Friday, 20 December 2013

A first look at the BritainsDNA Chromo 2 Y-DNA and mtDNA tests

Larry Vick has kindly shared screenshots of the results from his Chromo 2 test from BritainsDNA*. I wrote in my previous blog post about the results from his All My Ancestry admixture test. We will now have a look at his Y-DNA and mtDNA test results. The Chromo 2 test is a useful product for anyone wishing to have a detailed Y-DNA haplogroup assignment but who doesn't wish to pay out for one of the new but much more expensive comprehensive Y-chromosome sequencing tests. The test looks at around 15,000 Y-SNPs. For anyone with ancestry from the British Isles the Chromo 2 Y-DNA test is currently probably a better choice than the Geno 2.0 test from the Genographic Project. However, this is a rapidly changing market, and there are indications that the Genographic Project will be offering a new chip in 2014. For up-to-date comparisons of the various Y-SNP tests on the market see the Y-DNA SNP testing chart in the ISOGG Wiki.

There are a number of different options for the Chromo 2 test. The Chromo 2 Y-DNA test costs £189 ($299). A cheaper option is to purchase the Raw Y-DNA test for £129 ($199) which gives you your raw Y-DNA results without the ancestral and interpretative reports. If you are ordering the Raw Y test you will need to ensure that you share your results with the relevant haplogroup project administrators so that they can determine where your SNPs are placed on the Y-SNP tree as the position of many of the SNPs on the Chromo 2 chip is not yet known. The Chromo 2 test can also be purchased in packages in combination with the All My Ancestry test and a mitochondrial DNA haplogroup test. Larry had previously tested with Ethnoancestry (the former name of BritainsDNA) and was able to upgrade to the new test at a discounted price so he opted to have the full works. Make sure you click on all the images below to enlarge them to see the full details of each report.

The following screenshot shows the Y-DNA results welcome screen. Larry is haplogroup Q and BritainsDNA have identified his most downstream SNP as S324 (also known as L56). Larry tells me that he got a much better haplogroup assignment from BritainsDNA than he did from the Geno 2.0 test, and Chromo 2 has confirmed everything he already knew about his haplogroup except for what he has now discovered from the Full Genomes comprehensive sequencing test.

The Genetic Signature Report lists all the SNPs on the Chromo 2 chip for which Larry tested positive. Not all of these SNPs have been placed on the Y-tree and it is possible that his subclade assignment will be updated in future as the structure of the tree becomes clearer.

The Haplogroup Story provides a somewhat fanciful narrative about the origins of haplogroup Q which is defined by the SNP M242. It is of course mere speculation that haplogroup Q originated in the Altai mountains in Central Asia as they suggest. BritainsDNA give nicknames to the base haplogroups, and Altai is the name they have chosen in this case to represent haplogroup Q. Note that these nicknames have no scientific basis and should not be taken literally.

The World Distribution Map shows the percentage distribution of haplogroup Q in various populations around the world. BritainsDNA tell us that "the results for the world distribution have been brought to you from a combination of the published literature, our own data, and databases available from other research projects". It would have been helpful to have the full details of the sources used but unfortunately this information has not been provided. You can zoom in and out of the map to see the distribution of your haplogroup in different countries.

The Regional Distribution Map provides a breakdown of the distribution of haplogroup Q in the British Isles. The map represents "the locations of lineages 100 years ago" and is seemingly based on information provided by BritainsDNA customers who have been asked to give the birth place of their paternal grandfather.
This is an interesting feature which is not provided by any other companies. However, it would have been useful to have more details of the sampling process and, more specifically, the number of people sampled in each country. The date when the map was generated is not given and there is no indication as to how often the company plan to update the map.

The Four Nations map shows the distribution of Larry's haplogroup in the four countries that make up the British Isles. The company tell us: "The ancestral data that you and all of our customers provided on ordering has informed both the regional distribution across Britain and Ireland and uncovered the frequencies across our four home nations." The grandparents' place of birth is used for this chart which is again intended to represent "the location of lineages 100 years ago or more". As with the maps, this chart would have been more meaningful if details of the number of samples in each country had been provided. Presumably such information is considered to be commercially sensitive.

The Phylogenetic Tree shows the position of Larry's haplogroup in relation to the full Y-SNP tree. There is a slider to zoom around the tree, and a red line allows Larry to trace his lineage back to the root of the tree. With the anticipated SNP tsunami in 2014 the Y-tree is likely to undergo major restructuring, and this tree is likely to become out of date very quickly. ISOGG maintains the most up-to-date version of the Y-SNP tree.

The Y-DNA haplogroup frequencies chart shows the percentage of BritainsDNA customers who belong to each haplogroup.  Again, the underlying data are not provided, and it is not clear whether these frequencies include the whole customer base or just those customers who have a paternal grandfather who was born in the British Isles. The haplogroups are identified by their name and also by their BritainsDNA nickname. Note that the ISOGG Wiki has a chart which lists all these nicknames and the alternative SNP names.

BritainsDNA also offer the option to download the raw Y-SNP data. Larry sent me his raw data file which is in the form of a Notepad file with a list of all the SNPs tested. The results show whether Larry was positive or negative for each SNP tested and the genotype (the A, C, T and G letters) for each SNP. The file is provided in tab-delimited text file which can be opened up in a spreadsheet program.

Larry's mtDNA results follow the same format. Here is a screenshot of his mtDNA results welcome page.

Larry has been assigned to haplogroup H212b4, which is the same assignment he received for his full mitochondrial sequence test from Family Tree DNA. The Chromo 2 test covers around 3000 mt SNPs, and provides the same coverage as the Geno 2.0 chip. There are 16,569 base pairs in the full mitochondrial genome. 3000 SNPs is usually sufficient to give a reasonably detailed haplogroup assignment, but interpretation errors can occur and it is then necessary to have access to the raw data. There is, however, no option to download the raw mtDNA data. Larry tells me that BritainsDNA have advised him that they will not be providing the raw mtDNA data or indeed the raw autosomal DNA data. I would suggest that anyone who has taken an mtDNA or autosomal test with BritainsDNA should write to the company and ask for their raw data, and perhaps they will eventually change their mind. For a comparison of the mtDNA tests available see the ISOGG mtDNA testing comparison chart.

All in all I think the Chromo 2 test is a useful product for males wishing to have a detailed Y-DNA haplogroup assignment. It is certainly a big improvement on the previous offering from BritainsDNA/ScotlandsDNA which tested only 300 Y-DNA SNPs and 300 mtDNA SNPs, and was accompanied by a generic, melodramatic and fanciful narrative story with tales of the eruption of Mount Toba and ridiculous statements such as the supposed "fact" that "what directly caused populations to expand rapidly was the invention of porridge". The new haplogroup frequency charts and maps provide much more useful information, though the reports would have been more informative if details of the sample sizes had been provided. The experienced genetic genealogist is probably best advised to stick with the Raw Y test, unless he has a particular desire to have the charts and maps. If you've already taken a standard Y-STR test it is always best to seek advice first from the haplogroup project administrators or the relevant haplogroup-specific mailing list. In some cases it's possible to predict the most downstream Y-SNP with high confidence from a Y-STR signature and it is then only necessary to order a single SNP for $39 to confirm your placement on the Y-tree. It is also worth keeping up with the various genetic genealogy mailing lists and Facebook groups because there are likely to be many exciting new developments in 2014.

*Note that BritainsDNA also trades as ScotlandsDNA, IrelandsDNA and YorkshiresDNA.

Related blog posts
- A first look at the Chromo 2 All My Ancestry test from BritainsDNA
Alistair Moffat, BritainsDNA and the BBC - a "uniquely British farce"
- More pseudoscience from Alistair Moffat on the BBC
BritainsDNA, the BBC and Eddie Izzard
The British: a genetic muddle by Alistair Moffat
BritainsDNA, The Times and Prince William: the perils of publication by press release

© 2013 Debbie Kennett

A first look at the Chromo 2 All My Ancestry test from BritainsDNA

Larry Vick has very kindly shared some screenshots with me from his BritainsDNA* Chromo 2 test. Larry previously tested with the company in the days when it was known as Ethnoancestry. As an existing customer he was given the opportunity to order the Chromo 2 test at a very favourable price. Larry ordered the combination package which includes a Y-DNA (fatherline) test, an mtDNA (motherline) test and the All My Ancestry (biogeographical analysis) test. I will cover the All My Ancestry test in this post and will discuss the other tests in a follow-up post. Click on the images to enlarge them.

The All My Ancestry test analyses around 250,000 autosomal SNPs. The screenshot below shows the All My Ancestry welcome screen.  There are three different viewing options: Global Connections, Population Percentage, and Chromosome Painting.

The Global Connections menu compares your results with reference samples from around four thousand people from around the world. The results are plotted on a colour-coded chart and you can see which population is your closest match. There is a drop-down list which gives you the option to choose a variety of alternative views: Worldwide 1; Worldwide 2; African; Sub-Saharan; West Asian; South and Central Asian; East and Northern Asian; Hispanic and Afro-Caribbean 1; Hispanic and Afro-Caribbean 2; Native American mixture; and Jewish mixture. The image below shows the Worldwide 1 view.

This image shows the European view from the Global Connections menu:

The next menu allows you to look at your Population Percentages. This plot "uses a population genetic model to estimate your overall ancestry and puts this in context using nearly 4000 people from across the world". There is again a drop-down list which allows you to see your results compared to a number of different populations. The following options are available: global; Africa; Europe; West Asia; South and Central Asia; East and North Asia; and Hispanic-Afro-Caribbean-Native American. The following screenshot shows the global comparison:

This screenshot shows the European comparison:

The final viewing option is the Chromosome Painting. This allows you to see the contribution made to each of your chromosomes from three broad population groups: West Eurasian, Sub Saharan African and Asian-Native American. The company say "An ancestor six or more generations ago will have only contributed a small segment of DNA to your genome but this method can see these small segments which are not obvious in methods which provide a summary of the whole genome." As can be seen from the painting below this method has detected what are possibly small segments of African and Native American DNA.

Larry describes his documented ancestry as follows.
I think my ancestry would be best described as colonial American with a lot of UK, significant Irish, some German, and a little African and Native American mixture. I am not sure of the amount of African and Native American. My mother's 2nd great grandmother was from an area of tri-racial people, and I have no idea as to who her African or Native American ancestors were (in fact I don't even know my mother's 2nd great grandmother's parents' names). My mother's ancestry paintings have merely supported a family story about her 2nd great grandmother being from Newman's Ridge in Hancock County, Tennessee.  This 2nd great grandmother's maiden name was COLLINS, and that is a very prominent Melungeon surname (the reputed founder of this area was Vardy COLLINS).
I have to say I've personally never been able to work up much enthusiasm for these admixture tests. I already know that all my documented ancestors are from the British Isles and none of the tests are as yet able to tell me anything more than I already know from my genealogical research. However, Larry's genetic ancestry is much more interesting than mine which makes the results a little more appealing. I particularly liked the very colourful population percentage plots, a feature which is not available from any of the other testing companies. It would have been helpful to have information on the reference populations used for the analysis, something which all the other companies now provide. Another feature which is lacking is the ability to download the raw autosomal data. Compared to the alternative offerings on the market the All My Ancestry test is rather expensive at £169 ($269). It is a little cheaper when bought as part of a package in combination with the Chromo 2 Y-DNA and mtDNA tests. For a comparison of the autosomal DNA offerings from the other testing companies see Tim Janzen's autosomal DNA testing comparison chart in the ISOGG Wiki. The BritainsDNA All My Ancestry test is not yet included on this chart but Tim will no doubt wish to update it in due course when he's had the chance to assess his own results.

* Note that BritainsDNA also trades under the names ScotlandsDNA, IrelandsDNA and YorkshiresDNA.

Related blog posts
- A first look at the BritainsDNA Chromo 2 Y-DNA and mtDNA tests
Alistair Moffat, BritainsDNA and the BBC - a "uniquely British farce"
More pseudoscience from Alistair Moffat on the BBC
BritainsDNA, the BBC and Eddie Izzard
The British: a genetic muddle by Alistair Moffat
BritainsDNA, The Times and Prince William: the perils of publication by press release

© 2013 Debbie Kennett

Monday, 16 December 2013

The British: a genetic muddle by Alistair Moffat

The British: A Genetic Journey is the latest book by Alistair Moffat, the co-founder of the DNA testing companies BritainsDNA, ScotlandsDNA, IrelandsDNA and YorkshiresDNA. Moffat was previously the Director of the Edinburgh Fringe Festival and Director of Programmes at Scottish Television. He currently also serves as the Rector of St Andrew’s University. Moffat’s business partner is James Wilson, who works at the Centre for Population Health Sciences at the University of Edinburgh, and is BritainsDNA’s chief scientist.

According to the pre-publication publicity from the publisher Birlinn Books the book was originally planned to be written by both Alistair Moffat and James Wilson with the comedian Eddie Izzard lined up to write the foreword. It was originally scheduled for publication in March 2013 to coincide with the screening of the BBC programme Meet the Izzards in which Eddie Izzard, with the aid of Jim Wilson, went on a journey to explore his deep ancestry though DNA testing.

For whatever reasons the book was obviously extensively delayed but it was eventually published at the beginning of November. Until fairly close to the publication date the book was shown on Amazon.co.uk and other websites with both Jim Wilson and Alistair Moffat as co-authors and with the advertised foreword from Eddie Izzard. An example of the old cover can be seen here.

I was therefore somewhat surprised when I received my copy of the book from Amazon to find that Alistair Moffat was listed as the sole author. I could not find Jim Wilson’s name mentioned anywhere in the book. Furthermore, the long-promised foreword from Eddie Izzard is notable by its absence. Eddie Izzard similarly doesn’t get a mention in the book despite the fact that BritainsDNA did the DNA testing for Meet the Izzards and even went to the trouble of setting up a dedicated IzzardsDNA website.

The book is described on the dustjacket as being “based on exciting new research”. Having now read the book I’m at a loss to understand quite what this exciting new research actually is. The book itself mostly focuses on history and pre-history, with a heavy emphasis on pre-history, and there is very little on genetics. The genetics component largely consists of summaries of a small selection of genetics papers combined with a rehash of the many press releases issued by BritainsDNA over the last few years, some of which have attracted publicity in the British media.

Chapter 6 covers the Roman occupation of Britain. Alistair Moffat read out large extracts from this chapter during his lecture at Who Do You Think You Are? Live in February 2013.  I wrote about the misconceptions in this talk at the time. Sadly nothing has changed and no new evidence is offered.

In Chapter 9 on “The Royal British” we are regaled with the story of Prince William’s supposed Indian ancestry. This story was published in an advertorial in The Times newspaper in June this year and I discussed the problems with this research in an earlier blog post. Unfortunately, the book adds no further evidence to support the claims.

The casual reader of the book who is not familiar with the scientific literature will possibly have difficulty distinguishing between the genuine research published in peer-reviewed scientific journals and Alistair Moffat’s own somewhat unique take on our ancestral origins. There is not a single reference in the book and it is therefore not clear which genetics findings are based on peer-reviewed research, which sections are based on BritainsDNA’s unpublished research, and which sections are merely Moffat's own speculations. Some of the more ludicrous interpretations appear to be the product of Moffat’s fertile imagination.

The reader who is not familiar with the basics of genetic genealogy will probably also be somewhat confused by Moffat’s rather muddled terminology and his highly romanticised and at times laughable interpretations of our genetic history. He appears to have a very limited understanding of genetics. Confusingly he uses the word “marker” to describe both haplogroups (the branches of the human Y-chromosome DNA and mitochondrial DNA trees) and the markers known as SNPs – single-nucleotide polymorphisms –  that define those branches. For example, the mtDNA haplogroup L3 is described as being “a marker labelled L3”. This is particularly misleading for mitochondrial DNA because haplogroups are sometimes defined by several SNPs and, as can be seen on Phylotree, there are in fact three markers commonly used to define L3. Furthermore, especially for mtDNA, the same SNPs can occur in parallel in different haplogroups.

Moffat has a touching but misguided faith in the “ability of scientists to identify the origins and dates of DNA markers and to use them to track the movement of people across the Earth”. He tells us that “The dim and very distant prehistoric past can come brilliantly and movingly alive when the passage of a marker is traced from Manchuria and the shores of the Yellow Sea in the North Pacific clear across the Eurasian landmass to be found in Edinburgh in 2013.”  He attempts to correlate specific "markers" (more correctly, haplogroups) with ethnic groups or tribes such as the Vikings, the Picts, and the Maetae based on the flimsiest of evidence, conjuring up pictures in the reader’s mind of little bands of haplogroup armies migrating in unison in order to preserve the integrity of their markers. Unfortunately our genetic ancestry is somewhat more complicated than that. The problems of making such simplified interpretations and assigning arbitrary labels to groups and cultures are nicely summarised in Sense About Genetic Ancestry Testing, a pamphlet published earlier this year by Sense About Science.

Moffat unfortunately makes no attempt to explain any of the marker names and labels that he uses and provides no resources where the reader might seek clarification. The problem is readily apparent in the opening chapter of the book where Moffat’s imagination runs riot with the descriptive names used for the genetic groups that he describes:
     "On any London Monday morning packed trains rattle into King’s Cross, Euston, Cannon Street and Waterloo. The brakes hiss, the doors open and Saracens, Saxons, Berbers, Cave Painters, Vikings, Angles and Picts pour out onto the platforms. On any Saturday afternoon at Ibrox, St James’s Park, Old Trafford and Anfield crowds of Caledonians, Deer Hunters, Kurgans, Iberians, Rhinelanders and Anatolians roar on their teams, passionate in support, their sporting allegiances central to their identities. On any weekday morning all over Britain the school run delivers the children of the First Farmers, the Shell Collectors, the Foragers, the Shebans and the Yenesei to the gates of the playground.
     These are the British, named by their DNA markers, all of them immigrants, all of them descendants of men and women from somewhere else, from the distant, shadowy millennia of deep time, the survivors of many epic journeys lost in the darkness of the past."
The names he uses here are in fact the nicknames that BritainsDNA assigns to the various Y-DNA and mtDNA haplogroups and their sub-branches. There is a page in the ISOGG Wiki which provides a translation of the BritainsDNA nicknames for the Y-DNA haplogroups, but such names have no scientific basis. Furthermore, the ancestry we inherit on the Y-chromosome line (males only) and the mitochondrial DNA line represents only a decreasing fraction of our total ancestry as we look further back in time.

BritainsDNA mostly use their own proprietary S series names for the Y-SNPs that define the male-line branches of the tree, and these marker names are used throughout the book. A full list of the alternative and better known SNP names can be found in the ISOGG Y-SNP index.

In Moffat’s confused and simplified version of our genetic ancestry “Only 1.5% of all British and Irish Y-chromosome markers, principally M26 [the SNP that defines haplogroup I2a1a] from the ice age refuges and S185 [also known as L161.1, the SNP which defines haplogroup I2a1b2] from across Doggerland, certainly predated the arrival of the farmers c4000 BC, and a further 3.5% may have done.” We are then told that “Archaeology and DNA appear to agree on the origins of the vast majority of the incomers to Britain and Ireland after c4200 BC, those enriched for the G lineages.” The reason for this is supposed to be that the Y-chromosome “marker” of Ötzi the Iceman is “in the haplogroup G and it makes a clear link with the development of farming in Europe.” He then adds: “Almost certainly, those who carried the G markers sailed to Britain and Ireland in groups.”

The true story is of course much more complicated than that, and scientists and archaeologists don't have all the answers. There is no general agreement as to when and, most importantly, where the various haplogroups originated. There is also no evidence that any haplogroup was exclusive to any particular ethnic group in the past. Ancient DNA analysis and comprehensive Y-chromosome sequencing will provide further insights. Only a limited number of Y-DNA samples have been extracted from ancient DNA specimens to date. Richard Stevens provides a useful map showing the location of the finds together with details of the associated scientific papers where the results were published. Note that no ancient Y-DNA samples have yet been analysed from the British Isles. Comprehensive Y-chromosome sequencing is still in its infancy though we can expect to see a flood of new results in 2014 from genetic genealogists who have taken the state-of-the-art comprehensive Y-DNA sequencing tests. And of course the Y-chromosome markers, which are the primary focus of Moffat's book, only tell us about our ancestry on the fatherline or patriline, which represents only a small percentage of our total ancestry.

