Monday, 31 July 2017
Family Tree DNA summer sale
I've received notification from Family Tree DNA that their summer sale will be starting tomorrow 1st August. There are discounted prices on their most popular tests and upgrades are also included in the sale. Family Finder is reduced to $69 and the BigY is reduced to $395. The sale runs until 31st August. Any items ordered on invoice must be paid within a week of the ending of the sale. Here are the details of the sale prices (in US dollars):
Sunday, 30 July 2017
Living DNA updates and GEDmatch Genesis
While I was away on holiday in California in June Living DNA rolled out a couple of updates.
They have now provided us with the facility to download our raw data. You will find the new menu when you log into your Living DNA account.
We can use the raw data to do our own analyses and to upload the results to third-party sites to get additional interpretations. However, Living DNA uses a different chip from the other main testing companies (23andMe, AncestryDNA, Family Tree DNA and MyHeritage). The Living DNA test is run on the new Illumina Global Screening Array chip whereas the other companies are currently using the Illumina OmniExpress chip. As a result the Living DNA raw data is not compatible with other sites as there are not enough overlapping SNPs (markers) to make reliable relationship predictions. (Note, however, that if you are interested in getting health reports, you can upload your Living DNA raw data to Promethease.)
It's already been announced that 23andMe will be moving over to the GSA chip in due course, and it's likely that the other companies will eventually follow suit as the Illumina OmniExpress is being phased out. The GSA chip is designed for imputation. This is the process of inferring missing markers using statistical algorithms. Imputation can be done with a high degree of accuracy provided that sufficient reference populations are available. We will need to wait and see how the companies cope with the change but in theory the GSA chip is backwardly compatible with the OmniExpress. Much will depend on the quality of the imputation.
In the meantime the wonderful team at GEDmatch have come to the rescue. They are now beta-testing a new service called Genesis which will allow people to upload kits using formats that are not compatible with the main GEDmatch database. This includes Living DNA kits and exome sequences. The intention is that eventually the two databases will be merged.
GEDmatch are also in the process of developing an exciting new Genesis Algorithm which promises to provide more accurate matches. This is what the new Genesis home page looks like.
Here is a screenshot of the upload page.
I was successfully able to upload my Living DNA raw data to GEDmatch Genesis. When uploading your Living DNA data make sure you use the link for "Generic uploads (23andMe, FTDNA, Ancestry, most others)". Within a few minutes of uploading my raw data I was able to use the Genesis site to look at the various admixture calculators.
Here is a report using my Living DNA data with the Eurogenes K13 report. There are just 58623 SNPs used in this report.
When using the same Eurogenes K13 calculator on my standard GEDmatch kit 181512 SNPs are used in the comparison. However, as you can see from the screenshot below, the two reports are remarkably similar, despite the reduced number of SNPs used for the Living DNA comparison.
A few hours after I'd uploaded my results I was able to access my matches. Here is a screenshot of my matches with the kit numbers, names and e-mail addresses blurred out. Click on the image to enlarge it.
We are given information on the largest shared segment, the total cMs shared and the number of overlapping SNPs. Information is also provided about the confidence of the results. Confidence is very high for comparisons between two Living DNA kits but very low for comparisons with other companies.
All my matches are currently very low resolution and they go right down to matches that share a total of just 5 cMs. Few if any of these matches are likely to fall into a genealogical timeframe. Interestingly I've already spotted the names of four people I know amongst my Living DNA matches! As more people add their results to the Genesis database it will be a very useful way of making connections and doing comparisons across different testing companies. I look forward with interest to seeing how the Genesis algorithm develops.
The other new feature that Living DNA have rolled is what they call Family Views, which allows you to view your admixture results in Complete, Standard and Cautious modes. With the launch of this feature all our admixture results were completely rerun. This is because of teething problems with the new GSA chip. After initial quality control checks Illumina issued a new validation file to correct the errors. As validation continues it's possible that there will be further changes in the future. I will write separately about my updated Living DNA results in a future blog post.
There are also other updates in the pipeline as I learned at the Southern California Genealogical Society's Jamboree conference in June when a group of us attended a get-together with David Nicholson and Martin Blythe from Living DNA.
Living DNA should be able to accept uploads from other companies by the end of July. However, there are only a few days of July left and this hasn't yet happened so perhaps the launch of this feature has been delayed.
Living DNA are also working on a matching programme which they hope to start beta-testing in September.
A big update to our admixture results can be expected by the end of the year as more reference datasets are added to the collection. They will be including data from the Symons Genome Diversity Project, data from Asia and data from Aboriginals in Australia. Their Irish DNA Research Project is going well and they already have 1200 samples. They now have 450 people in their German DNA Research Project. Further projects are planned for France, Portugal, Austria, Belgium and the Netherlands.
We can look forward to some very exciting new developments in the next six months.
Further reading
They have now provided us with the facility to download our raw data. You will find the new menu when you log into your Living DNA account.
