Tuesday, 9 December 2014

Richard III and the use of DNA as evidence

The long-awaited scientific paper with details of the Richard III DNA analysis has finally been published. Twenty-two months have passed since the memorable press conference at the University of Leicester in February 2013 when Richard Buckley, the lead archaeologist on the Richard III dig, declared that "It is the academic conclusion of the University of Leicester that beyond reasonable doubt the individual exhumed at Greyfriars in September 2012 is indeed Richard the III, the last Plantagenet king of England." However, at that time most of the DNA work had yet to be done and none of the findings had been written up and published in peer-reviewed journals, though the evidence already seemed to be overwhelming. Since then five peer-reviewed papers have been published on different aspects of the study (see the list below). The DNA paper by Turi King et al “Identification of the remains of King Richard III” has been published in the journal Nature Communications and can be found here:

http://www.nature.com/ncomms/2014/141202/ncomms6631/full/ncomms6631.html

It is accompanied by 56 pages of supplementary material with all the technical details about the DNA testing (including Richard III's Y-DNA and mtDNA haplogroup assignments) and extensive genealogical information. This is perhaps the first time that a scientific paper has included such detailed genealogical content. It is well worth reading the paper in its entirety together with all the accompanying material. It is a masterclass in how to do ancient DNA research and how to correlate DNA with genealogical evidence. In addition, the University of Leicester have issued an official press release and this includes further information about the study as well as links to a number of interesting videos showing how the genetic and genealogical research was done.

The DNA results have been extensively covered in the media, with most reports, such as this one from the BBC, focusing on the lack of  a Y-DNA match and the possible implications for the monarchy, though many people have also commented that it might perhaps have been more of a surprise if the Y-DNA had matched!

In what is believed to be the first analysis of its kind, the authors brought together the genetic and genealogical evidence, along with previously reported non-genetic evidence, and used a probabilistic assessment to determine whether or not the remains found in the Leicester car park were actually those of Richard III. Such analyses are often presented in courtrooms but have never previously been used to answer genealogical and historical questions. I wonder if this might be the start of a new trend!

The statistical analysis was done by my colleagues at University College London, Professor Mark Thomas and Professor David Balding, working alongside Turi King. Two competing hypotheses were investigated:

                                       Hypothesis 1 (H1) Skeleton 1 is Richard III
                                       Hypothesis 2 (H2) Skeleton 1 is not Richard III

The analysis took into account the genetic evidence from the Y-DNA and mtDNA testing and the previously reported non-genetic evidence (radiocarbon data, estimated age at death, sex, presence of scoliosis, and presence of wounds suffered around the time of death). People always tend to over-estimate the importance of DNA test results which is why in genetic genealogy we always emphasise the need to use DNA in combination with genealogical evidence. DNA can effectively prove that two people are not related on a specific line, and it can generally be used to confirm relationships with very close blood relatives. However, for more distant relationships DNA can only indicate that two cousins share a common genetic ancestor. DNA cannot give us the precise date when that ancestor might have lived and there is always a very wide range of possible dates. Consequently DNA evidence can broadly support a hypothesis but is generally not conclusive in its own right. This is particularly the case with mitochondrial DNA testing. Although it is now possible to sequence the whole mitochondrial genome, mtDNA has a low mutation rate and two people can have an identical mtDNA sequence yet sometimes share a common ancestor who lived several thousand years ago.

The same limitations apply to the case of Richard III. Contrary to popular belief, the mtDNA match on its own did not "confirm" Richard III's identity; it was merely one of a number of pieces of supporting evidence which had to be considered in combination with the conflicting evidence from the lack of a Y-DNA match. Here's an extract from the UCL press release:
Contrary to what many may have expected, the genetic evidence alone is not conclusive, partly because only the mtDNA and Y chromosome are suitable for comparing distantly related individuals. In fact, the Y chromosome, did not match presumed male-line relatives of the king, and so counted against Hypothesis 1. However, this non-match could be explained by one or more false-paternity events (where the biological father is not the father recorded in family history) over 19 generations; such events are not uncommon so the male-line data only weakly favoured Hypothesis 2. The mtDNA evidence was found to support Hypothesis 1, but overall the genetic evidence was not enough to confidently identify Skeleton 1 as Richard III. 
However, when combined with the non-genetic evidence, even after making assumptions intended to count against Hypothesis 1, the authors obtained an overall likelihood ratio of 6.7 million. Even a sceptical translation of this likelihood ratio corresponds to a 99.9994% probability that ‘Skeleton 1’ is the remains of King Richard III, which the scientists believe puts the matter beyond reasonable doubt.
It would have been interesting to see how the probabilities would have worked out if there had also been a Y-DNA match. There is still scope for further DNA testing on descendants of other Y-lines from the higher branches of the tree if suitable candidates can be identified. Now that the Y-DNA results are in the public domain it's also possible that someone might take a DNA test and discover that he matches the Richard III Y-DNA signature which could perhaps encourage genealogical research to determine whether or not there is a connection.

