Tuesday, 27 September 2016

Living DNA – a new genetic ancestry test providing comparisons with the People of the British Isles dataset

Over five years ago I attended a one-day conference in Cardiff in Wales on Ancient Britons, Europe and Wales. At the conference Professor Sir Walter Bodmer presented the first results from the People of the British Isles (POBI) project which were hot off the press having only been analysed three weeks previously. The audience were completely blown away by the results. For the first time researchers had been able to detect regional differences between the people of Britain based on their DNA. Sir Walter shared a map with us and you could even see that some counties, such as Devon and Cornwall, stood out as distinct regions in their own right.

I don't have a photograph of the map that we saw that day in Cardiff but it was probably very little changed from the map that appeared in the published paper in Nature in 2015 and which you can see here on the Wellcome Trust website. I remember thinking at the time that this research opened up the tantalising possibility of being able to receive an admixture report from a genetic ancestry company which would allow you to compare your results with the POBI data and see how much of your ancestry came from Devon or Cornwall and other regions of Britain.

I am very pleased to report that that day has now arrived with the launch of a new DNA test from a company called Living DNA! This is the first genetic ancestry test to incorporate data from the POBI Project and to give customers the percentages of DNA that they share with people from different regions in Britain.

Disclosure. I should declare here that I have been involved in informal discussions with DNA Worldwide over the development of their product. I have not receive any payment but, in return for my advice, I will receive a free Living DNA account. The company have had access to my raw data files from AncestryDNA, 23andMe, Family Tree DNA for testing purposes. Yesterday I had a Skype briefing about the new test from David Nicholson of Living DNA. I also received a preview of my own results, though I don't yet have access to my online account. There is still some tweaking going on behind the scenes and the results I've received are likely to be changed, so I will report on my results once I have my account.

The original POBI map, which formed the centrepiece of the Nature paper, featured 17 regions. For the new Living DNA test the POBI data has been re-analysed using improved methods and the data has been clustered into 21 areas across the British Isles.

The Living DNA test also includes a standard ancestry report providing admixture percentages. This analysis is based on 80 worldwide regions. (Note that the test does not currently report Jewish or Aboriginal ancestry though hopefully these reference populations will be added in the future.)

A unique feature of the test is the "back in time" map which allows you to see how your DNA matches with populations across a range of historical dates. Historical population statistics have been used for the mapping. All the existing tests on the market are trying to pick up on the small and very recent differences in our DNA but this means that the bigger picture of our universal relatedness gets lost. Recent studies have shown that you only have to go back about 5000 years or so before we reach a point where we all share the same ancestors. I hope that this new test will go some way towards educating people about our common ancestry and the knowledge that there is no such thing as "race".

Here are some sample reports which have been provided by the company. The first map shows "the areas of the world where you share genetic ancestry in recent times" at the continental level.

This second map provides regional resolution.

On the regional map you can click through and see how your ancestry is broken down within the different regions. If you have ancestry from Britain you will be able to see your shared percentages of DNA in comparison with the local populations. The test has also been built so that people with mixed ancestry from other countries get more detail than ever before.
Here is the family ancestry visualisation.
The Living DNA test is currently available as a new standalone test but they are also planning to accept imported data from other companies for a small fee. It is hoped that this feature will be available by the end of the year. I understand that GedMatch are preparing to accept uploads of raw data from Living DNA. I hope that Family Tree DNA will also be able to accept the raw data as this test is likely to attract a lot of interest and we want to ensure that people who are interested in using their results for genealogical matching are able to do so.

The Living DNA test was offered to the public for the first time last weekend at the New Scientist Live show at the ExCeL arena in London. The test can be ordered from the website at www.livingdna.com and the kits will be shipped in mid-October.