We can use the raw data to do our own analyses and to upload the results to third-party sites to get additional interpretations. However, Living DNA uses a different chip from the other main testing companies (23andMe, AncestryDNA, Family Tree DNA and MyHeritage). The Living DNA test is run on the new Illumina Global Screening Array chip whereas the other companies are currently using the Illumina OmniExpress chip. As a result the Living DNA raw data is not compatible with other sites as there are not enough overlapping SNPs (markers) to make reliable relationship predictions. (Note, however, that if you are interested in getting health reports, you can upload your Living DNA raw data to Promethease.)
It's already been announced that 23andMe will be moving over to the GSA chip in due course, and it's likely that the other companies will eventually follow suit as the Illumina OmniExpress is being phased out. The GSA chip is designed for imputation. This is the process of inferring missing markers using statistical algorithms. Imputation can be done with a high degree of accuracy provided that sufficient reference populations are available. We will need to wait and see how the companies cope with the change but in theory the GSA chip is backwardly compatible with the OmniExpress. Much will depend on the quality of the imputation.
In the meantime the wonderful team at GEDmatch have come to the rescue. They are now beta-testing a new service called Genesis which will allow people to upload kits using formats that are not compatible with the main GEDmatch database. This includes Living DNA kits and exome sequences. The intention is that eventually the two databases will be merged.
GEDmatch are also in the process of developing an exciting new Genesis Algorithm which promises to provide more accurate matches. This is what the new Genesis home page looks like.
Here is a screenshot of the upload page.
I was successfully able to upload my Living DNA raw data to GEDmatch Genesis. When uploading your Living DNA data make sure you use the link for "Generic uploads (23andMe, FTDNA, Ancestry, most others)". Within a few minutes of uploading my raw data I was able to use the Genesis site to look at the various admixture calculators.
Here is a report using my Living DNA data with the Eurogenes K13 report. There are just 58623 SNPs used in this report.
When using the same Eurogenes K13 calculator on my standard GEDmatch kit 181512 SNPs are used in the comparison. However, as you can see from the screenshot below, the two reports are remarkably similar, despite the reduced number of SNPs used for the Living DNA comparison.
A few hours after I'd uploaded my results I was able to access my matches. Here is a screenshot of my matches with the kit numbers, names and e-mail addresses blurred out. Click on the image to enlarge it.
We are given information on the largest shared segment, the total cMs shared and the number of overlapping SNPs. Information is also provided about the confidence of the results. Confidence is very high for comparisons between two Living DNA kits but very low for comparisons with other companies.
All my matches are currently very low resolution and they go right down to matches that share a total of just 5 cMs. Few if any of these matches are likely to fall into a genealogical timeframe. Interestingly I've already spotted the names of four people I know amongst my Living DNA matches! As more people add their results to the Genesis database it will be a very useful way of making connections and doing comparisons across different testing companies. I look forward with interest to seeing how the Genesis algorithm develops.
The other new feature that Living DNA have rolled is what they call Family Views, which allows you to view your admixture results in Complete, Standard and Cautious modes. With the launch of this feature all our admixture results were completely rerun. This is because of teething problems with the new GSA chip. After initial quality control checks Illumina issued a new validation file to correct the errors. As validation continues it's possible that there will be further changes in the future. I will write separately about my updated Living DNA results in a future blog post.
There are also other updates in the pipeline as I learned at the Southern California Genealogical Society's Jamboree conference in June when a group of us attended a get-together with David Nicholson and Martin Blythe from Living DNA.
Living DNA should be able to accept uploads from other companies by the end of July. However, there are only a few days of July left and this hasn't yet happened so perhaps the launch of this feature has been delayed.
Living DNA are also working on a matching programme which they hope to start beta-testing in September.
A big update to our admixture results can be expected by the end of the year as more reference datasets are added to the collection. They will be including data from the Symons Genome Diversity Project, data from Asia and data from Aboriginals in Australia. Their Irish DNA Research Project is going well and they already have 1200 samples. They now have 450 people in their German DNA Research Project. Further projects are planned for France, Portugal, Austria, Belgium and the Netherlands.
We can look forward to some very exciting new developments in the next six months.
- New feature: downloading your raw data Living DNA blog, 15 June 2017.
- New feature: your family DNA views Living DNA blog, 15 June 2017.
Saturday, 29 July 2017
Comparing match tallies for family members with Family Tree DNA's Family Finder test
I've taken a look at the total number of matches for all my family members who have taken a Family Finder test at Family Tree DNA. I've also done a comparison with the data I extracted on 26th May 2016 just before Family Tree DNA updated their matching algorithms. The results are shown in the table below. Note that I have excluded immediate family members from the totals.
If my matches are representative of the wider Family Finder database then there has been over a 50% increase in the size of the database in the last 14 months.
I've also looked at the number of matches I share with my parents and taken stock of the number of matches which don't match either parent.
I share 501 matches with my dad. Of these, 320 were assigned to the paternal side with FTDNA's Family Matching tool. The remaining 181 matches were in common with my dad but did not meet the threshold for Family Matching.
I share 402 matches with my mum. Of these, 276 were assigned to the maternal side with the Family Matching tool. The remaining 126 matches did not meet the threshold for Family Matching.