Richard III's DNA
Richard III belongs to Y-DNA haplogroup G2 (G-P287). His 23-marker Y-STR profile has already been uploaded to the public ySsearch database and is available via two different ySearch IDs:

Richard III ySearch ID 45AER

Richard III ySearch ID B8YDF

I presume that the authors followed the NIST standards for reporting STR markers. There are different ways of counting the markers and different companies have reported results in different ways. Family Tree DNA have not yet converted their database to the NIST standards. When comparing the Richard III signature on Ysearch with FTDNA results an adjustment would need to be made to the STR marker known as GATA H4.1. See the Marker Standards page on the Sorenson Molecular Genealogy Foundation website for a conversion table:

http://www.smgf.org/ychromosome/marker_standards.jspx

Richard III's mtDNA places him in haplogroup J1c2c3, a new branch of J1c that is defined by the mutation A12397G. This new subclade was added to the mtDNA tree with the latest build of Phylotree thanks to the work of Ian Logan (see his posting on the Genealogy DNA mailing list). Richard III's mtDNA profile (control region only) has been uploaded to Mitosearch:

- Richard III's  Mitosearch ID T227G

All the mitochondrial sequences generated from the Richard III study have been deposited in GenBank under the accession codes KM676292 to KM676294. I cannot find the sequences on GenBank and presume they must have only been submitted very recently so it will take time for them to appear. In the meantime Ian Logan has provided a list of all publicly available J1c2c sequences that have been uploaded to GenBank and www.openSNP.org.

Other peer-reviewed papers on Richard III
The DNA paper is the sixth in a series of papers resulting from the Richard III study. The other papers are:


2)  Mitchell PD et al. The intestinal parasites of King Richard IIIThe Lancet 2013; 382 (989): 888.


4)  Lamb AL et al Multi-isotope analysis demonstrates significant lifestyle changes in King Richard IIIJournal of Archaeological Science 2014: 50: 559-565.

5) Appleby J et al. Perimortem trauma in King Richard III: a skeletal analysisThe Lancet, Early Online Publication, 17 September 2014.

© 2014 Debbie Kennett

Tuesday, 2 December 2014

23andMe relaunches health reports in the UK

It has been announced today that 23andMe have reintroduced their health test in the UK. The 23andMe test has been available in the UK since the company launched back in 2006, but in November 2013 23andMe were asked by the Food and Drugs Administration in America to withdraw their health reports pending regulatory approval. Existing customers were able to retain access to their health reports but new customers who ordered a kit on or after 22nd November 2013 were only able to receive the ancestry reports. The health reports were restored in Canada in October this year. The UK is now the second country to have renewed access to the 23andMe health reports. UK customers who ordered a 23andMe ancestry test between 22nd November 2013 and 1st December 2014 are now able to receive the new health reports free of charge. New customers in the UK who order a 23andMe test from today onwards will now have access to both health and ancestry reports. The 23andMe UK website can be found at: http://www.23andme.co.uk This URL redirects to: https://www.23andme.com/en-gb/

There has been a slight increase in price. The new test now costs £125 but this price is inclusive of shipping. The old test cost cost $178.95 ($99 for the test + $79.95 for shipping) which worked out at around £114 per test at the current exchange rate.

The new test is a pared down version of the previous test as can been in the comparison below.

New UK 23andMe health test
Old 23andMe health test
43 inherited conditions 
53 inherited conditions
12 drug responses
24 drug responses
11 genetic risk factors
122 health risks
38 traits                    
60 traits

A full list of the reports offered can be seen  here: https://www.23andme.com/en-gb/health/reports/#traits

I have access to a UK account which has the new health reports and I've had a chance to have a look around and see what is offered. Previously 23andMe used a star system to grade the confidence levels that they had assigned to reports. In my own 23andMe account I have reports that are graded from one star up to four stars. The grading system is explained as follows:

Four stars: Established Research. At least two studies examined more than 750 people with the trait or condition and/or the associations are widely accepted in the scientific community. The reports may cover rare conditions or include variants that do not greatly influence a person's absolute lifetime risk for a condition.

Three stars: Preliminary Research. More than 750 people with the condition were studied, but the findings still need to be confirmed by the scientific community in an independent study of similar size.

Two stars Preliminary Research. Fewer than 750 people were studied. Multiple large studies are needed to confirm these findings.

One star: Preliminary Research. Fewer than 100 people were studied. Multiple large studies are needed to confirm these findings.

With the new test only four-star reports are shown for genetic risk factors, drug responses and inherited conditions. The trait reports have star ratings of two, three or four stars.

Some four-star health reports are no longer available (for example, diabetes, age-related macular degeneration, bipolar disorder and stomach cancer). It is not clear why these reports are now excluded whereas potentially more controversial reports such as Alzheimer's are still available.

