Archive for the 'In The News' Category

On bad genetics reporting

05/12/2011
Categories: In The News
Written by Daniel MacArthur

This short article on the Independent’s website may not be the worst piece of genetics reporting ever, but given its brevity it may well take a new record for the density of errors and misconceptions. (To save you the trouble of hunting down the article it’s actually referring to, which of course is not linked, it’s this online article in Molecular Psychiatry).

Let’s start with the headline:

Sleeping is all in the genes

No. Data from twin studies suggest that the length of time people sleep for is around 44% heritable – that is, around 44% of the variation in this trait is due to inherited (and presumably mostly genetic) factors. The article being discussed in the piece provides no new information about the heritability of this trait.

Scientists have found the reason why some people need more sleep than others lies in their genes.

Scientists have found that one of the reasons people sleep longer than others is possibly a variant in a non-coding region of the gene ABCC9. Even if this association is real (and the evidence in the article is less than compelling), it explains just 5% of the variation in sleep length between people.

A survey of more than 10,000 people …

A survey of 4,251 people found the association between sleep length and the ABCC9 variant. This association was not replicated in a separate set of 5,949 individuals. The authors have a potential explanation for this lack of replication (based on the season in which the sleep length measurements were collected), and then did a post hoc re-analysis of their combined sample accounting for season that produced positive results.

showed those carrying the gene ABCC9, present in one in five of us,

The gene ABCC9 is present in all of us (hell, it’s even present in fruitflies). However, there is a genetic variation in one region of the ABCC9 gene, and one version of this variation is present in 17.3% of Europeans.
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Complete Genomics to sequence 1500 whole genomes for pre-term birth study

15/09/2011
Categories: In The News
Written by Daniel MacArthur

Genome sequencing provider Complete Genomics has announced a deal with the non-profit Inova Translational Medicine Institute, under which the company would sequence 1,500 complete human genomes to help explore the genetic basis of premature birth.

The Inova collaboration is one of many large-scale genome sequencing studies currently being planned and performed around the world. In some respects the study is actually quite a small one – only 250 “cases” (i.e. premature babies) are being sequenced, along with 250 normal-term control babies, which means the researchers will have low statistical power by the standards of modern genomics. However, sequencing this number of complete genomes to high depth is (as far as I know) unprecedented, and the inclusion of the parents of all of the children in the study will provide the team with the ability to do some very interesting analyses – for instance, looking at “de novo” mutations that arise in the babies but weren’t present in either parent, as well as exploring potential effects of the maternal genome. Maternal genetics are known to be important in determining the risk of premature birth: girls born prematurely have a higher risk of delivering a pre-term baby themselves (with twin studies suggesting between 15 and 40% of the risk is heritable), while paternal genes seem to have almost no effect.
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Inbreeding, Genetic Disease and the Royal Wedding

29/04/2011
Categories: In The News
Written by Luke Jostins

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?

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The genome hasn’t failed

21/04/2011
Categories: In The News
Written by Vincent Plagnol, Luke Jostins, and Daniel MacArthur

On Monday, the Guardian published an article by plant geneticist Jonathan Latham entitled “The failure of the genome”. Ironically given this is an article criticising allegedly exaggerated claims made about the power of the human genome, Latham does not spare us his own hyperbole:

Among all the genetic findings for common illnesses, such as heart disease, cancer and mental illnesses, only a handful are of genuine significance for human health. Faulty genes rarely cause, or even mildly predispose us, to disease, and as a consequence the science of human genetics is in deep crisis.

[...] The failure to find meaningful inherited genetic predispositions is likely to become the most profound crisis that science has faced. [emphasis added]

The claim that human genetics is in crisis is not novel. Latham made an extended version of this argument in a blog post at the Bioscience Resource Project in December last year, which Daniel critiqued at length at the time, and which contained a schoolboy statistical error corrected by Luke. And Latham is by no means the only genome-basher out there: the 10 year anniversary of the sequencing of the human genome triggered a spate of “genome fail” pieces (see Nicholas Wade, Andrew Pollack, Matt Ridley, and a particularly horrendous example from Oliver James, for instance).

We suspect for most of our readers Latham’s rather hysterical critique will fall on deaf ears, but it is part of a bizarre and disturbing trend that needs to be publicly countered. Here are several of the places where Latham’s screed gets it patently wrong:

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Why DTC genetic testing is good for research

10/03/2011
Categories: In The News, Law and Regulation and Opinion
Written by Joe Pickrell

I’ve been reading with interest Daniel’s coverage of the recent FDA hearings into DTC genetic testing. In this context, both he and Razib Khan are incensed by a video which seemingly shows an FDA official misleading Congress about the research done by 23andme:

You can think what you want about the value of the research done to date by 23andme [1], but in my mind, there’s one simple reason why the sorts of participant-driven research they’re doing can only be a good thing: all research is driven by curiosity, and the people most curious about a disease or trait are those who have it. While people may think of the academic research community as a machine with endless resources and limitless motivation, it’s not. People work on things they think are interesting; they sometimes follow “trendy” topics, or move into fields with more grant money, or get bored of a given problem and move on. So if the research in the trait you’re most interested in isn’t moving fast enough for you, well, tough luck.