I therefore have a total of 903 matches (74%) which match my mum or my dad. However, this means that 314 of my 1217 matches (26%) do not appear in the match lists of either of my parents.
All the matches that don't match my parents have a longest segment under 15 cMs. This is the breakdown.
The last time I did a comparison of parent and child matches I found that 23% of my matches did not match either of my parents.
These matches are either false positives or false negatives but without further investigation it is not possible to tell.
Have you tested both of your parents at Family Tree DNA? What are your statistics?
Related blog posts
| Relation | Number of matches 28 July 2017 |
Number of matches 26 May 2016 |
% increase |
| Debbie | 1217 | 592 | 51% |
| Debbie's dad | 1344 | 643 | 52% |
| Debbie's mum | 1038 | 495 | 52% |
| Debbie's husband | 905 | 443 | 51% |
| Debbie's eldest son | 1138 | 542 | 52% |
If my matches are representative of the wider Family Finder database then there has been over a 50% increase in the size of the database in the last 14 months.
I've also looked at the number of matches I share with my parents and taken stock of the number of matches which don't match either parent.
I share 501 matches with my dad. Of these, 320 were assigned to the paternal side with FTDNA's Family Matching tool. The remaining 181 matches were in common with my dad but did not meet the threshold for Family Matching.
I share 402 matches with my mum. Of these, 276 were assigned to the maternal side with the Family Matching tool. The remaining 126 matches did not meet the threshold for Family Matching.
I therefore have a total of 903 matches (74%) which match my mum or my dad. However, this means that 314 of my 1217 matches (26%) do not appear in the match lists of either of my parents.
All the matches that don't match my parents have a longest segment under 15 cMs. This is the breakdown.
| Longest block | Number |
| 10-14 cMs | 28 |
| 7-9 cMs | 286 |
The last time I did a comparison of parent and child matches I found that 23% of my matches did not match either of my parents.
These matches are either false positives or false negatives but without further investigation it is not possible to tell.
Have you tested both of your parents at Family Tree DNA? What are your statistics?
Related blog posts
Friday, 28 July 2017
DNA surprises
In all my genetic genealogy talks I always warn people to be prepared for the unexpected when taking a DNA test. DNA is a very powerful tool for the genealogist but it can also uncover family secrets and reveal close relations that we didn't know existed. Furthermore, we don't always get the answer we expected. As Bennett Greenspan of Family Tree DNA often says in his talks: "If you don't want to know the answer, don't ask the question". For some people DNA can completely overturn their concept of identity and they discover that they are not who they thought they were.
Sometimes DNA can reveal the most incredible stories that are stranger than anything in fiction. One such story has just been published this week in The Washington Post. The article focuses on a number of surprise findings from DNA testing but tells in detail the story of Alice Collins Plebuch who took a DNA test with AncestryDNA which was to change her life forever. The article is is a long read but a very worthwhile investment of your time. The journalist Libby Copeland is to be congratulated for her sensitive coverage of this story and her meticulous attention to detail. You can read the article by clicking on this link.
We have in fact known about this story in the genetic genealogy community for several years now, but this is the first time it has been picked up by the mainstream media. If you want some further background information check out this article on CeCe Moore's blog where the story was first revealed. There is an additional perspective in this blog post. Both of these blog posts also have additional photographs that weren't in The Washington Post article, but don't read the blog posts until you've read the article.
Wednesday, 26 July 2017
Parent and child comparisons at MyHeritage DNA
Update. See my blog post published on 14 January 2018 where I found that 32% of my matches did not match either of my parents compared to 71% in 2017 with the old matching algorithms.
I recently transferred my parents' data to the MyHeritage DNA database and I thought it would be an interesting exercise to compare their matches and admixture reports with my own. I transferred my AncestryDNA v1 raw data to MyHeritage and my parents' Family Finder raw data from Family Tree DNA. All three tests were done on the same Illumina OmniExpress chip so there should be an almost complete overlap of SNPs.
MyHeritage are the newest entrant into the genetic genealogy market. They launched their autosomal test in November 2016. If you've tested with AncestryDNA, Family Tree DNA or 23andMe it is currently possible to do a free transfer to MyHeritage. It is not clear if the transfer will be free in the long term so do take advantage while you have the chance.
While the MyHeritage database still has a long way to go to catch up with the other companies there are already early reports of DNA success stories. MyHeritage benefits from a website which is available in many different languages, and they are therefore likely to attract customers who will not be found in any of the other databases.
DNA matches
MyHeritage currently provide information about the amount of DNA shared (measured in centiMorgans), the number of shared segments, and the size of the largest segment. A chromosome browser is not provided though this feature is reportedly in development. It is also not yet possible to download a list of your matches, but hopefully this will be possible in future.
One of the most useful features of the MyHeritage matches feature is that there are country flags against the names of your matches. This allows you to focus on the matches who live in the countries where you are mostly likely to share recent genealogical ancestors.
My dad currently has 59 matches at MyHeritage (excluding me as his daughter). Most of his matches are in America but he has four matches with people from Great Britain, three from Sweden, and one each from the Czech Republic, Canada and Norway.
My mum has 20 matches at MyHeritage (excluding me as her daughter). Again the matches are predominantly with Americans but she has two matches with people from Great Britain and one with an Australian.
I have 24 matches at MyHeritage (excluding my parents). I have one match each from Luxembourg, Great Britain, Australia and Ireland. The rest of my matches are in America.
MyHeritage have a nice Shared DNA Matches feature which not only allows you to see which matches you have in common but also provides relationship predictions and the amount of shared DNA for both matches side by side. This is what the Shared DNA Matches page looks like for me and my mum.
I share two of my 24 matches with my mum and six matches with my dad. However this means that 17 of my 24 matches (71%) do not match either of my parents. These matches are either false positives or false negatives, but without further investigation it's not possible to tell.
I don't recognise any of the names in the match lists and it seems to me that, even if the matches are real, the relationship predictions are overly optimistic. Some of the matches are predicted to be second to fourth cousins, and even the most distant matches are predicted to be third to sixth cousins. However, I do not have any ancestors who emigrated to countries like Sweden, Norway and the Czech Republic. I also don't have any ancestors who emigrated to America. I do have a few cousins in America through a collateral line but I know them all by name. The Americans on my match list are likely to be very distant cousins, if they are related to me at all. Of the matches that I share with my parents all eight of them are in the US.
Clearly MyHeritage need to do some work on the matching algorithms, and I'm sure we will see some improvements in future. For the moment it doesn't seem worth investing too much time in researching these matches.
Comparing admixture percentages
In addition to cousin matching, the MyHeritage test also includes a free admixture report which they call an Ethnicity Estimate. Results are compared with 42 reference populations around the world, and there are plans to add further populations in the future. MyHeritage do not state what time depth their test is designed to cover.
Here are the details of my dad's genealogical ancestry:
I recently transferred my parents' data to the MyHeritage DNA database and I thought it would be an interesting exercise to compare their matches and admixture reports with my own. I transferred my AncestryDNA v1 raw data to MyHeritage and my parents' Family Finder raw data from Family Tree DNA. All three tests were done on the same Illumina OmniExpress chip so there should be an almost complete overlap of SNPs.
MyHeritage are the newest entrant into the genetic genealogy market. They launched their autosomal test in November 2016. If you've tested with AncestryDNA, Family Tree DNA or 23andMe it is currently possible to do a free transfer to MyHeritage. It is not clear if the transfer will be free in the long term so do take advantage while you have the chance.
While the MyHeritage database still has a long way to go to catch up with the other companies there are already early reports of DNA success stories. MyHeritage benefits from a website which is available in many different languages, and they are therefore likely to attract customers who will not be found in any of the other databases.
DNA matches
MyHeritage currently provide information about the amount of DNA shared (measured in centiMorgans), the number of shared segments, and the size of the largest segment. A chromosome browser is not provided though this feature is reportedly in development. It is also not yet possible to download a list of your matches, but hopefully this will be possible in future.
One of the most useful features of the MyHeritage matches feature is that there are country flags against the names of your matches. This allows you to focus on the matches who live in the countries where you are mostly likely to share recent genealogical ancestors.
My dad currently has 59 matches at MyHeritage (excluding me as his daughter). Most of his matches are in America but he has four matches with people from Great Britain, three from Sweden, and one each from the Czech Republic, Canada and Norway.
My mum has 20 matches at MyHeritage (excluding me as her daughter). Again the matches are predominantly with Americans but she has two matches with people from Great Britain and one with an Australian.
I have 24 matches at MyHeritage (excluding my parents). I have one match each from Luxembourg, Great Britain, Australia and Ireland. The rest of my matches are in America.
MyHeritage have a nice Shared DNA Matches feature which not only allows you to see which matches you have in common but also provides relationship predictions and the amount of shared DNA for both matches side by side. This is what the Shared DNA Matches page looks like for me and my mum.
I don't recognise any of the names in the match lists and it seems to me that, even if the matches are real, the relationship predictions are overly optimistic. Some of the matches are predicted to be second to fourth cousins, and even the most distant matches are predicted to be third to sixth cousins. However, I do not have any ancestors who emigrated to countries like Sweden, Norway and the Czech Republic. I also don't have any ancestors who emigrated to America. I do have a few cousins in America through a collateral line but I know them all by name. The Americans on my match list are likely to be very distant cousins, if they are related to me at all. Of the matches that I share with my parents all eight of them are in the US.
Clearly MyHeritage need to do some work on the matching algorithms, and I'm sure we will see some improvements in future. For the moment it doesn't seem worth investing too much time in researching these matches.
Comparing admixture percentages
In addition to cousin matching, the MyHeritage test also includes a free admixture report which they call an Ethnicity Estimate. Results are compared with 42 reference populations around the world, and there are plans to add further populations in the future. MyHeritage do not state what time depth their test is designed to cover.
Here are the details of my dad's genealogical ancestry:
- Four grandparents born in England: Bristol, Gloucestershire, London (x2).
- Eight great-grandparents born in England: Bristol (x2), Devon, Essex, Gloucestershire, Hertfordshire, London (x2).
- Fifteen great-great grandparents born in England: Devon (x2), Bristol, Essex, Gloucestershire, Hertfordshire (x 2), London. One great-great grandparent born in Scotland (location not known). The birthplace of seven of his English great-great-grandparents is unknown. Four were probably born in Bristol or in a nearby county. Three were Londoners who could have moved to London from anywhere in England.
Here are my dad's admixture percentages from MyHeritage.
Here are the details of my mum's genealogical ancestry:
- Four grandparents born in England: London (x2), Hampshire (x2).
- Eight great-grandparents born in England: Berkshire, Hampshire, London (x3), Somerset, Wiltshire. The birthplace of one great-grandparent is not known but he was probably born in London.
- One great-great-grandparent born in County Kerry, Ireland. Fifteen great-great-grandparents born in England: Bedfordshire, Berkshire (x2), Gloucestershire, Hampshire (x2), Hertfordshire, London (x2), Somerset (x2), Wiltshire. The birthplace of three of her English great-great-grandparents is unknown. One was probably born in Hampshire. The other two were probably Londoners who could have come from anywhere in the country.
Here are my mum's admixture percentages from MyHeritage:
Here are my admixture percentages from MyHeritage.
It's good to see that MyHeritage are at least trying to produce regional distributions within the British Isles, even though the results are somewhat off the mark. It's interesting to see that my parents come out with such very different results, despite the fact that they both have predominantly English ancestry. We have no Italian ancestry and the Italian component in the MyHeritage test does not show up in our results in tests with any other company. The admixture reports will no doubt be refined in future as the methodology improves and more reference datasets are added.
Update 12th November 2017
We have been getting reports of close matches which have been incorrectly reported at MyHeritage DNA. Lorna Henderson has reported problems with a second cousin match which was identified at other companies but not at MyHeritage DNA. CeCe Moore has blogged about a number of cases where half-siblings were reported as sharing an unexpectedly low amount of DNA. Yaniv Erlich, MyHeritage's Chief Scientific Officer, has responded on CeCe's blog and says that "We are well aware of these issues that affect a minority of our close matches. My team is actively working on this and we are in the final steps of a major overhaul to our matching system that resolves many of these issues and better tunes our parameters for our fast growing database." Let's hope that these issues are resolved sooner rather than later.
At present I do not advise trusting the matches reported by MyHeritage. If you've tested at MyHeritage I would recommend in the first instance that you download your raw data and take advantage of the free transfer to Family Tree DNA. Note that MyHeritage DNA transfers are exempt from the $19 fee to unlock the chromosome browser and MyOrigins reports. This will allow you to do a double check on the amount of shared DNA and access a different database of matches. When calculating the cM totals at FTDNA be sure to exclude all the small segments under 5 cMs or 7 cMs to get a more accurate reflection of the relationship.
Further reading
Update 12th November 2017
We have been getting reports of close matches which have been incorrectly reported at MyHeritage DNA. Lorna Henderson has reported problems with a second cousin match which was identified at other companies but not at MyHeritage DNA. CeCe Moore has blogged about a number of cases where half-siblings were reported as sharing an unexpectedly low amount of DNA. Yaniv Erlich, MyHeritage's Chief Scientific Officer, has responded on CeCe's blog and says that "We are well aware of these issues that affect a minority of our close matches. My team is actively working on this and we are in the final steps of a major overhaul to our matching system that resolves many of these issues and better tunes our parameters for our fast growing database." Let's hope that these issues are resolved sooner rather than later.
At present I do not advise trusting the matches reported by MyHeritage. If you've tested at MyHeritage I would recommend in the first instance that you download your raw data and take advantage of the free transfer to Family Tree DNA. Note that MyHeritage DNA transfers are exempt from the $19 fee to unlock the chromosome browser and MyOrigins reports. This will allow you to do a double check on the amount of shared DNA and access a different database of matches. When calculating the cM totals at FTDNA be sure to exclude all the small segments under 5 cMs or 7 cMs to get a more accurate reflection of the relationship.
Further reading
- Imprecise science Part 2: MyHeritage by Alex Coles, Winging It, 16 August 2017
- MyHeritage matching by Leah Larkin, The DNA Geek, 21 July 2017
- Introducing our new DNA ethnicity analysis, MyHeritage blog, 1 June 2017
- DNA articles in the MyHeritage Help Centre
Wednesday, 19 July 2017
The end of the road for BritainsDNA and myDNAGlobal
I wrote back in May last year that the BritainsDNA family of companies, which includes ScotlandsDNA, IrelandsDNA, CymruDNAWales and YorkshiresDNA, had been rebranded under the new name of MyDNAglobal after the company was taken over by Source BioScience.
On checking the MyDNAglobal website today I discovered that the company is no longer taking orders. The following notice now appears on the website
Dear Customers
It is with regret that effective from 3rd July 2017 MyDNA.global will no longer be accepting new orders.
Whilst we have enjoyed offering this individual service it is unfortunately not something we are able to provide going forwards.
All existing orders will be honoured – if you have recently purchased a test and have yet to return your sample please do so by 31 August 2017 so we can process your results.
Unfortunately we cannot guarantee that samples received after 31 August 2017 will be processed.
For those customers who have already received their results these will be available to you via our website until 31 August 2018, after which they will no longer be available.
If you have any queries please email our support team: support@myDNA.global.
Thank you for your custom.
If you've tested with any of these companies I would suggest that you download all your data while you have the chance.
Update
For further information on the demise of BritainsDNA and background information on Source Bioscience see the article by Ewan Lamb BritainsDNA - a thing of the past.
Update
For further information on the demise of BritainsDNA and background information on Source Bioscience see the article by Ewan Lamb BritainsDNA - a thing of the past.
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.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.
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!
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
Friday, 14 July 2017
An update to the AncestryDNA kit management system
AncestryDNA have announced that the process for activating kits will change from 18th July onwards. Up until now it has been possible to add multiple kits for your relatives to your own DNA account. The disadvantage of this process is that the person taking the test does not have full control of their own DNA and data, and there is the potential for misuse. Under the new system every person who takes a DNA test will be required to set up their own Ancestry account. They can then choose to assign sharing roles to their friends and family members. There are different levels of sharing which are explained in this graphic provided by AncestryDNA.
As can be seen, if Manager status is granted, you will be able to have full access to your relative's account and do everything that was previously possible when sharing kits under a single account. The notable and important exception is that the owner of the DNA sample is the only one who can remove Manager status. This means that the person who has taken the test will always have the right to access his or own data. Unfortunately we have sometimes had cases in the genetic genealogy community where a kit manager has blocked the tester from accessing his or her own account. This will ensure that such situations will not arise in the future.
There are no extra costs involved. If you already have an Ancestry subscription and your relatives are sharing with you it will still be possible to benefit from all the additional features available to subscribers for the kits you manage on behalf of your relatives (eg, the ability to view the full trees of their matches, and the ability to see features such as the shared ancestor hints and DNA Circles).
AncestryDNA have written a blog post with information about the changes which you can read here. This post has been updated since I read it late last night to provide clarification of points raised in the comments.
This change brings AncestryDNA into line with Family Tree DNA, who already require each customer to have their own individual account. It also ensures that AncestryDNA comply with the Genetic Genealogy Standards which state that "Genealogists believe that testers have an inalienable right to their own DNA test results and raw data, even if someone other than the tester purchased the DNA test."
I don't know what motivated this change but it seems likely that AncestryDNA were influenced by the forthcoming General Data Protection Regulation (GDPR) which will apply throughout the European Union and also in the UK from 25th May 2018 onwards. For further details on the new data protection laws see the leaflet from the Information Commissioner's Office on Preparing for the General Data Protection Regulation (GDPR): 12 Steps to Take Now.
A key tenet of data protection legislation is that the individual has right of access to his or her own data. By ensuring that each person has their own AncestryDNA account it will be much easier to ensure that this happens. Although Ancestry is not required to comply with European legislation for customers outside Europe it seems sensible to provide their international customers with the same levels of data protection as their European customers.
Further reading
As can be seen, if Manager status is granted, you will be able to have full access to your relative's account and do everything that was previously possible when sharing kits under a single account. The notable and important exception is that the owner of the DNA sample is the only one who can remove Manager status. This means that the person who has taken the test will always have the right to access his or own data. Unfortunately we have sometimes had cases in the genetic genealogy community where a kit manager has blocked the tester from accessing his or her own account. This will ensure that such situations will not arise in the future.
There are no extra costs involved. If you already have an Ancestry subscription and your relatives are sharing with you it will still be possible to benefit from all the additional features available to subscribers for the kits you manage on behalf of your relatives (eg, the ability to view the full trees of their matches, and the ability to see features such as the shared ancestor hints and DNA Circles).
AncestryDNA have written a blog post with information about the changes which you can read here. This post has been updated since I read it late last night to provide clarification of points raised in the comments.
This change brings AncestryDNA into line with Family Tree DNA, who already require each customer to have their own individual account. It also ensures that AncestryDNA comply with the Genetic Genealogy Standards which state that "Genealogists believe that testers have an inalienable right to their own DNA test results and raw data, even if someone other than the tester purchased the DNA test."
I don't know what motivated this change but it seems likely that AncestryDNA were influenced by the forthcoming General Data Protection Regulation (GDPR) which will apply throughout the European Union and also in the UK from 25th May 2018 onwards. For further details on the new data protection laws see the leaflet from the Information Commissioner's Office on Preparing for the General Data Protection Regulation (GDPR): 12 Steps to Take Now.
A key tenet of data protection legislation is that the individual has right of access to his or her own data. By ensuring that each person has their own AncestryDNA account it will be much easier to ensure that this happens. Although Ancestry is not required to comply with European legislation for customers outside Europe it seems sensible to provide their international customers with the same levels of data protection as their European customers.