The display of the health reports has changed. 23andMe no longer show your risk compared to the average. This was previously presented in a somewhat alarming and confusing way so that all the conditions for which you had a higher than average risk factor, however small, were highlighted in red as though they were potentially a cause for concern. For example, in my own report I supposedly have a 0.2 % risk of bipolar disorder compared to an average risk of 0.1%. In contrast I have a 50.6% risk of obesity compared to an average risk of 59%, but because my risk was lower than average, it was not picked out in the report as being of special concern even though I am much more at risk of obesity than I am of bipolar disorder.

I had hoped that a test aimed at the UK market would be customised with links to UK resources. However, as far as I can gather most of the resources are in fact American resources. Confusingly when the word "national" appears it is used to refer to the US and not the UK. Similarly 23andMe advise talking to a genetic counsellor if you have concerns about your results, but they provide a link to an American company called InformedDNA and a link to the US National Society of Genetic Counselors. It would have been much more helpful to provide information about genetic counsellors in the UK and links to NHS resources.

Regardless of these minor quibbles, it's good news that the 23andMe health reports are once again available in the UK.

I have provided links to further coverage of the story below:

- 23andMe press release: http://mediacenter.23andme.com/en-gb/blog/2014/12/01/23andme-brings-ce-marked-personal-genome-service-to-the-uk/

- BBC interview with Anne Wojcicki: http://www.bbc.co.uk/news/science-environment-30288939

- BBC: http://www.bbc.co.uk/news/science-environment-30285581

- The Guardian: http://www.theguardian.com/technology/2014/dec/02/google-genetic-testing-23andme-uk-launch

- Daily Mail: http://www.dailymail.co.uk/health/article-2856789/125-DNA-test-checks-100-conditions-assess-risk-Alzheimer-s-cancer-going-bald.html

- GenomeWeb: https://www.genomeweb.com/microarrays-multiplexing/23andme-gets-ce-mark-launches-pgs-offering-uk-125

- The Verge (US): http://www.theverge.com/science/2014/12/1/7316089/23andme-expands-to-the-uk-despite-us-restrictions

Further reading
My series of articles on my 23andMe test - Note that my test was done on the Version 2 chip before the launch of the new test on the v4 chip in the UK
- Tim Janzen's autosomal DNA testing comparison chart

Saturday, 29 November 2014

Death of Valerie Hedgecock née Cruse

I am very saddened to learn of the death of Valerie Hedgecock née Cruse. Valerie is descended from the Ogbourne St George Cruse tree.  An obituary has been published in The Argus, her local newspaper in Brighton, Sussex:

http://www.theargus.co.uk/announcements/deaths/deaths/11575181.Valerie_HEDGECOCK/

Valerie had been researching her family tree for many years, and I'd corresponded with her on many occasions. She very kindly made a generous contribution towards the Cruwys/Cruse/Cruise DNA Project, and the last time I heard from her she was still maintaining an active interest in the Cruse research.

I would like to pass on my condolences to Valerie's family and friends.

With thanks to Geoffrey Lloyd

Tuesday, 25 November 2014

Family Tree DNA holiday sale

Family Tree DNA have announced that their holiday sale is now on. The Family Finder test is reduced to $89 (£57). The 37-marker Y-DNA test is $129 (£82). The mtDNA full sequence test is $169 (£108). The Big Y test for advanced users is $525 (£334). A full list of prices is shown below. Upgrades are also included in the sale so it's a good opportunity to upgrade your kit if you've not already done so. E-mails are in the process of being sent out to group administrators. FTDNA customers will be notified separately. The sale prices are provided below. There is a new mystery reward discount scheme so you might be able to get a further reduction on the sale prices. If you receive a mystery award and you are unable to use it for any reason do make sure you share it with the fellow project members. I've copied below for reference the e-mail that was sent out to the genetic genealogy bloggers.

Family Tree DNA Sale



For this holiday season we’ve got an exciting new twist to the sale - Mystery Reward discounts! The Mystery Reward will be a randomized discount (up to $100 off) that can be applied on top of the already reduced Holiday Sale prices. 

The Mystery Reward icon will appear on testers’ myFTDNA dashboard each week and the code will expire the night before the next Mystery Reward appears. When you click the icon, you'll to go to the reward page to open the Mystery Reward for savings up to $100. We’ll also send an email notification to the kit’s primary email address when a new code is available for use or sharing.


Best of all, there will be a new Mystery Reward every week. Customers can use the discount or can share it with a friend. 


In addition, all customers who have purchased the Big Y test will receive a coupon for $50 off a Big Y test. That's ON TOP of the sale price. Yes, you read that right. A coupon that can be used on top of a sale price. The coupon can also be "regifted," meaning shared with a friend or fellow project member.


Thank you for helping us to generate excitement about the holiday sale. We appreciate all the cooperation you give us throughout the year!

Here are the prices: