe v4 chip.

The DREAM chip was developed by Dr Eran Elhaik who is currently based at the University of Sheffield. In February this year Dr Elhaik gave a presentation at Rootstech about the DREAM chip. I was not at Rootstech, but the handout from the presentation is available online and this provides some technical details about the chip:

DREAM consists of ~800,000 markers: 730,000 autosomal,50,000 X-chromosomal, 18,000 Ychromosomal, and 1,300 mitochondrial markers. DREAM includes unique ancestry informative markers for 500 worldwide populations. It also includes a large number of ancient markers unique to over 300 ancient genomes that allows inferring relatedness to our ancestors (1000 to 50,000 years ago). These powerful markers allows DREAM full compatibility with the Geographical Population Structure Origins (GPS Origins^TM technology. GPS Origins^TM traces the geographical origins of your parental ancestries, down to home village in some cases, trace their migration routes, and date their arrival to these locations. GPS Origins^TM has a time resolution that ranges from 100 to 10,000 years.

In addition DREAM tests around 2,000 genes to "determine ~40 adaptations (e.g., high altitudes) and special traits (e.g., eye color)".

The GPS Origins test does not currently match you with your genetic cousins but it's possible that this feature will added in the future. The chip includes around 400 copy number variants (CNVs) which it is claimed will help to improve the accuracy of relationship predictions for 4th and 5th degree relatives (first cousins and first cousins once removed). It should be noted that the currently available cousin-matching tests from AncestryDNA, 23andMe and Family Tree DNA can already be used to make reliable inferences about relationships up to about the fourth cousin level when the results are used in combination with genealogical information. It may that the use of CNVs is intended to improve inferences when contextual information is not available.

The developer describes DREAM on his blog as "a new microarray that can support concepts that do not yet exist. The difference between DREAM and the old-generation arrays is the same as between smartphones and plain cell phones. They can both make phone calls and text one another, but only smartphones allow running apps. In other words, some of the tests that would be developed on DREAM may work on the old arrays, but not all tests. We’ll do our best to support to all microarrays, of course". (The full blog post can be read here.)

I don't know what the overlap of markers is on the DREAM chip compared with the chips used by AncestryDNA, 23andMe and Family Tree DNA but with additional markers, many of which were specifically selected for biogeographical ancestry, it seems plausible that if a test was done on the chip for which it was designed the results might be much improved. However, it is apparent that many of the problems with this test are related to the methodology, which cannot be replicated and is conceptually unsound. (See my previous review of the GPS Origins test for a fuller discussion of these issues and links to sources.)

Peter Moriarty contacted me after stumbling upon my original review. He has tested on the DREAM chip but he had also previously transferred his raw data to GPS Origins from both 23andMe and AncestryDNA. He has very kindly given me permission to share his reports. This gives us a unique opportunity to compare the results obtained from the DREAM chip with results from AncestryDNA and 23andMe transfers. Here is what Peter says:

Like some of your other contributors I was disappointed with the 1st raw date upload results, which was from my Family Tree results, so I thought I would retry by supplying the raw data from 23andMe. Again the results were disappointing (to say the least), and curiously they show different locations where my DNA apparently first showed a traceable origin. SO, having dug a hole, and having received responses/explanations from GPS Origins that they couldn’t be responsible for raw DNA data from other sources, I jumped in the hole I dug, and ordered a full GPS Origins DNA test. The total costs of these tests was $357.00! So I hope they can be of some benefit to at least expose GPS Origins for what they are.

Here is the migration map that Peter received from his first data upload.

Here is the migration map from Peter's second data upload. Peter does not know which of these maps relate to AncestryDNA and 23andMe and so far the company have not been able to tell him which one is which.

Here are the results that Peter received after being re-tested on the DREAM chip.

Peter also sent me a copy of his Gene Pool percentages which he said were "close to identical from all three test results":

GENE POOL % s

Complete Results

#1 Fennoscandia 20.6% Origin: Peaks in the Iceland and Norway and declines in Finland, England, and France

#2 Southern France 14.5% Origin: Peaks in south France and declines in north France, England, Orkney islands, and Scandinavia

#3 Orkney Islands 12% Origin: Peaks in the Orkney islands and declines in England, France, Germany, Belarus, and Poland

#4 Western Siberia 10.4% Origin: Peaks in Krasnoyarsk Krai and declines towards east Russia

#5 Basque Country 9.5% Origin: Peaks in France and Spain Basque regions and declines in Spain, France, and Germany

#6 Sardinia 8.1% Origin: Peaks in Sardinia and declines in weaker in Italy, Greece, Albania, and The Balkans

#7 Southeastern India 8% Origin: Endemic to south eastern india with residues in Pakistan

#8 Tuva 7% Origin: Peaks in south Siberia (Russians: Tuvinian) and declines in North Mongolia

#9 Northern India 4.3% Origin: Peaks in North India (Dharkars, Kanjars) and declines in Pakistan

#10 Arabia 1.6% Origin: Peaks in Saudi Arabia and Yemen and declines in Israel, Jordan, Iraq, and Egypt

#11 The Southern Levant 1.4% Origin: This gene pool is localized to Israel with residues in Syria

#12 Western South America 0.8% Origin: Peaks in Peru, Mexico, and North America and declines in Eastern Russia

#13 Pima County: The Sonora 0.8% Origin: Peaks in Central-North America and declines towards Greenland and Eskimos

#14 Bougainville 0.6% Origin: Peaks in Bougainville and declines in Australia

#15 Northwestern Africa 0.1% Origin: Peaks in Algeria and declines in Morocco and Tunisia

#16 West Africa 0.1% Origin: Peaks in Senegal and Gambia and declines in Algeria and Morocco

Peter comments on his test results as follows:

My whole and almost only interest in genealogy started as a quest to find out where my Irish Moriarty ancestors lived in Ireland prior to emigrating from Ireland to America. I know the names of the parents of the first ancestor who left arrived in America via Canada in 1961, and am sure they lived in County Kerry, probably on or near the Dingle Peninsula. Of course the 3 autosomal DNA tests contributed little to this quest, so I also took Family Tree’s Y-DNA and mtDNA tests. Interestingly I was contacted by a surname project administrator who told me that I was related to a group of 11 people (so far) who had surnames indicating Irish and English ancestry. They encouraged me to purchase a BigY analysis. I mention all of this because this report indicates that my Irish heritage goes back to at least 365 AD. So this shows, if not proves, that I have Irish ancestry going back at least to that time. The three GPS Origins test results indicate the places where my ancestors’ formations are traceable. As you can see from my GPS Origins results, these locations range from England to Estonia to Switzerland to Sweden to Albania to Georgia and end up in Germany, Russia, Norway, and England! All depending upon which test to believe.

GPS Origins explained away the fact that I don’t show any Irish ancestry results is that their test results probably preceded my records. They also said that probably my maternal and paternal ancestors were from different locations and therefore the GPS Origins results would split the difference and indicate locations somewhere in the middle. Huh? So much for the claim to locate the actual village of origin! Although the paper and historic documentation I have from family records only goes back from 200 years (Irish) and 400 years (German), I believe that my mother was 75% Scotch/Irish + 25% Germanic, and my father was 50% Irish and 50% English, so at least for the past 6 to 10+ generations, they were predominately English/Scotch/Irish. (We also believe there is a little Scandinavian DNA mixed in with the Scotch and perhaps the Irish ancestors), so the GPS Origins results are baffling to say the least.

That having been said, I am only a beginner in understanding DNA. I understand that atDNA tests are good for genealogical research for about 6 generations back, and are also good for describing one’s deep ancestral ethnic makeup. The GPS Origins test results contributed zero to the former, and as far at the latter is concerned, the results may be accurate, but it seems unlikely that my ancestral make up is from such disparate locations as Russia/Siberia (17.4%) and India (12.3%) in addition to Sardinia and Basque Country etc, especially since none of these geographic locations showed up in any of the 3 other autosomal DNA tests that I took, all of which pegged my ancestors as 96-99% Western European!

I should point out that the BigY test Peter took is a Y-chromosome test. The Y-chromosome is passed on from father to son and provides information about ancestry on the direct male line. Y-DNA testing is often used in surname projects because the transmission of the Y-chromosome usually corresponds with the inheritance of surnames. The Y-chromosome doesn't get chopped up like autosomal DNA through the process of recombination and so it can be used to trace male lines back for hundreds or thousands of years.

Autosomal DNA provides information about our ancestors on all our family lines, but because it is diluted with each new generation you only have to go back a few generations before we find ancestors who drop off our genetic family tree. Peter has 64 gggg grandparents, only one of whom was a Moriarty, and so this line represents a tiny fraction of his total pedigree. Although he clearly has deep Irish connections on his Y-DNA line, these results would not be expected to correlate with his genetic ancestry from an autosomal DNA test. In addition, our DNA can only be matched to reference datasets that are in the company's database. If a population is not included then you will be matched to the next closest population. I have been unable to find a full list of the reference populations used by GPS Origins to determine whether or not they have any data from Ireland.

Clearly Peter gained no benefit from being tested on the DREAM chip. In fact the results he received from the full test were even more off the mark than the reports from the transfers. He has paid a hefty price to find this out. Thank you Peter for sharing your results so that others can learn from your experience and will not be tempted to waste their money.

Note
The GPS Origins test was previously sold by DNA Diagnostics Center and had its own dedicated website. The test is now being sold through HomeDNA which appears to be a subsidiary of DNA Diagnostics Center. If you previously tested with the company you will now need to get your account authorised on the new site in order to access your results. The test is currently only sold in the US and Canada.

Update
Within a few hours of publishing this article I was informed by Peter Moriarty that, following a complaint he made to GPS Origins, they provided him with a full refund for all three tests.

Related blog posts

• A review of the GPS Origins test: four ethnicities and four reports
• The new GPS Origins test from DNA Diagnostics Center - caveat emptor

A review of the GPS Origins test: four ethnicities and four reports

I wrote about the GPS Origins test from DNA Diagnostics Center back in August this year when the test was first launched. There was recently a special offer via Geneabloggers to upload your raw data and receive an interpretation for $29, a big saving on the usual transfer price of $79. I thought I would it give it a try out of curiosity. As a comparison three other people with different ancestries have also shared their reports with me and given permission for me to use them on this blog.

First of all let's have a look at what the GPS Origins test claims to offer. Here are the descriptions from the how it works page:

The GPS Origins report is split into two parts. In the first section you are provided with your gene pool percentages. Here is the explanation of gene pools from the Understanding Your Results page:

The second part of the test provides two migration stories for each customer. Here is the explanation from the Understanding Your Results page:

There is further information about the test on the FAQs page:

The company makes the following claims with regards to the accuracy of the test:

Now let's move on to look at some actual results, starting with my own GPS Origins test.

Debbie Kennett's GPS Origins results
I've done a lot of research on my family tree over the last 15 years. All my known ancestors within the last 500 years are from Britain and Ireland. I have one great-great-great-grandmother who was born in Ireland and one great-great-great-grandfather who was born in Scotland. All my remaining ancestors were born in England and are predominantly from the south and west of the country. I've previously tested with AncestryDNA, 23andMe and Family Tree DNA. My admixture results from these three companies are fairly typical for someone with British ancestry. Each company uses different reference populations and therefore produces different results, but my ancestry comes out at between 41% and 58% British and Irish with the balance made up from a mixture of other European populations. You can see my full admixture results from all three companies here.

For the GPS Origins test I uploaded my raw data from AncestryDNA (v1). Here are my gene pool percentages:

# 1 Fennoscandia 19.8%
Origin: Peaks in the Iceland and Norway and declines in Finland, England, and France

# 2 Western Siberia 12.9%
Origin: Peaks in Krasnoyarsk Krai and declines towards east Russia

# 3 Sardinia 12.4%
Origin: Peaks in Sardinia and declines in weaker [sic] in Italy, Greece, Albania, and The Balkans

# 4 Orkney Islands 11.8%
Origin: Peaks in the Orkney islands and declines in England, France, Germany, Belarus, and Poland

# 5 Southern France 11.3%
Origin: Peaks in south France and declines in north France, England, Orkney islands, and Scandinavia

# 6 Basque Country 11.2%
Origin: Peaks in France and Spain Basque regions and declines in Spain, France, and Germany

# 7 Southeastern India 9.1%
Origin: Endemic to south eastern india with residues in Pakistan

# 8 Tuva 6%
Origin: Peaks in south Siberia (Russians: Tuvinian) and declines in North Mongolia

# 9 Northern India 4%
Origin: Peaks in North India (Dharkars, Kanjars) and declines in Pakistan

# 10 Western South America 1.1%
Origin: Peaks in Peru, Mexico, and North America and declines in Eastern Russia

# 11 Central America 0.2%
Origin: Peaks in Mexico and Central America with residues in Peru

# 12 Northwestern Africa 0.2%

Origin: Peaks in Algeria and declines in Morocco and Tunisia

In the second part of the test I am given a map showing my two migration routes with accompanying migration stories.

You can see an interactive version of my migration routes here. You can view a PDF file with my full GPS Origins report here.

For the blue migration route I am told that my ancestors came from around Croatia prior to 211 AD. They then moved to Ireland at some point before 211 AD and moved to England between 211 AD and 1950 AD. According to my red migration route my ancestors came from Russia prior to 659 AD and arrived in north-western Russia between 659 AD and 1366 AD.

Ann Turner's GPS Origins results
The next report has been shared with me by Ann Turner. Ann's known ancestry is 3/16 German and 1/16 Irish from the early 1800s. The remainder is colonial American, and presumably English. Ann has also tested at 23andMe (v2 and V4), AncestryDNA and Family Tree DNA. Here are her 23andMe results at the speculative setting:

At AncestryDNA Ann's results are: Europe 98% and West Asia 1%. Europe is broken down as follows: Scandinavia 50%, Europe West 15%, Iberian Peninsula 12%, Ireland 12%, Great Britain 6%, trace regions 3%.

With Family Tree DNA's Family Finder test Ann's MyOrigins results are: European 97%, Central South Asia 2%. Europe is broken down into: Western and Central Europe 44%, Scandinavia 35%, British Isles 16%, Southern Europe 1%.

Ann uploaded her AncestryDNA data (v1) to GPS Origins. Here are Ann's gene pools:

# 1 Fennoscandia 22%
Origin: Peaks in the Iceland and Norway and declines in Finland, England, and France

# 2 Southern France 15.5%
Origin: Peaks in south France and declines in north France, England, Orkney islands, and Scandinavia

# 3 Western Siberia 10.9%
Origin: Peaks in Krasnoyarsk Krai and declines towards east Russia

# 4 Southeastern India 10.7%
Origin: Endemic to south eastern india with residues in Pakistan

# 5 Orkney Islands 10.6%
Origin: Peaks in the Orkney islands and declines in England, France, Germany, Belarus, and Poland

# 6 Basque Country 10%
Origin: Peaks in France and Spain Basque regions and declines in Spain, France, and Germany

# 7 Sardinia 9.3%
Origin: Peaks in Sardinia and declines in weaker in Italy, Greece, Albania, and The Balkans

# 8 Tuva 7%
Origin: Peaks in south Siberia (Russians: Tuvinian) and declines in North Mongolia

# 9 Northern India 2.5%
Origin: Peaks in North India (Dharkars, Kanjars) and declines in Pakistan

# 10 The Southern Levant 1.4%
Origin: This gene pool is localized to Israel with residues in Syria

# 11 Western South America 0.2%
Origin: Peaks in Peru, Mexico, and North America and declines in Eastern Russia

Here are Ann's migration routes.



You can see an interactive version of Ann's migration routes here. The PDF File with Ann's full GPS Origins report can be seen here.

Ann's migration stories show that her ancestors came from Greece prior to 696 AD, and from Russia prior to 696 AD. Both of Ann's routes converge on the same location in Germany some time between 696 AD and 1935 AD. 

Piya Changmai's GPS Origins results

From the above two results it would appear that this test is not very helpful for people of Northern European ancestry. Let's now have a look at some results for someone with Asian ancestry. Piya Changmai has kindly shared his results with me. According to his family history Piya has 5/8 of his ancestry from Thailand and 3/8 from Southern China. He describes his ancestry as follows:

I have a Chinese paternal great-grandfather, so he contributed 1/8 of my ancestry. I have also a Chinese maternal grandmother, so her contribution is 2/8. Other ancestors are Thai and Laotian ethnics from Thailand. Thai and Laotian are closely related ethnics, like Czech and Slovak. In summary, I have Chinese ancestry 2/8+1/8 = 3/8 and Thailand (Thai and Laotian) ancestry 5/8. Both Chinese ancestors are from Southern part of China, also reflected by Y and mt haplogroups (O2a1a and F4b, respectively).

Piya has also tested at 23andMe. Here are his 23andMe results at the standard setting:

Here are Piya's 23andMe results at the speculative setting:

Piva uploaded his 23andMe (v4) data to GPS Origins. Here are Piya's gene pool results:

# 1 Austronesian Oceania 33.4%

Origin: Peaks in Korea, Chinese (Han), Mynamar, Japan, and Vietnam and declines towards West China and India

# 2 Austronesian Southeast Asia 27.1%

Origin: Peaks in Taiwan and Malay and declines in Thailand, Vietnam, Cambodia, and South China

# 3 Central America 6.4%

Origin: Peaks in Mexico and Central America with residues in Peru

# 4 Sino-Tibetan and Hmongic Southeast Asia 5.8%

Origin: Peaks in East Asia, Central-south China (Lahu, Naxi, Yi) and declines towards India

# 5 Tuva 4.2%

Origin: Peaks in south Siberia (Russians: Tuvinian) and declines in North Mongolia

# 6 Central Southern China: Yunnan and Guangxi 4%

Origin: Peaks in East Asia (East) and Chinese (She, Dai) with residues in Central south China (Han, Miao, Tujia)

# 7 Western Siberia 3.2%

Origin: Peaks in Krasnoyarsk Krai and declines towards east Russia

# 8 Pima County: The Sonora 3.1%

Origin: Peaks in Central-North America and declines towards Greenland and Eskimos

# 9 Southeastern India 2.9%

Origin: Endemic to south eastern india with residues in Pakistan

# 10 Papuan New Guinea 1.8%

Origin: Peaks in Papua New Guinea and declines in Australia

# 11 Bougainville 1.6%

Origin: Peaks in Bougainville and declines in Australia

# 12 Southern France 1.3%

Origin: Peaks in south France and declines in north France, England, Orkney islands, and Scandinavia

# 13 Southwestern India 1.3%

Origin: Endemic to Indian (Pulayar) with residues in India (Paniya, Savara, Bengali, Juang, Savara, Ho, Bonda)

# 14 Northern India 1.1%

Origin: Peaks in North India (Dharkars, Kanjars) and declines in Pakistan

# 15 Western South America 1%

Origin: Peaks in Peru, Mexico, and North America and declines in Eastern Russia

# 16 Northern Mongolia and Eastern Siberia 1%

Origin: Peaks in North Mongolia and declines in Siberia

# 17 Northwestern Africa 0.5%

Origin: Peaks in Algeria and declines in Morocco and Tunisia

# 18 The Southern Levant 0.3%

Origin: This gene pool is localized to Israel with residues in Syria

Here is Piya's migration map.

You can see an interactive version of Piya's migration map here. (His report is under the pseudonym Mee Panda.) A PDF file with Piya's full GPS Origins results is available here.

Both of Piya's migration routes start in the same place in Kyrgyzstan. Piya is told that his ancestors came from Kyrgyzstan prior to 1183 AD. His ancestors on the northern route arrived in northern China between 1183 AD and 1617 AD. Piya's southern migration route ends up in Singapore and arrived there some time between 1150 AD and 1751 AD. 

Ezgi Altinisik's GPS Origins results
The final set of results I'll be looking at are from Ezgi Altinisik. She is from Turkey. Her paternal grandfather was born in Bulgaria and her paternal grandmother was born in Romania but both were Turkish and moved back to Anatolia around 1930. Her maternal grandmother is from Siverek in Turkey. Her maternal grandfather is from Samsun on the north coast of Turkey. As far as she knows, all her maternal ancestors have resided in Turkey for a long time.

Ezgi has also tested at 23andMe. Here are her 23andMe results at the standard level:

Here are her 23andMe results at the speculative level.

Ezgi uploaded her 23andMe data (v4) to GPS Origins. Here are Ezgi's gene pool results:

# 1 Southern France 14.6%

Origin: Peaks in south France and declines in north France, England, Orkney islands, and Scandinavia

# 2 Fennoscandia 14.6%

Origin: Peaks in the Iceland and Norway and declines in Finland, England, and France

# 3 Southeastern India 12.8%

Origin: Endemic to south eastern india with residues in Pakistan

# 4 Western Siberia 10.9%

Origin: Peaks in Krasnoyarsk Krai and declines towards east Russia

# 5 Orkney Islands 9.7%

Origin: Peaks in the Orkney islands and declines in England, France, Germany, Belarus, and Poland

# 6 Tuva 7.9%

Origin: Peaks in south Siberia (Russians: Tuvinian) and declines in North Mongolia

# 7 Sardinia 7.8%

Origin: Peaks in Sardinia and declines in weaker in Italy, Greece, Albania, and The Balkans

# 8 Arabia 5.7%

Origin: Peaks in Saudi Arabia and Yemen and declines in Israel, Jordan, Iraq, and Egypt

# 9 The Southern Levant 5.5%

Origin: This gene pool is localized to Israel with residues in Syria

# 10 Basque Country 3.9%

Origin: Peaks in France and Spain Basque regions and declines in Spain, France, and Germany

# 11 Northern India 3.8%

Origin: Peaks in North India (Dharkars, Kanjars) and declines in Pakistan

# 12 Austronesian Southeast Asia 1.3%

Origin: Peaks in Taiwan and Malay and declines in Thailand, Vietnam, Cambodia, and South China

# 13 Central America 0.8%

Origin: Peaks in Mexico and Central America with residues in Peru

# 14 Western South America 0.8%

Origin: Peaks in Peru, Mexico, and North America and declines in Eastern Russia

Here is Ezgi's migration map.

Ezgi's interactive migration map can be seen here. A PDF file with Ezgi's full GPS Origins results is available here.

The blue migration route shows that Ezgi's ancestors came from Russia prior to 1244 AD. Her ancestors then passed through Turkey on their DNA journey and ended up in Crete some time between 1244 AD and 1557 AD. According to the red migration route Ezgi's ancestors came from Turkey prior to 1037 AD, and arrived in Armenia some time between 1037 AD and 1527 AD.

Discussion

This is only a very small sample of four test results, but if these results are representative it would appear that the GPS Origins test is not very helpful.

The gene pool results are very strange and correlate poorly with the results we might expect for the reported ethnicities. For instance, both North European persons (Ann and I) and the Turkish person (Ezgi) in this small sample have unexpectedly high and very similar percentages of ancestry components from Siberia (18% - 19%) and India (13 - 17%). The model seems to overestimate these components for all West Eurasians. The components from Orkney (9.7% - 11.8%) and Sardinia (7.8%  - 12.4%) are also similar in these three individuals.

The Thai person (Piya) has an unexpectedly high component of around 10% Native American, but only just over 5% from India. Both Ann and I, who have recent all-European ancestry, came out with more than double this Indian component. We would expect much more Indian ancestry in a Thai person as compared to a European person, based on the history of Thailand and recent genetic research (Mörseburg et al 2016).

The maps do not always correspond with the countries in the gene pools. Fennoscandia is supposed to encompass Norway, Sweden, Finland, Denmark and "a part of Russia known as the Kola Peninsula". However, on the map it covers Iceland, Norway, Finland, Britain and France but excludes Sweden and Denmark. The map for the Western Siberian gene pool covers the whole of Russia. The Austronesian Oceania gene pool seems to be misnamed given its geographical distribution and probably should be renamed as Northeast Asia. Only Korea, Japan, Vietnam and Myanmar (Burma) are highlighted on the map yet these countries are not in Oceania and the people do not speak any Austronesian languages. China is missing from the map, although the text states that the component peaks in Han Chinese, among other populations. Pavel Flegontov, a geneticist at the University of Ostrava in the Czech Republic, tells me that in all other ADMIXTURE analyses he's seen, this Northeast Asian component has a much wider distribution in Siberia and much lower percentages in Myanmar and Vietnam. He suggests that if the components really have the distributions shown on the maps, that clearly demonstrates that GPS Origins reports artefacts of an overly complex admixture model with 36 components.

According to the legend on the migration maps "Although the Migration Patterns represent your Maternal and Paternal DNA route, we cannot differentiate which route is specifically your parents’ individual route at this time." However, the GPS Origins test does not phase the genetic data (phasing is the process of sorting the alleles onto the maternal and paternal chromosomes) so it is not clear how the paternal and maternal routes are defined in the first place. If an individual has reported ancestry from predominantly one region then surely we would expect the migration routes to be broadly similar for both the maternal and paternal lines.

The co-ordinates are supposed to represent places where "significant genetic mixture took place at the gene pool level", but the proposed migration routes are at times bizarre and do not correspond with historical records. For example, there are no large-scale historical migrations from Croatia to Ireland, from Kyrgyzstan to Singapore, or from Russia to Crete. The precision of the geographical co-ordinates down to three decimal places gives a false sense of accuracy, but the methodology is opaque.

The concept of the dual migration pathways is difficult to understand. If we go back one thousand years, in theory we all have over 8,000 million genealogical ancestors. It is inconceivable that half of these ancestors would all go off on their travels in one direction and the other half would go in a different direction.

The algorithms for the GPS Origins test have been developed by scientists at the University of Sheffield led by Eran Elhaik. However, as mentioned in a previous blog post, the underlying research by Elhaik et al (Nature Communications, 2014) on which this test is based has proved to be controversial. The results have been called into question by Flegontov et al (2016) who conclude that GPS is a "genetic provenancing approach" which is "at best only suited to inferring the most likely geographic location of modern and relatively unadmixed genomes, and tells nothing of population history and origin".

Since then a further analysis has been published by Andrew Millard, an archaeological scientist at the University of Durham. He was unable to reproduce the mathematical calculations and concluded:

...the mathematical methods described are incoherent, the supplementary data is not that used to create the figures or equations in the paper, and the supplementary code does not implement the methods described. The paper is methodologically unsound and not reproducible.

There have also been additional concerns about an undeclared conflict of interest on the part of Eran Elhaik and Tatiana Tatarinova, the lead authors of the GPS paper in Nature Communications. This omission has now been partially rectified, somewhat belatedly, with the publication on 31 October 2016 of a corrigendum. However, the new conflict of interest statement does not mention the relationship that the two authors already appear to have had in place with Prosapia Genetics prior to publication. The Prosapia Genetics domain name was originally registered to Tatarinova. On the very day that the paper was released Prosapia started selling a commercial GPS test. In a video published to accompany the press release issued by the University of Sheffield Eran Elhaik suggested that people should upload their genotype data to "our website" to find out their geographical homeland. The Prosapia URL (www.prosapiagenetics.com) was included at the end of this video. The video has since been edited to remove the URL but the original unedited video can be viewed on the Daily Mail website. The original Prosapia GPS test no longer seems to be available and the website now returns a warning message. An early version of the website dating from 3 May 2014, a few days after the publication of the paper, can be found in the Internet Archive.

Conclusion
The GPS Origins test does not provide meaningful results and has no practical application for the genetic genealogist. If you wish to use your raw autosomal DNA data from one of the commercial testing companies to get an alternative admixture analysis I recommend using one of the free services such as DNA.Land or GedMatch instead.

Update 1st December 2016
Eran Elhaik has published a response to this article GPS Origins results for four participants on his Khazar DNA Project blog.

Update 8th December 2017
The GPS Origins test is now marketed by a company known as Home DNA. See the article Genome culture: a holiday gift-giving guide by genetics counsellor Laura Hercher one the deficiencies of the Home DNA privacy policy and the limitations of their tests.

Acknowledgements

Thanks to Ann Turner, Piya Changmai and Ezgi Altinisik for sharing their results. Thanks to Pavel Flegontov and Ann Turner for helpful comments on early drafts of this blog post.

Related blog posts

• The GPS Origins test - the DREAM chip compared with AncestryDNA and 23andMe transfers
• The new GPS Origins test from DNA Diagnostics Center - caveat emptor

 © 2016 Debbie Kennett

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:

• Is Yiddish to be traced to Turkey? 29 April 2016
• Turkey, Shmurkey! — A Response to Das et al. (2016) 10 June 2016

Update 18th July 2017

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

Driving in the wrong direction with a dodgy DNA satnav

I've been receiving a lot of questions in the last couple of days about the new DNA "satnav" tool called GPS (Geographic Population Structure) which purports to pinpoint the village that your ancestors lived in one thousand years ago. See, for example, the articles in the Daily Mail and the Washington Post. There was also some prominent and uncritical coverage on BBC Breakfast News on Thursday featuring a segment in which the BBC weather presenter Carol Kirkwood was given the results of her DNA test on air and told that her ancestors were from the town of Crieff in Scotland. As Chris Jiggins has pointed out on Twitter the acronym GPS seems to have been chosen deliberately to "promote a completely false sense of accuracy".  

The company which is offering this service is a new start up by the name of Prosapia Genetics, which has been set up by Tatiana Tatarinova from the Children's Hospital Los Angeles. The company proudly proclaim on their website: "Our first tool, GPS, will tell you where your DNA was forged, and is accurate to home village with a time resolution of the past 1,000 years."

The reports are based on an analysis of autosomal SNPs. You can either order a test through Prosapia Genetics, who appear to have an affiliate relationship with Family Tree DNA, or you can submit your raw data file from a test you've already taken with one of the companies that offers autosomal DNA testing - AncestryDNA (US only),  23andMe, Family Tree DNA, Geno 2.0 or BritainsDNA/ScotlandsDNA. A range of reports is offered with prices varying depending on the number of reference populations used for the analysis. The reports simply give you a set of geographical co-ordinates, which are supposed to represent the "ancient home" of all of your ancestors, and a map showing where your ancestors lived. We are now getting feedback from a number of people who've paid for this service and it would appear, not surprisingly, that the reality does not match the hype.

Julie Matthews bought the Basic Test, which covers 100 reference populations. She commented in the Facebook R1b-L21 group:

I spent $29 to discover that my "homeland" was in the middle of the River Humber in England. I knew we all descended from fish - here's proof. Don't waste your money!

Teresa Vega paid for the Super Test, which includes 500 reference populations. She writes in the ISOGG Facebook group:

Totally unconvincing. Stupid me paid $42.99 for nada! My ancestral home is smack dab west of Puerto Rico in the Atlantic Ocean! I learned nothing and it told me to upgrade to another test for more detailed results -- a test they don't even have listed! Don't believe the hype!!!!

Teresa's report can be seen online here.

JoAnn O'Linger had a similarly misleading result. She reports in the ISOGG Facebook group:

I had a similarly disappointing result from Prosapia (paid for), it was the "Super Test" as well: 

" JoAnn ordered a Super GPS Test of her DNA data. We found the following GPS Co-ordinates : Latitude 56.7811288256845 and Longitude 4.26921663910535 

A map pointing the location is given below with a short guide on how to interpret this results.

How to interpret your results? 

GPS coordinates indicate the place where your DNA was forged before your family may have moved to your current location. Because borders changed throughout history, your ancestors may have been part of an ancient country once ruled the region. If your GPS coordinates are in the water, it indicates mixture between two populations on the two ends of the body of water, in which case we suggest you register to the upcoming GPS2 tool that would provide you with the origins of your parents. If you wish to learn more about your past, we suggest you try the Advanced test or the Super test, which provide much higher accuracy." 

JoAnn says: "Those coordinates are squarely in the North Sea, which does make sense as I am the typical American mutt, with mostly Irish and English heritage, but if one goes further back, much of that is from Norman French and Gaelic-Norse Orcadians. So it makes sense, but in my opinion it's not worth the high price."

Prosapia Genetics have a Forum where you can read the comments from their customers, many of whom have expressed similar disappointment at the service offered:

http://prosapiagenetics.com/community/viewforum.php?f=2

[Update 10th May 2014 The Prosapia Genetics Forum is now restricted to members only. I am told that complaints and negative comments have been deleted and comments are being moderated.]

This is not surprising as the whole concept of the test is fundamentally flawed. If we assume 30 years per generation and we go back 35 generations to the year 1050 theoretically we will have 34,359,738,367 ancestors. This figure does of course exceed the population of the world at that time and in reality there will be lots of pedigree collapse which will reduce the number of ancestors considerably. Even so, the mind-boggling figures demonstrate that it is quite meaningless to try and pinpoint a single geographical location as the origin of all those diverse ancestors one thousand years ago. Furthermore, we only inherit the DNA of a tiny subset of our ancestors. To understand why this is the case read Luke Jostin's blog post "How many ancestors share our DNA" and the posts from Graham Coop and Blaine Bettinger that are linked in that article.

Even if it were possible to pinpoint a single location to represent our millions of ancestors from a thousand years ago, we would need accurate "maps" in the form of carefully sampled reference populations in order to be able to use our DNA satnav. Unfortunately, we only have a limited number of reference populations available, many of which have been sampled for medical purposes with no attempt made to collect the relevant "co-ordinates" in the form of  detailed genealogical information. Consequently, any maps included in a reference genome "satnav" are going to have massive black holes. It is therefore not surprising that this DNA satnav is misdirecting people into rivers and oceans!

The methodology behind the GPS tool was outlined in a paper by Elhaik et al entitled Geographic population structure analysis of worldwide human populations infers their biogeographical origins. The paper was published in the scientific journal Nature Communications. Despite the fact that the Prosapia Genetics website appears to have been launched on the same day that the paper was published Tatiana Tatarinova, the founder of the Prosapia Genetics website and one of the lead authors, has not declared any "competing financial interests". The paper has already been the subject of controversy. The technique described in the paper offers nothing new and it is claimed that the methodology has been copied from that used by the blogger Dienekes Pontikos, who writes under a pseudonym. For background see Dienekes' two blog posts on the subject:

- Nature Communications, the Genographic Project, Elhaik et al. re-discover zombies, the Oracle, etc. 3 years after the fact...
- The Geographic Position Structure (GPS) algorithm of Elhaik et al. (2014) is basically wrong

See in particular the comments section of the first of the above two posts where Eran Elhaik attempts to defend the charge of plagiarism.

Joe Pickrell, one of the reviewers of the paper, has posted a summary of his critique which is well worth a read. The review can be found here:

http://jkplab.org/2014/04/30/review-geographic-population-structure-gps-of-worldwide-human-populations-infers-biogeographical-origin/

The authors themselves concede in the paper that the technique has its limitations and will only work if "the appropriate samples are available in the reference population data set". They appear to have cherry-picked some conveniently isolated populations such as the Sardinians for the purposes of their study, but the technique did not work for other populations:

To test GPS’s accuracy with individuals from populations that were not included in the reference population set, we conducted two analyses. We first repeated the previous analysis using the leave-one-out procedure at the population level. As expected, GPS accuracy decreased with 50% of worldwide individuals predicted to be 450 km away from their true origin. The predicted distance increased to 1,100 and 1,750 km for 80 and 90% of the individuals, respectively (Fig. 4a). Because GPS best localizes individuals surrounded by M genetically related populations, populations from island nations (for example, Japan and United Kingdom) or populations whose most related populations were under-represented in our reference population data set (for example, Peru and Russia) were most poorly predicted. Consequently, the median distances to the true origin were much smaller for individuals residing in Europe (250 km), Africa (300 km) and Asia (450 km) due to their being more commonly represented in the reference population data set compared with Native Americans and Oceanians. These results represent the upper limit of GPS’s accuracy when the specific population of the test individual is absent from the reference population data set.

A hyped up press release was issued by the University of Sheffield which also includes a link to a video on YouTube. As is often the case, the media have picked up on the hype in the press release and have made no attempt to read the scientific paper and understand the limitations of the methodology. I hope that there have not been too many people who have paid out good money for these misleading DNA satnav reports.

Note that if you've taken a test with one of the genetic genealogy companies there are many free services that you can use to get an alternative reading of your data and a prediction of your "ethnicity", all of which will give much better results than the commercial offerings from Prosapia. One of the best free websites is GedMatch which allows you to get readings from a wide range of different services. You can find a full list of services in the ISOGG Wiki article on admixture analyses. However, it is still very difficult to distinguish between populations at anything more than the Continental level, and all such reports should be treated with a very large pinch of salt.

Update 6 May 2014
Teresa Vega now tells me that she has received a full refund for her test from PayPal. She told PayPal that she had felt misled by the company's claims and she was unhappy that they had recommended upgrading to a test that they did not even have on their site. JoAnn O'Linger is now also in the process of applying for a refund.

Update 3rd September 2014
Although the Prosapia Genetics domain name was originally registered to Dr Tatiana Tatarinova, it was subsequently transferred to Vladimir Makarov.

Update 30th May 2015
In April 2015 Dr Eran Elhaik gave a presentation at Who Do You Think You Are? Live on the subject of "Reaching the Holy Grail in genetic genealogy: from genome to home village". For further details see the summary on the DNA sat nav page on the UCL website. In particular do listen to the recording of the exchange in the Q&A session between Eran Elhaik and Professor Mark Thomas.

Update 16th July 2016
A new paper by Pavel Flegontov, Alexei Kassian, Mark G. Thomas, Valentina Fedchenko, Piya Changmai and George Starostin "Pitfalls of the geographic population structure (GPS) approach applied to human genetic history: a case study of Ashkenazi Jews" provides a critique of the GPS methodology used for the Prosapia Genetics test with specific reference to its application to infer the origins of the Yiddish language.

Update 31st October 2016
A corrigendum to the Elhaik et al 2014 paper on geographic population structure has been published by Nature Communications. It contains a conflict of interests statement from the authors. The statement includes an acknowledgement that one of the authors (Tatiana Tatarinova) has a link with Prosapia Genetics.

Acknowledgements

Many thanks to Julie Matthews, JoAnn O'Linger and Teresa Vega for permission to use their quotes and reports.

Related blog posts
- My letter in Family Tree Magazine about "genetic homeland" stories

See also
Since writing this article I have discovered other discussions on the subject. I have posted the relevant links below and will update the list if further links become available:
- Prosapia Genetics - Worth the money? A review by Lorine McGinnis Schulze
- Researchers develop DNA GPS tool to accurately trace geographical ancestry -  a discussion on the Reddit forum
- Is GPS DNA tracking too good to be true? An article by Peter Calver in the Lost Cousins newsletter, May 2014
- So many genes, so close to home by Matthew Thomas, BioNews, 12 May 2014.
- Ancestral home pinpointed by DNA by Julie Lutter, Family History Research by Jodi, 13 May 2014.

© 2014-2016 Debbie Kennett