At times the prose is so melodramatic as to be unintentionally hilarious. For example, Moffat correctly notes that R1b-M269 is the most common haplogroup in Europe, and that it increases in frequency from east to west, but then goes on to offer the following explanation for the dominance of R1b (pages 99-100):
     "This increase in frequency from east to west obviously shows the direction of travel and the marker’s origins. R1b-M269 is the DNA of a second wave of farmers and as this revolutionary way of life, of producing food, washed across Europe, this marker, which first arose in the Near East, became tremendously widespread. And its dynamic movement to every corner of the continent shows something unarguable, that this new wave of farming and farmers was not a process of acculturation or adoption. Rather, it was the cultural cargo of an invasion, the deposit of a takeover by new people, the bearers of the marker of R1b-M269.
     Recent research has dated the origin of the cluster of R1b Y-chromosome markers to the middle of the third millennium BC and attached its dramatic spread across Europe to the advance of the Beaker People. And it seems that there was conflict, perhaps even something close to genocide. When the carriers of the R1b lineages arrived in Britain and Ireland, they took over, and this process must have involved the elimination of many of the men who carried the G lineages of the first farmers." 
Y-DNA haplogroup G is indeed the predominant haplogroup found in the very limited range of ancient DNA samples from the Neolithic period and only one R1b sample has been published to date, but we cannot extrapolate from 40 or so samples and conclude that all of the first farmers were haplogroup G. The published scientific papers on R1b are in fact contradictory and do not agree on the date of the origin of R1b. Mass genocide is one far-fetched hypothesis to account for the present-day dominance of R1b in Europe, but it is equally possible that R1b has spread dramatically purely by chance. Moffat is seemingly unaware of the work of his Chief Scientist, Jim Wilson, who was one of the authors of a recent paper entitled The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269 (Busby GBJ, Brisighelli F, Sanchez-Diz P et al. Proceedings of the Royal Society B 2012; 279: 884–892) in which the authors concluded that "the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution". A recent paper by Sikora et al in Investigative Genetics (2013; 4: 25) entitled Modeling the contrasting Neolithic male lineage expansions in Europe and Africa provides a summary of the contrasting findings in the literature. The authors use a simple demographic model which suggests that "in Europe, the R1b lineage experienced an extremely rapid and extensive increase as soon as it entered the continent, expanding more than a thousandfold in a few generations".

The lack of basic research that has gone into the genetics aspects of the book is evidenced in the statement in the final chapter on Comings and Goings: “Near Eastern markers can be distinguished in the modern population of Britain but specifically Jewish DNA is hard to find.” Moffat goes on to provide an outdated description of the Cohen Modal Haplotype, but seems to be blissfully unaware of the large number of scientific studies investigating “Jewish” DNA. It has been found that there are a number of Y-DNA and mtDNA subclades that are almost exclusively confined to people with Jewish ancestry. This oversight might perhaps explain why, as I wrote in an earlier blog post, his company mistakenly ascribed a Japanese origin to an Ashkenazi Jewish customer.

Some of the genetic findings he discusses may be more plausible, but it is a shame that the company’s scientists have so far failed to publish any of their research. I do not feel qualified to comment on the historical content which comprises the majority of the book. This subject matter might well be of interest to the general reader who wishes to have an overview of British history and pre-history. However, the lack of references is a cause for concern, especially in view of the fact that Moffat has a background in journalism rather than academic research.

However, if you are interested in the genetic history of the British then I regret that this genetic jumble of a book cannot be recommended. I can only think that Jim Wilson and Eddie Izzard are very grateful that they do not have their names associated with it.

Note
Despite my reservations about Alistair Moffat's book, please note that the Chromo 2 test offered by his company BritainsDNA is a credible and useful test for males wishing to explore their deep ancestry and who would like to have a detailed Y-DNA haplogroup assignment. There are also a number of other tests on the market at varying prices. For details see the ISOGG Y-SNP testing chart. For an explanation of the different deep ancestry tests and possible future developments in this fast-changing market see my article on a confusion of SNPs. Y-SNP testing is best co-ordinated through a Y-DNA haplogroup project. Please note that Y-SNP tests do not currently have a direct application for genealogy. For information on suitable tests for genealogical purposes see the beginners' guides to genetic genealogy in the ISOGG Wiki.

See also
Genetic astrology: a tale of misleading claims and legal threats

Related blog posts
- BritainsDNA, the BBC and Eddie Izzard
Alistair Moffat, BritainsDNA and the BBC - a "uniquely British farce"
More pseudoscience from Alistair Moffat
BritainsDNA, The Times and Prince William: the perils of publication by press release

© 2013 Debbie Kennett

Thursday, 12 December 2013

Recordings of Royal Society's Ancient DNA talks now online

In November I attend the Royal Society's two-day meeting on Ancient DNA. The recordings of the presentations are now available online on the Society's website:

http://royalsociety.org/events/2013/ancient-dna/

I previously posted my notes from the meeting which might help you to decide which talks you would like to listen to:

- Day 1 at the Royal Society's Ancient DNA meeting

Day 2 at the Royal Society's Ancient DNA meeting

My personal favourites were the talks by Carles Lalueza Fox, David Reich, Johannes Krause, Greger Larson and Alice Storey.

Sunday, 8 December 2013

Setting the record straight about Sara Sheridan’s “Japanese” DNA

I’ve previously written about the exaggerated and misleading haplogroup stories provided by some DNA testing companies. BritainsDNA, which also trades under the names ScotlandsDNA, IrelandsDNA and YorkshiresDNA, has been one of the worst offenders in this regard in the last year or so. I commented previously on the problems with their story about Prince William’s supposed Indian ancestry. In May this year a Scottish novelist by the name of Sara Sheridan told the story of the unusual findings from her ScotlandsDNA test in an article for the Huffington Post. She was informed by ScotlandsDNA that, despite her family history of Jewish ancestry, she descends “from a female line called 9Na [sic] that developed 17000 years ago in the area around Japan's most northerly island and on the mainland just opposite”. 9NA is a typo in the article and does in fact refer to N9a which is a mitochondrial DNA haplogroup. While haplogroup N9a might well have arisen 17,000 years ago, plus or minus several thousand years, determining precisely where a haplogroup originated is a different matter altogether. We are mostly reliant on the mtDNA of living people to make inferences about the genetic make-up of our matrilineal ancestors, but the present-day location of the bearers of a specific haplogroup does not necessarily correlate with its ancient origins. An awful lot of migration can happen in 17,000 years! In addition, the population today will probably only represent a tiny fraction of the mtDNA diversity of our distant ancestors because so many lineages will have become extinct. It is therefore quite preposterous to propose such a precise origin for a haplogroup so many thousands of years ago. Any theories on the origins of the various haplogroups should be regarded as highly speculative and should not be taken too seriously. They most certainly should not be presented as fact as they were here.

The test Sara would have taken with ScotlandsDNA is what they now call their Standard mtDNA Test. This test looks at just 300 mtDNA markers – known as SNPs (single-nucleotide polymorphisms) – from across the mtDNA genome and costs £170.  An improved higher-resolution test known as Chromo 2 was introduced by the company in June 2013. The newer test looks at around 3000 mt SNPs and costs £189 (males also benefit from a Y-chromosome analysis from the same test). The 300 mt SNPs covered in Sara Sheridan’s ScotlandsDNA test represent just under 2% of the mtDNA genome. The new Chromo 2 test covers around 18% of the mt genome.

There are in fact many daughter branches below N9a as can be seen from the most up-to-date version of the mtDNA tree on Phylotree. However, in order to determine the sub-branch it is necessary to test many more than the 300 mt SNPs covered by ScotlandsDNA, and ideally the whole mtDNA genome (all 16569 base pairs) should be sequenced. The sub-branches are of more recent origin and can sometimes provide better geographical resolution, though there are currently not enough full mtDNA sequences available in the literature to draw reasonable conclusions.

For females the ScotlandsDNA/BritainsDNA mitochondrial DNA tests are very poor value for money. Sara Sheridan could have had her entire mitochondrial genome tested at Family Tree DNA, the market leader for mtDNA testing, for much less than the price she paid for her low-resolution and very expensive mtDNA test from ScotlandsDNA. The full mitochondrial sequence (FMS), which literally sequences all 16569 base pairs in the mt genome, normally costs $199 (about £122) and is currently on offer for $169 (about £103) in the FTDNA sale which closes at the end of December. FTDNA are currently the only company to offer a full mitochondrial sequence test direct to the consumer. The FMS test gives you the most detailed possible haplogroup assignment, which can be further refined as new sub-branches are discovered. FTDNA also have the advantage of a large genealogical matching database and the ability to join the appropriate mtDNA haplogroup project for further comparisons.

Note that although the BritainsDNA/ScotlandsDNA Chromo 2 test is poor value for females it is a useful test for males of British ancestry who wish to have a detailed Y-DNA haplogroup assignment (females do not of course have a Y-chromosome). For a comparison of the different Y-SNP tests on the market see the ISOGG Y-SNP testing chart.

