Tag Archive for 'ancestry'

Response to “Exaggerations and errors in the promotion of genetic ancestry testing”

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Following the Genomes Unzipped post entitled “Exaggerations and errors in the promotion of genetic ancestry testing”, we received a request to reply from Jim Wilson. Jim Wilson is the chief scientist of BritainsDNA. He is not the one who gave the BBC interview that prompted the Genomes Unzipped post but he is a key contributor to the science behind BritainsDNA. We are keen to tell both sides of this story and this post is an opportunity for BritainsDNA to state their arguments and motivation. -VP

I saw Vincent Plagnol’s post here on Genomes Unzipped about the promotion of genetic ancestry testing and felt compelled to respond. While I did not give the interview that was the subject of the post, I am the chief scientist at BritainsDNA and I feel that the post was biased in presenting only one side of the story and thus misrepresenting the situation. Perhaps I can offer another perspective for readers.

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Exaggerations and errors in the promotion of genetic ancestry testing

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One thing we have done in Genomes Unzipped is to report on what is on the market for consumers interested in getting information about their genetic data. While we have found generally positive things to say about this market, there are also many exaggerated claims especially when it comes to making inferences about an individual’s ancestors from direct-to-consumer genetics companies. An example came up last summer with a BBC radio 4 interview of Alistair Moffat of Britain’s DNA.  This post will discuss the scientific basis of some of the claims made in the interview.

But first of all, what is my motivation to write this post? After all, there are quite a few genetic ancestry companies like Britain’s DNA, making similar claims. Why specifically discuss this BBC radio 4 interview? The main reason is that listening to this radio interview prompted my UCL colleagues David Balding and Mark Thomas to ask questions to the Britain’s DNA scientific team; the questions have not been satisfactorily answered. Instead, a threat of legal action was issued by solicitors for Mr Moffat. Any type of legal threat is an ominous sign for an academic debate. This motivated me to point out some of the incorrect, or at the very least exaggerated, statements made in this interview. Importantly, while I received comments from several people for this post, the opinion presented here is entirely mine and does not involve any of my colleagues at Genomes Unzipped.
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Inbreeding, Genetic Disease and the Royal Wedding

Today is, of course, the day of the Royal Wedding, with new blood entering the British royal line, and the hope of new heirs to our throne. And of course the question on the lips of all British geneticists is: will there be any new royal genetic diseases in this crop? The European royal lines have always been prone to the odd loss-of-function mutation. An unlucky mutation in Queen Victoria’s Factor IX gene caused a nasty case X-linked Haemophilia B in her male descendants (a mutation that was only mapped in 2009 by sequencing the bones of the murdered Romanov branch). Luckily for them, this mutation hasn’t been observed in any of Victoria’s descendants lately; while it can hide undetected in women, this obviously doesn’t apply to William. More systemic genetic problems have been the result of heavy inbreeding; Charles II of Spain, with his distressingly bushy family tree (left), suffered from severe Habsburg jaw, along with a host of other genetic complaints.

In terms of inbreeding, there has been a bunch of digging around in the press to find the closest common ancestor of William and Kate: Channel Four turned up fourteen and fifteenth cousinships, and the Daily Mail managed to find a eleventh cousinship. For comparison, William’s parents Diana and Charles were also 11th cousins, and the Queen and Prince Philip were a far more regal 2nd cousins once removed. Eleventh cousins share on average 60-parts-per-billion of DNA, or about 180bp (although with wide variation due to the spotty nature of meiotic recombination: in fact, 99.5% of 11th cousins will share no stretches of DNA through recent descent at all, while the remaining 0.5% will typically share tens of thousands of bases). Given that the average person harbours about 10 recessive diseases, this gives about a 1 in 1.6 million chance of Kate and Will’s offspring developing a royal disease due to a piece of DNA shared between them. So, not very likely then.

In fact, eleventh cousins is a pretty low degree of relatedness, by the standard of these things. A study of inbreeding in European populations found that couples from the UK are, on average, as genetically related as 6th cousins (the study looked at inbreeding in Scots, and in children of one Orkadian and one non-Orkadian. No English people, but I would be very suprised if we differed significantly). 6th cousins share about 0.006% of their DNA, and thus have about a 0.06% chance of developing a genetic disease via a common ancestor. Giving that the Royal Family are better than most at genealogy, we can probably conclude that the royal couple are less closely related than the average UK couple, and thus their children are less likely than most to suffer from a genetic disease. Good news for them, bad news for geneticists, perhaps?

Analysing your own genome, bloggers respond to the FDA and more reporting on bogus GWAS results

Razib Khan, more known for his detailed low-downs of population biology and history, has written an important post on Gene Expression, explaining in careful detail exactly how to run some simple population genetic analysis on public genomes, as well as on your own personal genomics data. The outcome of the tutorial is an ADMIXTURE plot (like the one to the left), showing what proportion of your genome comes from different ancestral populations. This sort of analysis is not difficult, but it can often be hard to know how to start, so Razib’s post gives a good landing point for people who want to dig deaper into their own genomes.

This tutorial also ties in to some political ideas that Razib has been talking about since the recent call to allow access to genomic information only via prescription. If you are worried about losing access to your genome, one option is to ensure that you do not require companies to generate and interpret your genome. As sequencing, genotyping and computing prices fall, DIY genetics becomes more and more plausible. Learn to discover things about your own genome, and no-one will be able to take that away from you. [LJ]

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Guest post by Razib Khan: My personal genome

I’ve been following Razib Khan’s scholarly and analytical exploration of his family’s genetic history – using data from 23andMe – over at Gene Expression with increasing fascination. When last week he noted that his findings appeared to be (finally) converging on a consensus, I asked if he’d be willing to summarise his journey for Genomes Unzipped readers. Here it is. –DM.

I’ve always been interested in genetics, anthropology, and history. Many may perceive me to be a collector of obscure facts, but summing up infinitesimals does produce something substantial in aggregation. One of the most influential books in my life has been History and Geography of Genes. So with that, the shift from classical markers to uniparental lineages, and now to the dense SNP-chips, has been a boon for my own intellectual interests which reside in part at the intersection of history and population genetics.

However, I’ve never been deeply curious as to the history of my own personal genome. I’m not adopted. All four of my grandparents were ethnic Bengalis, albeit from relatively diverse communal backgrounds. I look typically South Asian. Genealogy has never been a family fascination, and I’m going to be honest and admit that until five years ago I didn’t even know the names of my grandparents (in the Bengali language there are distinctive terms for maternal and paternal grandparents, so this wasn’t needed). Both sides of my family are from the Comilla district of Bengal, and that’s all I really cared about (and I didn’t care that much, I don’t put much stock in “heritage” as determinative).

As for other yields of personal genomics, I was skeptical. My parents have many siblings, and many, many, cousins. I had a general sense of my risks for diseases through an inspection of the pedigree of my family and their medical histories. Additionally, many of the risk alleles have been identified in European study populations, and I wasn’t totally sure about the between-population portability of these inferences. And I won’t even address the fact that effect size of many of the markers isn’t something to shout home about.

But last spring Daniel alerted me to the 23andMe “DNA Day” sale. It was affordable, and at that point enough of the readers of my weblog had been typed that I kept getting questions as to my own background (e.g., my family has the title Khan, so there was a question as to whether I carried the “Genghis Khan haplotype”). So I bit. At the time I recall emailing Dan and being excited that I’d be told I likely had brown eyes and was 75% “European” and 25% “Asian.” When my results came back, I was in for a mild surprise. The proportion to the left are calculated by 23andMe’s “ancestry painting” algorithm. As you can see, I’m more than 25% “Asian.” My initial reaction was that this seemed a touch high, but no worries, I would ask around and see which other South Asians had such a high value. After dozens of instances of “gene sharing,” the answer came back: none.
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Am I partly Jewish? Testing ancestry hypotheses with 23andMe data

I agreed to make my 23andMe genotyping results publicly available as part of GNZ without a moment’s hesitation. This is in part because I knew the results were actually a bit dull (in a good way, I suppose) – I’m not at vastly increased or decreased risk for any diseases (based on research so far), and I was unsurprised to find out that I have blue eyes. I was also unsurprised that 23andMe identified me as most likely of north European ancestry.

Several hours after we released our data, however, I was pointed to a post where Dienekes Pontikos wrote about the results of running all our data through his ancestry prediction program. While just about everyone was quite confidently predicted to be almost entirely of northwestern European descent, this analysis gave me a point estimate of 20% Ashkenazi Jewish ancestry. Within hours, several people had asked me about this, and I had no real response. So I decided to take a look at the data myself; some basic analyses are below.
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Friday Links

This will be somewhat of an introspective Friday Links, looking at what other people have had to say about our recent announcement. We’ll resume our regular programming next week.

It’s been a big week here at Genomes Unzipped, with the announcement that all of the group members have released their genetic data publicly. The announcement was accompanied by a story by Mark Henderson in The Times (subscription only, unfortunately, but also syndicated here) along with commentary from Misha Angrist, Linda Avey and Christine Patch.

You can also listen to Daniel talk about the project on the BBC World Service (starts 19m30s), and Carl on BBC Radio Scotland (starts 38m). Finally, Luke and Daniel were on CBC Radio’s The Current today.

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Testing for traces of Neanderthal in your own genome

I’m guessing everyone reading this post is familiar with recent research from Svante Paabo’s group indicating that modern humans interbred with Neanderthals during their long co-existence in Eurasia between 30,000 and 80,000 years ago. According to the researchers’ calculations, somewhere between 1 and 4% of the DNA in modern non-African humans is derived from these interbreeding events – in other words, many of us are walking around with Neanderthal DNA sitting in our genomes.

So how much of your genome is Neanderthal? Over at The Genetic Genealogist, Blaine Bettinger takes a look at the options currently available to those interested in digging for Neanderthal ancestry in their own genetic backyard. Blaine notes that one company is already offering a test labelled as looking for Neanderthal ancestry based on a limited number of variable (microsatellite) markers. However, this test doesn’t actually look directly for putative Neanderthal-derived variants; instead, it (rather quaintly) tests for “strong matches between your DNA fingerprint [...] and populations identified as “archaic,” that is, whose composition retains the earliest earmarks of out‐of‐Africa genetics.” This is a very rough approach to the problem, to put it mildly.

Added in edit 15/07/10: John Hawks has a justifiably scathing review of the test on his blog; I’ve removed links to the company from this post to avoid giving them extra publicity.

People who have already had their genomes scanned by a company like 23andMe theoretically have sufficient data already available to perform a much higher-resolution analysis. However, sadly there’s not yet any readily available algorithm out there for doing this, despite there being (as Blaine notes) substantial interest for such a test from amongst the 23andMe community.

Seems like there’s some real scope for a DIY genomics tool here. Is anyone out there already working on this? Let us know in the comments.


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