Recall that one of the key players in the discovery of the gene for Huntington’s disease was a foundation started by a man whose wife had the disease (startlingly, the current president of the foundation apparently accused DTC companies of “raping” the human genome during the present FDA hearing). Recall also that James Lupski, curious about the cause of his Charcot-Marie-Tooth disease, simply sequenced his own genome to find it. These are simply well-connected and trained people driven to find a gene involved in a disease. Patient communities that currently exist are also curious and driven, but in many cases are dealing with complex diseases that are amenable to genetics only with large sample sizes and extensive organization; what these communities can now do is outsource, in a sense, their research to 23andme (see, eg., 23andme’s Parkinson’s study). For scientific knowledge, this can only be a good thing.

[1] To date, the novel associations discovered by 23andme are in hair morphology, freckling, photic sneeze reflex, and “asparagus anosmia”. What these things have in common is that they’re biologically interesting, but not particularly medically interesting; it’s pretty much only curiosity that would drive you to map these traits. Medical researchers tend to scoff at this sort of thing; I think it’s actually pretty cool.


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A Googol of Genomes?

12/01/2011
Categories: In The News and Technology
Written by Dan Vorhaus

[Editor's Note: this was originally posted over at the Genomics Law Report but we'd like to survey Genomes Unzipped readers as well. How many complete genomes do you think will be sequenced in 2011? Poll is at bottom.]

Earlier this week we took a look back at 2010 and offered our projections for the coming year in personal genomics. Topic #1, just as it was last year: the $1,000 genome.

In hindsight, it might have been ill-advised to offer predictions about the near-term future of genome sequencing during the same week in which one of the year’s major industry conferences (the JP Morgan annual Healthcare Conference) is taking place.

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Saturday Links

23/10/2010
Categories: Friday Links, In The News and Technology
Written by Luke Jostins

Due to a communication breakdown, no-one wrote a Friday Links post yesterday, so today we have a Saturday Links to make up for it.

Steve Hsu has a very appropriately named post, News from the future, about the Beijing Genomics Institute. The BGI is the largest genome sequencing center in China, and one of the largest in the world, and is growing faster than any other, and loading up on a shedload of high-tech HiSeq machines.

Steve reports that the BGI are claiming that their sequencing rate will soon be at 1000 genomes per day, with a cost of about $5k (£3.2k) each. To put a slight downer on these amazing numbers, he clarifies that this might be referring to 10X genomes, which would realistically mean ~300 high quality genomes a day, at $15k (£9.6). Either way, if you want to keep an eye on how fast whole-genome sequencing is progressing, perhaps with an eye to when you’re ready to shell out to get your own done.

A question for the comments: how cheap would a whole-genome sequence have to get before you’d order one?

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Friday Links

15/10/2010
Categories: Friday Links and In The News
Written by Daniel MacArthur and Luke Jostins

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.

Continue reading ‘Friday Links’

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A missed opportunity: what the GAO report could have told us about DTC genetic testing

19/08/2010
Categories: In The News, Law and Regulation and Opinion
Written by Luke Jostins, Katherine Morley, and Daniel MacArthur

The recent United States Government Accountability Office report on direct-to-consumer (DTC) genetic tests was the star attraction of a bruising Congressional hearing into the DTC industry, and sparked widespread headlines about “bogus” results from the genetic testing industry.

The report is prefaced by the statement:

GAO did not conduct a scientific study but instead documented observations that could be made by any consumer.

While it is the GAO’s prerogative to conduct their study as they see fit, we believe that they missed a valuable opportunity to survey the DTC genetic testing industry and systematically evaluate what is and isn’t being done well. In this post, we discuss how the discoveries that the GAO reported were already largely known, and assess the opportunities that the GAO missed to provide genuine insight. What could the data they collected have told us if they had decided to add a little more scientific rigour to their investigation?  

Continue reading ‘A missed opportunity: what the GAO report could have told us about DTC genetic testing’

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The past, present and future of DTC genetic testing regulation

05/08/2010
Categories: In The News and Law and Regulation
Written by Daniel MacArthur

(Newsweek reporter Mary Carmichael has a DNA dilemma: should she buy a direct-to-consumer genetic test? To help answer that question, she’s recruited people with expertise in various areas related to personal genomics – and a diverse range of opinions about the industry – to address specific areas of concern. At the end of the week she’ll announce her decision.

This post is a brief version of Dan Vorhaus’ response to one of Mary’s questions: how should these tests be regulated? Check out the Newsweek website for other answers to the question, as well as a fantastic extended interview with two senior FDA officials. The full version of Dan’s response is now up at Genomics Law Report.

For other Unzipped contributions to Mary’s project, see Jeff Barrett’s post about risk predictions on Tuesday, and my post on test reliability and the balance between knowledge and fear yesterday. –DM)

The regulation of DTC genetic testing has been consistently characterized as confusing, incomplete and irregularly applied. Recent events – Pathway and Walgreens, a bevy of ominous FDA letters, a Congressional Hearing and a GAO report criticizing DTC genetic tests – indicate that the tide may finally be turning. Yet a brief historical review discloses that DTC has actually been down this road before. A GAO report decrying the evils of DTC genetic testing and a subsequent Congressional hearing? 2010 and 2006. Threatening regulatory letters to DTC companies? 2010 and 2008. DTC genetic testing has faced down the specter of heightened regulation before, and over the long term I am confident it will continue to do so.

Nevertheless, in the short term it is possible that DTC genetic testing will be subjected to a substantially more restrictive regulatory framework. Will DTC continue unchanged while regulators and companies engage in protracted negotiations? Will oversight weed out the ‘snake oil salesmen’ and permit legitimate companies to flourish? Or will it drive all genetic testing (temporarily) out of the hands of consumers?

I cannot advise you to take the test or not, but I can say that if you want to proceed there is no time like the present, for there is no guarantee that the option will still be on the table tomorrow.


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