Living DNA is a partnership between the British company DNA Worldwide and the European company Eurofins. Here are the company details from the website:
Living DNA is a collaboration of over 100 world-leading scientists, academic researchers and genetic experts. The team is led by DNA Worldwide Group, a DNA testing company, whose services are used by every court in the UK. The company is run by David Nicholson and Hannah Morden who saw an opportunity to show humanity that we are all made up of all of us, dissolving the concept of race. It was launched in 2016 after two years of intensive development but its parent company DNA Worldwide Group has been operating since 2004, and employs over 35 people from its head office in Somerset, UK.
Although Living DNA is a for profit company they also intend to use their test for educational purposes to show how we are all connected to each other. They are working with an organisation called Show Racism the Red Card, a UK charity which works to combat racism. The company are working with a school in East London and ten schools around Europe. They also have PhD students working with them on different projects.

The following video provides further information about the company and the philosophy behind the test.

Who are Living DNA from Living DNA on Vimeo.

Technical details
Here are some of the technical details which I have gleaned from the website or which have been given to me by David Nicholson during my Skype briefing:
  • The tests are being done on a new custom Illumina Global Screening Array chip. Living DNA are the first company in the world to have access to this chip. This chip is a replacement for the Illumina OmniExpress chip which is in the process of being phased out. The new chip has been designed specifically for imputation and achieves a very high accuracy rate of 99.9%. (The datasheet for the Illumina chip can be found here.)
  • Medical SNPs are included on the chip and there is considerable overlap with the 23andMe chip. (I note from the Illumina press release that 23andMe have signed up to the Global Screening Array chip and I wonder if a v5 23andMe test might be in the pipeline.)
  • The following SNPs are on the Living DNA chip:
638,000 autosomal SNPs
17,800 X-chromosome SNPs
22,500 Y-SNPs
4,700 mtDNA SNPs
  • The Y-DNA SNPs have been selected from the 1000 Genomes Project and research papers, and checked and reviewed on the ISOGG SNP tree, The Y-SNP test has been developed in collaboration with Professor Mark Jobling and Pille Hallast at the University of Leicester.
  • The mtDNA SNPs have been selected by a team of scientists at Innsbruck University in Austria. They have used Phylotree and the latest tree builds to select the most useful mtDNA SNPs.
  • The autosomal component of the test has been developed by Daniel Lawson, Grady Weinberg, Daniel Falush, Garrett Hellenthal and Simon Myers. Lawson, Falush, Hellenthal and Myers were the team who developed the fineSTRUCTURE program used for the analysis of the POBI data and they were all authors on the POBI paper. The Living DNA test uses a refined version of that program upscaled for commercial use. fineSTRUCTURE is a haplotype-based method which takes advantage of the fact that SNPs travel together, and provides a more detailed analysis.
  • The autosomal DNA data is phased prior to processing.
  • White papers will be published soon with more information.
  • It will be possible to share results on the platform with friends and family and to manage multiple kits from a single account.
  • The test is done using a mouth swab. There is no liquid involved. This method has been chosen to facilitate international shipping. 
  • The developers have worked hard to ensure that the new chip is backwards compatible with other chips so that data can be accepted from all companies. The intention is to make the transfer process as easy as possible, preferably by interfacing with company APIs where available.
  • Customers will be able to download their raw data. Raw data will be imputable so that it is backwards compatible with older chips.
  • The test is available worldwide but prices will vary from country to country depending on local taxes and shipping rates. Negotiating global shipping rates and regulations is an extremely complicated process and prices are subject to change. There will be no hidden extras and the cost of shipping (including return shipping) will be included in the advertised price. The website currently shows prices for the UK, USA, Canada, Australia and Europe, and a standardised international price for other countries.
  • Participants will have the opportunity to opt into academic research studies.
Future plans
  • It is planned to add in more data as it becomes available. It is hoped in particular to get some samples from Ireland.
  • Updated ancestry reports will be provided free of charge and there will be no subscription fees to receive the updates.
  • There are plans to incorporate ancient DNA data.
  • A chromosome browser view is in the pipeline.
  • There is a long feature list in development, and the company hope to receive feedback from the community and will develop the tools that people want.
  • There is a major focus on privacy.  The customer decides what happens to their data.
  • All the processing is done within the European Union.
  • Data will not be sold on to pharmaceutical companies.
  • Care has been taken to ensure that people understand the implications of testing.
  • Children under the age of 18 can take the test but will be required to re-consent once they reach the age of 18.
  • There will be an option to nominate a beneficiary.
  • For full details read the company's page on Privacy and Security.
This is a very exciting new test. It is a very pleasant change to have a test that specifically caters for the British and European market. The admixture tests currently provided by the big three genetic genealogy companies are primarily serving the very different needs of the American market. Access to the POBI dataset is what we've all been waiting for and I'm sure that everyone is going to be keen to see how their results compare. I'm also particularly pleased to see the back in time map which I hope will be a useful educational tool and will help to improve our understanding of our shared human ancestry. This is a very welcome addition to the genetic ancestry marketplace, and I look forward to seeing some interesting new developments in the future.

Update 10 October 2016
The Living DNA team are hoping to improve their Irish reference panel. To this end they would like to recruit people with four grandparents born within 80 km (50 miles) of each other in Ireland. If you have already tested with 23andMe, Family Tree DNA or AncestryDNA you can transfer your results free of charge (23andMe data is preferred if available). If not, you can benefit from a discounted rate for a new test. Here is the link to transfer your results: https://www.livingdna.com/en-gb/irish-dna-research-project

Further reading
- See Chris Paton's blog for the official press release.
- For further commentary see John Reid's blog post More on the Living DNA genetic ancestry test and plans.
- Razib Khan provides some insights on admixture in his blog post on Scale of time and space in admixture.

© 2016 Debbie Kennett

Sunday, 4 September 2016

Rockstar Genealogists 2016 - the voting is now open

John Reid, who writes the Anglo-Celtic Connections blog, is once again organising the annual Rockstar Genealogists poll.

There have been a few changes this year to try to overcome the problem of multiple voting, and there are also changes in the way that the votes will be reported, so it will be interesting to see if there will be any surprises in store.

I'm pleased to see that so many of my fellow members of the Guild of One-Name Studies are on this list including our Chairman Paul Howes who is a very welcome first-time addition. I have fond memories of the recent Guild of One-Name Studies conference where Paul volunteered to fill a hole in the programme at the last minute and held the audience spellbound with an inspiring, unscripted and Powerpoint-free talk on some of the success stories of his one-name study.

All the respected UK genealogy speakers and writers, such as Nick Barratt, Peter Calver (who writes the Lost Cousins newsletter), Colin Chapman, Else Churchill, Audrey Collins, John Hanson, Celia Heritage, Janet Few, Michael Gandy, Emma Jolly, Chris Paton, Alec Tritton and John Titford, are included in the list. I feel very honoured to be included in such illustrious company.

Genetic genealogy is well represented with all the big names from the US receiving nominations. I'm one of four genetic genealogists flying the flag for the UK. I am in excellent company with Maurice Gleeson, Chris Pomery and Geoff Swinfield.

John Reid's intention is to provide a resource to help volunteers select speakers for their events. The nominations on the list can serve as a useful starting point but it's also a good idea to get feedback from other genealogists in each country who have worked with the individuals concerned before booking a speaker or commissioning an article or book.

Before you vote I urge you to read Janet Few's blog post on Rockstars and unsung heroes. Janet very eloquently and humorously sums up my thoughts on the contest, and says all that needs to be said.

Thank you to John Reid for organising the poll.

Make sure you cast your vote here. You can vote for as many people as you want but make sure you use your votes wisely.

Thank you to everyone who voted for me. I was honoured to be placed third in the list for England. Scotland and Wales though I'm still very uncomfortable with the whole idea of holding such a poll.

Here is the full list of gold medallists: http://anglo-celtic-connections.blogspot.co.uk/2014/09/rockstar-genealogists-gold-medalists.html

Here is the list of silver and bronze medallists;

John Reid published a further blog post in which he published the comments received by the voters. There were some interesting comments raised some of which, if true, are a cause for concern for the genealogy community: http://anglo-celtic-connections.blogspot.co.uk/2016/09/rockstar-genealogist-2016-comments.html

Kerry Scott at the Clue Wagon blog questions the validity of holding such a contest and I share her concerns: http://www.cluewagon.com/2016/09/the-rockstar-genealogist-contest-is-a-fiesta-of-awkward-lets-change-this/