When the news of Sara Sheridan’s supposed “Japanese” ancestry was first published I discussed the story with Jill Whitehead who, like Sara, has Ashkenazi Jewish ancestry from Scotland. As the Jewish community is very inter-connected it is highly likely that Jill and Sara are related within a fairly recent time frame, so Jill took a particular interest in this case. Jill is one of the pioneers in the genetic genealogy community. She had her mitochondrial DNA tested with Family Tree DNA back in 2003, and has also tested with 23andMe. Jill is a member of the Jewish Genealogical Society of Great Britain and has written several articles on Jewish genetic genealogy for the society’s journal. Jill wanted to have the opportunity to set the record straight about Sara Sheridan’s erroneous haplogroup interpretation, and has kindly provided below a much more plausible explanation of Sara's matrilineal origins:
A number of us in the DNA community are aware of the presentation of DNA results used by the company BritainsDNA/ScotlandsDNA. These have been cursory to say the least, especially in terms of unusual DNA haplogroups that are not of British origins. ScotlandsDNA advised the Scottish author Sara Sheridan that her N9a haplogroup was Japanese or Korean even though she was of Jewish Ashkenazi origins. Surely alarm bells should have rung? Instead of paying for an expensive DNA test (and ScotlandsDNA can be pricey in comparison with others) she would have been better advised to carry out a paper trail search first. 
I traced her family back through the ScotlandsPeople website, and also using the naturalisation records on the National Archives website and the JewishGen shtetl finder. I found her ancestral town of origin in Belarus within half an hour of searching. The cost was only £14 worth of credits on ScotlandsPeople. If you can get back to a naturalisation record, and bearing in mind that Scottish records show dates and places of marriages of parents (even those overseas), then it is quite a simple process to trace Jewish families (provided the name is not a common one). This was how I found my own Jewish Brown family of Edinburgh twenty years ago, before I tried DNA testing eleven years ago now. 
I could not believe the description of the N9 haplogroup given by BritainsDNA. I match up with several thousand Ashkenazi Jews on both FTDNA's Family Finder and 23andMe's DNA Relatives feature. Their tests are much more sensitive and they recognise that the Jewish sub-haplogroup of N9 is in fact N9a3. I match half a dozen people of Ashkenazi Jewish origin who are also haplogroup N9a3. There has also been quite a bit of recent international research on N9 haplogroups, and FTDNA for one always publishes recent research papers. ScotlandsDNA obviously had no idea this research existed otherwise they would have known the difference between a Jewish N9 and a non-Jewish N9. 
I reproduce below the comments I made on the Scotsman newspaper website after an article appeared in that newspaper which again described Ms Sheridan's haplogroup as being Japanese/Korean
"I come from a prominent Edinburgh Jewish family that came to the city in the 1860s. I have also been interested in genetic genealogy for over ten years having published articles on this for Shemot, the Journal of the Jewish Genealogical Society of Great Britain, e.g. their recent specialist Jewish Genetics edition. 
I was somewhat surprised to read the description of Sara Sheridan's N9a3 maternal mtdna haplogroup. The Japanese make up only one small part of N9, there are many other N9s to be found throughout the world, as shown in a number of academic genetics journals recently. I have never come across a Japanese Jew, but there is a Jewish subclade of N called N9a3 with recent origins in Poland/ Belarus/ Lithuania. In fact, a very recent academic paper from 2012 by Derenko et al from the Russian Academy of Sciences points to a series of Neolithic skeletons found in Hungary as being N9a3. 
To add to that, I have no less than four assigned third cousins on the DNA testing site 23andMe, who are all N9a3, and they are all American Ashkenazi Jews originally from Poland/Lithuania/Belarus, who are related to me some time back in about the late 18th/early 19th century. I think ScotlandsDNA needs to be more accurate in its assessment and description of haplogroups. When haplogroups were being formed in ancient times, not all humans went in one direction, they scattered east and west. That is why we have Hungarian Neolithic skeletons, East European Jews and Asian populations who make up N9 haplogroups."
Further reading and resources
-  A list of Jewish DNA projects provided by JewishGen

The Haplogroup N Project at Family Tree DNA

- The ISOGG list of mtDNA haplogroup projects

- The ISOGG mtDNA testing comparison chart

- The Jewish Genealogical Society of Great Britain. The April 2013 issue of the society's journal Shemot was a special edition devoted to DNA testing and provides a useful introduction to Jewish genetic genealogy.

Scientific papers
- Costa MD, Pereira JB, and Pala M. A substantial prehistoric European ancestry amongst Ashkenazi maternal lineagesNature Communications 2013; 4 (2543).

- Ostrer H and Skorecki S. The population genetics of the Jewish peopleHuman Genetics 2013; 132 (2): 119-127.

- Derenko M, Malyarchuk B, Denisova G et al.  Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe.  PLoS One 2012;7(2).

- Behar DM, Yunusbayev B, Metspalu M et al. The genome-wide structure of the Jewish peopleNature 2010; 466 (7303): 238-242.

- Atzmon G, Hao L, Li Hao, Pe’er I et al. Abraham’s children in the genome era: major Jewish Diaspora populations comprise distinct genetic clusters with shared Middle Eastern ancestryAmerican Journal of Human Genetics 2010; 86 (6): 850-859.
  

- Behar DM, Metspalu E, Kivisild T et al. Counting the founders: the matrilineal genetic ancestry of the Jewish Diaspora. American Journal of Human Genetics 2006 78 (3): 487-497.

- Behar DM, Metspalu E, Kivisild T et al. The matrilineal ancestry of Ashkenazi Jewry: portrait of a recent founder event. American Journal of Human Genetics 2006; 78 (3): 487-497.

- Shriver MD, Kittles RA. Genetic ancestry and the search for personalized genetic histories. Nature Reviews Genetics 2004; 5: 611-618.

