Tuesday, 11 July 2017

AncestryDNA - Genetic Communities

Back in February, when I wrote about my LivingDNA results, I commented on the upcoming release of AncestryDNA's "Genetic Communities" feature, which I'd heard about through others who could see their communities as part of the beta testing.  Unfortunately, general "busy-ness" got in the way of me posting about my own Genetic Communities, when I received them soon after that.  So this is a 'catch up' post.  I'm not going to cover all the details of how the Genetic Communities work - information about that is already available on the blogs of other genetic genealogists, such as Blaine Bettinger* or Debbie Kennett*, or on the Ancestry site itself. In this post I'm just going to focus on my own results and explore how useful (or otherwise) the information might be.

This is from my AncestryDNA Home Page, showing my general ethnicity and also that I am in three of the genetic communities.

Clicking though to view my "genetic ancestry" gives me the details of which communities I am in, and a map showing both the communities and the estimated general ethnicity areas (I only have traces of 'ancestry' from the "three more regions" so they aren't shown in detail.)

There are over 300 Genetic Communities currently available (Blaine Bettinger has provided a pdf of the full list, from a link on his blog), and it is possible to click down from a continental level, to explore what communities have been identified in different regions of the world, by clicking the "view all" button.  However, I find this a bit inconsistent, and potentially "buggy", when trying to explore the regions where I am in a community.

For example, If I look at the "Scots", which I am not part of, all of the communities show separately in white:

But, when I view a region where I am part of a community, I can only see my own community. For example "The Welsh and English West Midlanders" contains three communities:

But I only seem to get shown the one that I am in, when I try to view these:

This is virtually the same view I get when viewing my own Genetic Community, "English in the West Midlands". 

Based on the list provided by Blaine Bettinger, the "Welsh and English West Midlanders" region also contains the "North Walians" and the "South Walians", but I don't seem able to access the view similar to the one I see for the Scots region, showing all three of the communities in the region - although I can (sometimes) see the whole region, if I access it from the drop down on my own genetic communities view above:

For the other two community regions that I am in, the "English Midlanders and Northerners" and the "Southern English", I seem to be in the overall region but not allocated  to a more specific community within that, but again, the only view I can obtain is the same as my personal view, so I cannot see what the three more refined communities in each of these regions are.

 I would be interested in seeing how the three regions my Genetic Communities are in look like to someone who is not in them.

Comparison to LivingDNA
Since LivingDNA is the only other company that provides ethnicity estimates in fine detail within the UK, I thought it might be interesting to compare the results from them to my Ancestry Genetic Community regions.  My LivingDNA results have been updated since I wrote about them at http://notjusttheparrys.blogspot.co.uk/2017/02/a-slight-sidetrack-my-livingdna-results.html so, for now, I am including an image from both versions of LivingDNA to compare to AncestryDNA's Genetic Communities. (I will do a more detailed post about the updated LivingDNA results later.)

The three Genetic Communities I am in on Ancestry cover a large area of England, but do not include any of Scotland and only cover the border area of Wales.  In some ways, the earlier version of the LivingDNA results was a better match to the Genetic Communities, as it included down into Devon and Cornwall, and did not include much of Scotland, whereas the updated results no longer show any Devon or Cornish DNA, and now include Aberdeenshire.  However, we are talking about fairly low percentages for these counties.  Both Ancestry and LivingDNA place my main 'ancestry' as being from the West Midlands/Welsh Border areas - which does tie in with my known family history.

So I do feel that both companies are identifying connections to similar areas within the UK and, as the details continue to be refined, potentially the results will be very useful in furthering my family history.

Debbie Kennett has pointed out that, given the current predominance of Americans in the database, the Genetic Communities can help those of us in the UK to filter our match lists so as to focus on the more relevant matches, ie those who do have an identifiable connection to the same UK areas that we have.  However, although the Genetic Communities are created initially from the DNA analysis, with pedigrees then being used to supply historical information that helps to 'identify' the community, it isn't necessary to have a pedigree in order to be in a community, so finding the connections to matches who are in communities will usually involve further research (and, ultimately, might still be impossible in some cases). 

But the very fact that a pedigree isn't required, in order to appear in a community, does make the Genetic Communities a useful feature for anyone who does not know their family history, as it can help to identify some "times and places" for them to explore potential connections to their matches.

So, as confirming my family history and discovering new relatives are my main aims in using DNA, how useful are the communities for finding the connections between my matches and my own family history, beyond the general benefit of narrowing down my match lists? 

 The story views on the Genetic Communities help to provide more detail about the places where my matches' ancestors were from.

And also where they went to:

And the connection page indicates some of the surnames that are more prominent in the particular community, as well as indicating my own strength of connection to the Community:

(I love the background photo, by the way - definitely a place with relevance to my family history!)

As you can see, there is overlap between the three communities that I am in.

Just as I am in several communities, so are many of my matches.  The following diagram illustrates the numbers of my matches in each of the overlapping Community groupings:

(For anyone who does the maths, yes, there is an inconsistency between the images, with 23 matches being listed as in the "English in the West Midlands" community, and only 22 shown in my diagram - that's because another person was added in the four days between extracting the community match lists to produce the diagram and then copying the "Your Connection" image above.  Keeping data up to date is not easy!)

Since the "English in the West Midlands" is a subset of the "Welsh and English in the West Midlands", it does seem strange that two of the matches are in the subset but not in the higher level community (but that's just a minor anomaly that I've noticed, rather than something I'm looking into).

It seems clear that, at the moment, whilst it is helpful to know these matches have a UK connection, the Communities don't necessarily narrow that down to a particular branch of my family - partly because my genetic matches and I might both be in the same multiple communities but also because, as Blaine points out in his post, just because a match shares a particular community with me, it doesn't mean that, that is definitely where the shared ancestry is from.  But the Genetic Communities certainly could be helpful 'pointers' to potential connections and I imagine they will also improve over time, so may eventually even hint at specific family lines, especially when combined with other information from known family history and shared matches. 

What about those DNA matches that I have already identified some shared ancestry with - how do the Genetic Communities match up to our shared ancestry? 

Unfortunately, only two of those 'identified matches' appear in the same communities that I am in.  In one case, the match is in three of the communities I am in - the 'Welsh & English West Midlanders', 'English in the West Midlands' and 'English Midlanders and Northerners'.  There is quite an overlap between these three communities anyway, but it is reassuring that our shared ancestry is from around the Bromyard area, in north eastern Herefordshire.  The other match is in both the 'Southern English' and the 'English Midlanders and Northerners'.  In this case, our shared ancestry is in London in the later 1800s and then traces back to Wiltshire by the beginning of that century, so it looks as if the 'Southern English' community may be relevant to this - but, if I didn’t already know the connection, the shared 'English Midlanders and Northerners' could send us looking in the wrong place.

There is one other match who, whilst I don't know exactly how we relate, is known to be related to me on my mother's side, thanks to comparisons at Gedmatch.  They are in both the 'Southern English' and the 'English Midlanders and Northerners', either of which could be relevant to my mother's side of my family.  However, I have noticed that a third match, who is shared between the two of us, is showing as just in the 'Southern English' community, so that may possibly hint at where the shared ancestry is (although that community does take in everything under a line from South Wales to the Wash, so that's hardly narrowing things down :-) )

In another example, I do have a match who is in all four communities that I can see, but is a shared match to someone who is only in one of the four.  So the combination of the Genetic Communities with shared matches may be another topic to explore, to see if it can help indicate the potentially more relevant areas of the country to be researching in. 

However,  this may not be without its problems and may still be misleading to me.  For example, I have a match who shows up in just the 'Southern English' community, but both his profile and a shared match indicate there's likely to be a high level of Welsh ancestry.  Since I assume that I am not seeing any communities that my matches are in, but which I am not in, it's possible that they both share in a Welsh community,  and it's probably more likely that one of my West Midlands ancestors headed into Wales and connects into their trees that way, than the connection being in the south of England.

Shared matches are something I will write about in a separate post soon, so I shall perhaps consider the combined use of these two tools further in that.  I'm certainly grateful to AncestryDNA for the various tools they provide and look forward to future developments.  

I just know that I still have a lot to learn, to be able to work with the tools effectively!


Tuesday, 4 July 2017

A Day Out at UCL

It was with some slight trepidation that I set out last Tuesday morning for the Workshop on “Personal Genetic Testing: Challenges and Benefits in and Beyond the Clinic” at the University College London (UCL). PGT covers more than just the ‘direct-to-customer’ DNA tests that we genetic genealogists use and this was clearly going to be an “academic” day. Was it all going to be “over my head”?

But, considering my interest in DNA testing, and with people such as Debbie Kennett involved in the event, I had decided it was worth taking the risk. In the end, whilst I imagine the day might not have appealed to the ‘average’ genetic genealogist, I did find it interesting and useful, even if some of the topics were not directly relevant to me.

Following a non-eventful train journey to Euston (would you believe that first class on London Midland was actually the cheapest ticket!), I arrived with plenty of time to spare, so took a few minutes to sit in the garden at the Friends meeting house, which was between Euston and UCL, to enjoy the experience of being in London.

The first talk of the day was by Adam Rutherford.  Although he is well known as an author and presenter, it was actually the first time I’ve heard him speak. I may not fully grasp the issues of “identity politics” but his talk was interesting and informative, and gave me a better understanding of how genetics-related topics I’d previously learnt about, such as Mendelian inheritance from biology lessons at school, and the “Nature vs Nurture” debate from when I was studying psychology, fit into the wider picture of genetics.  I also learnt a new term (‘European Genetic isopoint’ – “the time at which everyone alive is the ancestor of everyone alive today, or no-one”*, which is said to be approximately the tenth century.)  It was enlightening (and slightly shocking) to hear how some topics, which Dr Rutherford described as “non-controversial” to geneticists, can be extremely controversial amongst some members of the general public.  Unfortunately, it would seem that the simplistic understanding many of us possibly have about genetics can lead to undesirable consequences, such as when a concept like the “warrior gene” becomes an accepted excuse for criminal behaviour.

Coffee break was followed by a focus group on the Science of Ancestry Testing, dealing with the tests we take for genealogy.  Rather than the panel members doing presentations, as in the later sessions, this was initiated by the moderator, Mark Thomas, posing some questions about what we actually mean when we use terms such as “ethnicity” and “ancestry”, and whether genetic testing is helping to debunk myths, or whether it is reinforcing them.  The representatives of two testing companies (Dave Nicholson, from LivingDNA, and Mike Mulligan, from Ancestry) made good points about their companies’ activities in education, and about the need to be trusted by their customers (and therefore having a solid scientific basis to their claims).  But there’s clearly some differences of opinion with the scientists as to how scientific the simple ‘one-liners’ that often appear in adverts actually are.  And of course, it is often similar, simple one-liners that make the news headlines about DNA testing. There was a good comment from someone to the effect that phrases such as ‘the seven daughters of Eve’ may provide a “clear narrative” but are “scientifically problematic”.

So one “take home point” for me, from this session, was that I should try to be more critical and analytical about the things I read (and write) about genetic genealogy – people place their own interpretations on what they read, based on their own understanding and biases, and even terms such as “ancient ancestry” and “recent ancestry” often have different meanings, for example, when used by a genetic genealogist, as opposed to a population geneticist.  There is a need for clarity about how terms are being used in any particular context, as well as more awareness of the details underlying the headlines.

After the lunch break (when I joined most of the other genetic genealogists for an enjoyable lunch in the nearby Wellcome Institute Cafe), the first afternoon session concerned ethical issues in PGT.  This involved three presentations which were all thought-provoking, for different reasons.  Concepts such as “genomic sovereignty”, and the “forensic microbiome”, have certainly given me a few things to look up since I returned home*.  Whilst I cannot even imagine what it is like to live in a country such as Mexico, where thousands have been killed, or have disappeared, the second presentation, involving the question of the “personal or social” nature of genetic testing was one I could relate to more easily, having considered some of the issues myself when deciding to test at 23andMe (and in asking relatives to also test).  To know, or not to know, that is the question.  I was glad that one conclusion of the study was that people can make ethical decisions, if they have the relevant information.  The third presentation, concerning the ethical issues that arise in the use of DNA when dealing with disaster settings, is one I hope I never need to consider from a personal viewpoint.  Sadly very timely in the light of recent events, this was an insight into the very real challenges, and difficult decisions, faced by those who work in this field and raised many questions about the “Pandora’s box” that the ability to carry out DNA testing has opened.

The next session was a panel presenting social scientific perspectives on PGT and Identity. Unfortunately, I’ve always struggled with the “wordiness” of the social sciences so, for me, this was the least interesting session and reminded me of why I didn’t go into research following my psychology degree.

After another coffee break, there was a useful tutorial on the challenges of security and privacy in genomics.  It’s an important point to remember that, unlike passwords or bank details, there’s no “reset button” for our genomic data, which is why, even at the level of data we genealogists deal with, we should consider carefully what we share about it, and about those we connect to.

The final panel concerned medical and research aspects of PGT.  Again, these were interesting, even though not directly relevant to me.  The first, concerning personalised medicine and whole genome sequencing for genetic diagnosis, again illustrated some of the difficult decisions organisations such as the NHS face, when considering issues such as population screening, where the benefit of potentially discovering a curable disease at an early stage, needs to be weighed against the possibility of discovering other, untreatable, diseases at the same time. The second talk in this panel, and the final one of the day, was an enthusiastic presentation about open-access medical genomics, with particular concentration on the Personal Genome Project UK (PGP-UK). This introduced me to a few more “omics” terms (epigenomics and transcriptomics) to go with ‘genomics’, as well as describing how different types of data access affected ease of research. The PGP has a very intense application procedure, including an exam that even someone with a genetics PhD can fail, if they don’t read the information properly. So participants are very clear about what the project involves, and what open access of their data will mean, before they take part in the project.  I doubt there’ll be any concerns regarding a lack of informed consent in that project!

The day ended with an informal reception, which was another opportunity to catch up with the other genetic genealogists, and to hear their views of the day.

So, to sum up, I enjoyed the day and it opened my eyes to some of the wider issues concerning PGT and it wasn’t (entirely) over my head. I do feel that there is a gap between what the academics are focusing on and the priorities for many genetic genealogists. I imagine that the time some scientists have had to spend ‘debunking’ the more ridiculous claims that have been made regarding genetic identities of groups (such as of the Vikings), has influenced this. There clearly is scope for research into the relationship between DNA testing and identity, or ‘belonging’ – but I suspect that the majority of those testing initially do so from a sense of curiosity, rather than as a way of finding their place in the world or, as one participant put it, an “identity grab”, finding “distinctiveness in a complex world, with fractured identities”.  However, at the moment, there seems to be an overemphasis on the ancestry/ethnicity side of the tests and the claims relating to that aspect, rather than on the other aspects, such as “cousin matching” (in order to confirm researched family history, or to discover unknown parentage), which is a very important aspect for many genealogists who test.  Although I admit to having had a variety of reasons for the specific tests I have taken, or arranged to be taken, over the years, including curiosity and health issues, as well as using it as a tool for my one-name study, it is confirming my family history and finding new relatives that are the priority for me.  

Why does any of this matter?

There’s probably several reasons, but here’s a couple: I have visited societies that have had a talk by a scientist about DNA testing, who have been left with the impression that direct-to-customer DNA tests are overly expensive and not worth doing.  This concerns me, given that I am trying to encourage the use of such tests for genealogy.  I don’t mind people deciding against testing - I have several relatives who have done that and it is entirely their choice – but I’d like people to be making the decision based on accurate information.   Also, during the day I spoke to at least one person who supported the idea of regulation of the direct-to-customer DNA tests.  This wasn’t the first time that I’d found myself involved in such a conversation, having previously experienced it at WDYTYA. It’s no surprise that the topic of regulation comes up, not just because of the concerns about unscientific “ancestry” claims, but when one considers that there are now companies claiming they can use your DNA to help you with your diet, your exercise, even your wine choice*, it can seem as if the general public might need protecting.

So I think it is important that we continue to engage with the scientists and academic community to ensure that how we are using DNA testing is based on sound scientific principles, and that the way we are using it is then properly understood and represented by those who may, one day, be involved in any potential regulation.  I am very grateful to the other genetic genealogists who attended last week, as I know most of them have a better understanding of these issues than I do.  I’m also grateful to the scientists and staff at UCL, who are enabling ongoing debate about the issues surrounding PGT.  Long may it continue.

And, hopefully, we will all end up better for it.

* Sources, references or other relevant links
Personal Genetic Testing: Challenges and Benefits in and Beyond the Clinic

Genetic Sovereignty - 
Genomic Sovereignty and "The Mexican Genome" - https://ore.exeter.ac.uk/repository/handle/10036/3500
Genomic sovereignty and the African promise: mining the African genome for the benefit of Africa

The increasing use of DNA in other aspects of life:
Diet and fitness – examples of scientific literature I found:
http://www.bmj.com/content/324/7351/1438 (Summary free, main article behind a paywall)
(And a search on google for “DNA diet” will give results from companies aiming to sell you such a test.  Caveat emptor!)
Wine choice