Further reading
- Leah Larkin has put together a very helpful blog post entitled Reality check - impending changes at AncestryDNA. She answers all the questions that have arisen as a result of this impending change. Do have a read.
- See also the blog post from Diahan Southard AncestryDNA's Privacy Policy - why it's a good thing
Tuesday, 11 July 2017
Parent and child comparisons at AncestryDNA
I've now had both my parents tested at AncestryDNA and their results have recently come in. By testing my parents I will be able to assign matches to paternal and maternal sides. My parents will potentially match people who are not on my own match list and they will have more robust matches than I do with more distant matches. I thought it would be a useful exercise to take stock of our matches, admixture reports and genetic communities to serve as a baseline for future comparisons.
DNA results and matches pages
Here is my dad's results page. He currently has 54 fourth cousins or closer, and 157 pages of matches making a total of 7850 matches. He has three shared ancestor hints, no DNA Circles and no New Ancestor Discoveries.
Here is my mum's results page. She currently has 116 fourth cousins or closer, and 212 pages of matches making a total of 10600 matches. She has no shared ancestor hints, no DNA Circles and no New Ancestor Discoveries.
Here is my results page. I currently have 66 fourth cousins or closer and 193 pages of matches (9650 matches). I have two shared ancestor hints, no DNA Circles and no New Ancestor Discoveries.
Note that the shared hints shown above do not include shaky leaf hints for the parent/child relationships. When I first checked the results hints were provided but the relationships were shown as aunt/uncle and nephew/niece rather than parent/child. I presume this was a bug as these hints have now disappeared.
As a result of testing my parents I've now gained one new shaky leaf hint. This is a predicted 5th to 8th cousin who shares a single segment of 11 centimorgans with my dad. According to the family trees they are third cousins twice removed and their common ancestors are William Cruwys (1793-1846) and Margaret Eastmond (1792-1874) who married in 1814 in Rose Ash, Devon. One of their sons emigrated to Prince Edward Island in Canada and this match is a descendant of this PEI family. Fortunately she has provided a detailed family tree, but I shall also look forward to corresponding with her and comparing notes. Interestingly this lady does not appear in my own match list so it looks as though I have not inherited this single segment from my dad.
I now also have a new filter on my match page
This filter allows me to see at a glance which matches I share with my mum and which matches I share with my dad. However, the list is restricted to those matches which are fourth cousins or closer. I can understand the restriction on shared matches for cousin relationships but it would be useful if AncestryDNA would let us sort our entire match list by paternal and maternal matches.
Comparing admixture percentages
Now let's have a look at the admixture results in more detail. AncestryDNA call this report an "Ethnicity Estimate" though strictly speaking ethnicity is self-determined and has no bearing on our genetic ancestry. AncestryDNA say that the admixture reports reflect our ancestry from "thousands of years ago". I cannot trace our family tree back thousands of years but here are the details of my dad's recent genealogical ancestry:
Here are the details of my mum's genealogical ancestry:
Here is my own Ethnicity Estimate.
As can be seen, there is a wide variation in the results and there is little correlation between the admixture percentages and our known genealogical ancestry. Admixture results can sometimes provide useful insights but the results should not be taken too literally. It's also worth remembering that, although the percentages have been given labels based on modern nation states, the regions which these labels cover extend well beyond the present-day national boundaries, as can be seen from my ancestry map below. The Irish component actually extends over much of the United Kingdom. The Great Britain component overlaps with Ireland and extends into northern Europe. The Europe West component extends into southern and eastern England.
Genetic communities
Genetic communities provide information about our genetic ancestry within the last few hundred years. They are also a useful way of filtering your matches so that you can focus on the matches who have family trees from the same country and the same locations as you where you stand the greatest chance of identifying a genealogical connection. I'm currently in one genetic community for the Southern English. The confidence level is 95%. I have 63 matches amongst the 204,681 AncestryDNA members in this community.
My mum and dad both have two communities: Southern English and The Welsh & English West Midlanders. In both cases the confidence level for the Southern English community is 95% and the confidence level for the Welsh community is 20%.
My dad has 45 matches in the Southern English community and nine matches amongst the 58,768 Ancestry DNA members who are in the Welsh & English West Midlanders community.
My mum has 77 matches in the Southern English community and 14 matches in the Welsh & English West Midlanders community
Neither my mum nor my dad have any known ancestry from Wales or the West Midlands. However, on looking at the map of this community, you can see that it covers a wider area and actually extends into Gloucestershire, Wiltshire, Oxfordshire and North Somerset where we do have known ancestry.
Conclusion
I now have a lot of new matches to work with, and it's going to be a great help having my parents' results available for comparison. With autosomal DNA it always helps to test as many close relatives as possible. If you can't test your parents you should try and test aunts and uncles, siblings and cousins to get the best possible representation of the DNA of all your ancestors.
DNA results and matches pages
Here is my dad's results page. He currently has 54 fourth cousins or closer, and 157 pages of matches making a total of 7850 matches. He has three shared ancestor hints, no DNA Circles and no New Ancestor Discoveries.