Books
Ostrer H. Legacy: A Genetic History of the Jewish People. Oxford University Press, 2012.
Abulafia D. The Great Sea: A Human History of the Mediterranean. Allen Lane/Penguin, 2011.
Goldstein D. Jacob’s Legacy: A Genetic View of Jewish History. Yale University Press. 2008.
Entine J. Abraham’s Children: Race, Identity and the DNA of the Chosen People. Grand Central Publishing, 2007.

See also
- Mitochondrial DNA testing at a new low price

© 2013 Debbie Kennett

Friday, 6 December 2013

23andMe update, third party tools and alternative personal genomics companies

Following on from the warning letter received by 23andMe from the FDA, the company have now announced that in order to comply with the FDA's requirements new customers will not receive health reports "while the company moves forward with the agency’s regulatory review". The ancestry reports are not affected, and new customers will also have access to their raw data files. Raw data files can be uploaded to third-party services such as Promethease or Interpretome where you can generate your own health reports. A full list of autosomal DNA tools can be found in the ISOGG Wiki:

www.isogg.org/wiki/Autosomal DNA tools

The FDA is not concerned with customers interpreting their own raw data and as far I understand these third-party tools do not fall under the FDA's remit.

The health reports have only been withdrawn for customers who have ordered a 23andMe test from 22nd November onwards.  This was the date when the warning letter was received from the FDA. Existing customers who ordered a test before 22nd November will continue to have access to their health reports.

Anne Wojcicki of 23andMe has posted a personal message to 23andMe users on the company blog:

http://blog.23andme.com/news/23andme-provides-an-update-regarding-fdas-review/

More detailed FAQs can be found on the 23andMe website:

https://23andme.zendesk.com/entries/23273619-FDA-Update-December-5th

The official press release can be found here:

http://mediacenter.23andme.com/press-releases/23andme-inc-provides-update-on-fda-regulatory-review/

Blaine Bettinger, who writes the Genetic Genealogist blog, has provided some useful commentary on the latest developments and links to other posts on the subject:

http://www.thegeneticgenealogist.com/2013/12/06/23andme-will-continue-to-sell-genetic-tests-for-ancestry/

Margaret A. Hamburg, a Commissioner for Food and Drugs at the FDA, has written a letter to the Wall Street Journal in which she states that the FDA "remain committed to continuing our ongoing dialogue with the company in order to bring a safe, effective and trusted product to the market". The full letter can be read here:

http://online.wsj.com/news/articles/SB10001424052702304011304579222111609444156

It is not yet known how long the regulatory process will take but I hope that a resolution will be reached sooner rather than later and that 23andMe will once again be able to market their DNA testing service.

In the meantime if you are interested in getting your DNA tested for the health reports there are a number of different companies outside the US which offer a similar service to 23andMe. A full list can be found in the ISOGG Wiki:

www.isogg.org/wiki/List of personal genomics companies

All the other American companies now require that the testing is done through a doctor. However, many of the companies in other countries still offer a direct-to-consumer service. Unfortunately, none of the other personal genomics companies have the advantage of a large database and a vibrant community forum which are the biggest benefits of the 23andMe service.

For the background on the 23andMe story read my earlier blog post on 23andMe and the FDA.

© 2013 Debbie Kennett

Tuesday, 3 December 2013

A new exome sequencing and interpretation service from Belgian company Gentle Labs

While the spotlight has been very much on 23andMe and the FDA this last week the launch of a new high-end genomics service has attracted little attention. Gentle Labs is a new company based in Belgium. They are offering an exome sequencing service with interpretation for $1990. The results are provided through a doctor. This is from their FAQs:
Why would I pay $1990 if I can get my DNA sequenced for $99?        Some companies are offering 'insights into your DNA' for only $99. These tests, however, are only based on 0.03% of your genome (corresponding with 1.9 % of your genes). It's like reading a novel by reading a letter on every page: you won't get much of the story. These cheaper tests do not allow for accurate or complete results or interpretation: some of these tests have false negative rates of 50% or more! In fact, companies offering these tests admit this themselves. One company clearly displays on their website that "The information on this page is intended for research and educational purposes only, and is not for diagnostic use." In other words: these tests should not be relied on for any medical purposes, nor for diagnostic use.
   
        In contrast, our Gentle test not only offers complete coverage of all your genes, it also includes counseling with some of the world's best medical geneticists provided by Royal Doctors. Other advantages include:
        *       a free subscription service through which we will keep you informed about your DNA as science evolves
        *       free DNA data storage (so that you can provide your medical doctors access to your DNA data in case of a health issue or emergency)
        *       user friendly iPad and web apps to explore your genetic results and - in the end - yourself
The Royal Doctors have no connection with royalty but offer a network of doctors who will provide advice for a fee of one Euro per day. Their website can be found at www.royaldoctors.com 

Dr. Bertalan Meskó, who writes the Science Roll blog, has signed up for the Gentle service and has published an interview with Peter Schols, the CEO of Gentle Labs, which can be found here.

The launch of Gentle Labs was covered by GenomeWeb but the story is behind a paywall.

Interestingly 23andMe launched their own exome sequencing pilot programme back in 2011. Exome sequencing is the logical next step for personal genomics tests but the costs are still prohibitively high for the average consumer. It will be interesting to see what transpires in the next five years.

© Debbie Kennett