Tuesday, 18 July 2017

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 OriginsTM technology. GPS OriginsTM 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 OriginsTM 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

No comments: