Archive for the 'In The News' Category

Exaggerations and errors in the promotion of genetic ancestry testing

Early_diversification

 

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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Genome interpretation costs will not spiral out of control

Mo' genomes, mo' money?

An article in Genetic Engineering & Biotechnology News argues that as the cost of genome sequencing decreases, the cost of analysing the resulting data will balloon to extraordinary levels. Here is the crux of the argument:

We predict that in the future a large sum of money will be invested in recruiting highly trained and skilled personnel for data handling and downstream analysis. Various physicians, bioinformaticians, biologists, statisticians, geneticists, and scientific researchers will be required for genomic interpretation due to the ever increasing data.

Hence, for cost estimation, it is assumed that at least one bioinformatician (at $75,000), physician (at $110,000), biologist ($72,000), statistician ($70,000), geneticist ($90,000), and a technician ($30,000) will be required for interpretation of one genome. The number of technicians required in the future will decrease as processes are predicted to be automated. Also the bioinformatics software costs will plummet due to the decrease in computing costs as per Moore’s law.

Thus, the cost in 2011 for data handling and downstream processing is $285,000 per genome as compared to $517,000 per genome in 2017. These costs are calculated by tallying salaries of each person involved as well as the software costs.

These numbers would be seriously bad news for the future of genomic medicine, if they were even remotely connected with reality. Fortunately this is not the case. In fact this article (and other alarmist pieces on the “$1000 genome, $1M interpretation” theme) wildly overstate the economic challenges of genomic interpretation.

Since this meme appears to be growing in popularity, it’s worth pointing out why genome analysis costs will go down rather than up over time:
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Identical twins usually do not die from the same thing

Over at Nature News, Erika Check Hayden has a post about a recent Science Translational Medicine paper by Bert Vogelstein and colleages looking at the potential predictive power of genetics. The take-home message from the study (or at least the message that has been taken home by, e.g., this NYT article) is that DNA does not perfectly determine which disease or diseases you may get in the future. This take home message is true, and to me relatively obvious (in the same way that smoking doesn’t perfectly determine lung cancer, or body weight and dietary health doesn’t perfectly determine diabetes status).

A lot of researchers have had a pretty negative reaction to this paper (see Erika’s storify of the twitter coverage). There are lots of legitimate criticism (see Erika’s post for details), but to be honest I suspect that a lot of this is a mixture of indignation and sour grapes that this paper, a not particularly original or particularly well done attempt to answer a question that many other people have answered before, got so much press (including a feature in the NYT). A very large number of people have tried to quantify the potential predictive power of genetics for a number of years – why was there no news feature for me and Jeff, or David Clayton, or Naomi Wray and Peter Visccher, or any of the other large number of stat-gen folks who have been doing exactly these studies for years. ANGER RISING and so forth.

But of course, the reason is relatively obvious. Continue reading ‘Identical twins usually do not die from the same thing’

On bad genetics reporting

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

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

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?

The genome hasn’t failed

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

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.

A Googol of Genomes?

[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.

Continue reading ‘A Googol of Genomes?’

Saturday Links

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?

Continue reading ‘Saturday Links’


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