Here is my mum's results page. She currently has 116 fourth cousins or closer, and 212 pages of matches making a total of 10600 matches. She has no shared ancestor hints, no DNA Circles and no New Ancestor Discoveries.
Here is my results page. I currently have 66 fourth cousins or closer and 193 pages of matches (9650 matches). I have two shared ancestor hints, no DNA Circles and no New Ancestor Discoveries.
Note that the shared hints shown above do not include shaky leaf hints for the parent/child relationships. When I first checked the results hints were provided but the relationships were shown as aunt/uncle and nephew/niece rather than parent/child. I presume this was a bug as these hints have now disappeared.
As a result of testing my parents I've now gained one new shaky leaf hint. This is a predicted 5th to 8th cousin who shares a single segment of 11 centimorgans with my dad. According to the family trees they are third cousins twice removed and their common ancestors are William Cruwys (1793-1846) and Margaret Eastmond (1792-1874) who married in 1814 in Rose Ash, Devon. One of their sons emigrated to Prince Edward Island in Canada and this match is a descendant of this PEI family. Fortunately she has provided a detailed family tree, but I shall also look forward to corresponding with her and comparing notes. Interestingly this lady does not appear in my own match list so it looks as though I have not inherited this single segment from my dad.
I now also have a new filter on my match page
This filter allows me to see at a glance which matches I share with my mum and which matches I share with my dad. However, the list is restricted to those matches which are fourth cousins or closer. I can understand the restriction on shared matches for cousin relationships but it would be useful if AncestryDNA would let us sort our entire match list by paternal and maternal matches.
Comparing admixture percentages
Now let's have a look at the admixture results in more detail. AncestryDNA call this report an "Ethnicity Estimate" though strictly speaking ethnicity is self-determined and has no bearing on our genetic ancestry. AncestryDNA say that the admixture reports reflect our ancestry from "thousands of years ago". I cannot trace our family tree back thousands of years but here are the details of my dad's recent genealogical ancestry:
- Four grandparents born in England: Bristol, Gloucestershire, London (x2).
- Eight great-grandparents born in England: Bristol (x2), Devon, Essex, Gloucestershire, Hertfordshire, London (x2).
- Fifteen great-great grandparents born in England: Devon (x2), Bristol, Essex, Gloucestershire, Hertfordshire (x 2), London. One great-great grandparent born in Scotland (location not known). The birthplace of seven of his English great-great-grandparents is unknown. Four were probably born in Bristol or in a nearby county. Three were Londoners who could have moved to London from anywhere in England.
Here are the details of my mum's genealogical ancestry:
- Four grandparents born in England: London (x2), Hampshire (x2).
- Eight great-grandparents born in England: Berkshire, Hampshire, London (x3), Somerset, Wiltshire. The birthplace of one great-grandparent is not known but he was probably born in London.
- Fifteen great-great-grandparents born in England: Bedfordshire, Berkshire (x2), Gloucestershire, Hampshire (x2), Hertfordshire, London (x2), Somerset (x2), Wiltshire.
- One great-great-grandparent born in Ireland: County Kerry. The birthplace of three of her English great-great-grandparents is unknown. One was probably born in Hampshire. The other two were probably Londoners who could have come from anywhere in the country.
As can be seen, there is a wide variation in the results and there is little correlation between the admixture percentages and our known genealogical ancestry. Admixture results can sometimes provide useful insights but the results should not be taken too literally. It's also worth remembering that, although the percentages have been given labels based on modern nation states, the regions which these labels cover extend well beyond the present-day national boundaries, as can be seen from my ancestry map below. The Irish component actually extends over much of the United Kingdom. The Great Britain component overlaps with Ireland and extends into northern Europe. The Europe West component extends into southern and eastern England.
Genetic communities
Genetic communities provide information about our genetic ancestry within the last few hundred years. They are also a useful way of filtering your matches so that you can focus on the matches who have family trees from the same country and the same locations as you where you stand the greatest chance of identifying a genealogical connection. I'm currently in one genetic community for the Southern English. The confidence level is 95%. I have 63 matches amongst the 204,681 AncestryDNA members in this community.
My mum and dad both have two communities: Southern English and The Welsh & English West Midlanders. In both cases the confidence level for the Southern English community is 95% and the confidence level for the Welsh community is 20%.
My dad has 45 matches in the Southern English community and nine matches amongst the 58,768 Ancestry DNA members who are in the Welsh & English West Midlanders community.
My mum has 77 matches in the Southern English community and 14 matches in the Welsh & English West Midlanders community
Neither my mum nor my dad have any known ancestry from Wales or the West Midlands. However, on looking at the map of this community, you can see that it covers a wider area and actually extends into Gloucestershire, Wiltshire, Oxfordshire and North Somerset where we do have known ancestry.
Conclusion
I now have a lot of new matches to work with, and it's going to be a great help having my parents' results available for comparison. With autosomal DNA it always helps to test as many close relatives as possible. If you can't test your parents you should try and test aunts and uncles, siblings and cousins to get the best possible representation of the DNA of all your ancestors.