Author Archive for Daniel MacArthur

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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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Nature poll for scientists on personal genomic analysis

Brendan Maher from Nature has alerted us to a new poll that may well be of interest to many of our readers – an investigation of the attitudes of researchers towards personal genetic testing. Here’s the summary:

We aim to get a sense of how many researchers are actually peering into their own genomes. The responses will be analysed in aggregate to aid in a news story, and no identifying individual information will be used unless you agree to be contacted by a reporter. At the end of the survey you will have the chance to enter our prize draw to win a £100/$150 Amazon gift card.

You can fill in the survey here.

Direct-to-consumer genetic test results in a clinical setting: a case report

Dr Neeta Tailor is an anaesthetist working at the Royal Gwent Hospital in Wales. Dr Tailor recently treated a friend of Genomes Unzipped members (referred to here as Patient X) who required emergency surgery following some unusual and fairly horrible complications (believe me, I’ve seen the photos!) from wisdom tooth removal. The remarkable thing about this case: prior to surgery the patient volunteered information about her potential drug responses based on her 23andMe profile, including variation in one gene that could have had a profound effect on her response to a standard muscle relaxant. Dr Tailor kindly agreed to write up her experience in this guest post.

For those interested in the genetic details: Patient X’s 23andMe results suggest she is heterozygous for the rs1799807 SNP, which induces an aspartate to glycine change in the BCHE gene and is associated with a substantially prolonged apnea (loss of breathing) following administration of succinylcholine. This is one of three separate mutations in the BCHE gene tested by 23andMe. Although in this case the clinicians had already decided independently to avoid the use of succinylcholine, it’s intriguing to think about how rapidly this type of information could become useful to clinicians – and what steps will need to be taken to ensure DTC genetic testing results are trustworthy enough to justify their consideration in this kind of emergency setting. [DM]

Anaesthesia is classically described as the pharmacologically induced triad of amnesia (memory loss), analgesia (pain reduction) and the loss of muscle reflexes. Patients usually come across anaesthetists during their pre-operative anaesthetic assessment; we are the ones telling you that our job is to pop you off to sleep, although it is usually more complicated than that!

The patient described below works in the world of genetics and invited me to describe her case in order to illustrate how pharmacogenomics and person specific genetic characteristics may affect the choice of general anaesthesia.

A 37 year old woman (Patient X) was booked onto the emergency theatre list on a Sunday morning. The planned operation was incision and drainage of an infected haematoma in the cheek, an unusual complication which had developed quickly over 48 hours following the extraction of a wisdom tooth by her own dentist. By the time she was admitted to hospital, she had extensive facial swelling, not just of her gum, but also the whole of the left side of her face from her forehead to her neck. In addition, she had reduced jaw movement, as well as limited mouth opening of less than one finger breadth. She was also feeling quite unwell having vomited during the night and her blood tests showed raised markers of infection. She was in pain requiring several different types of analgesia.

This presentation in itself poses some difficulty. One of our jobs as anaesthetists involves administering drugs to cause unconsciousness which subsequently requires maintenance of a patent airway using either a mask, an airway device that sits above the vocal cords, or by a tube in the trachea. We usually then maintain unconsciousness using an inhaled volatile anaesthetic via the chosen device.

During this operation we knew we were going to need to share the airway with our maxillo-facial surgery colleagues performing the procedure. To ensure the optimal outcome for all (an anaesthetised patient for us and access to the mouth for the maxfax team), a tube in the trachea was the most ideal option. However, to get to the trachea, we have to get in the mouth and get a good view of the vocal cords and this is where the potential problem could arise.
Continue reading ‘Direct-to-consumer genetic test results in a clinical setting: a case report’

Heritability and twins, yet again

Slate’s Brian Palmer has written an astonishingly ignorant critique of the use of twin studies to estimate the heritability of complex traits. Razib has a pithy response, in which he refers to the Slate piece as “a sloppy mishmash”: there’s just so much wrong with the piece (beginning with its first sentence: “One of the main messages of science over the last couple of decades is that genes are destiny”) that it’s hard to know where to start pulling it apart.

Fortunately there’s no need for a point-by-point response here: Luke wrote a lengthy response to another ignorant critique of twin studies late last year, and his cautious defense of the methodology is just as pertinent here. In addition, it’s been reassuring to see that the comments thread at Slate has been almost universally negative.

As Luke noted last year, there are some valid criticisms that can be pointed at twin studies, although none of these fundamentally undermine the value of these studies for understanding human genetics. It’s a shame that Palmer chose to ignore these substantive criticisms in favour of sweeping dismissals and eugenic slurs.

Friday Links: New genes for multiple sclerosis, and a new list of DTC genomics companies

This week sees the publication of a large study of the genetics of multiple sclerosis. A consortium of 23 research groups gathered together data on nearly 10,000 MS suffers, and discovered 29 new genetic variants that contribute to disease risk. Overall, genetic variants for MS can now explain around 20% of the overall heritability of the disease, and these genetic variants highlight pathways that are likely to be important in the disease (such as T-helper-cell differentiation). Notably, this study is published in Nature, which is pretty rare for genome-wide association studies such as this. Perhaps related to this is the wonderful degree of detail included in the figures, such as in the ancestry plots of individuals in the study (see left). It is also surprisingly readable, containing just 4 pages of main article, with the nitty-gritty relegated to 100 pages of supplemental text. [LJ]

The Genetics and Public Policy Center have released an updated version of their list of direct-to-consumer genetic testing companies. You can view the list as a rather user-unfriendly massive PDF matrix of companies versus diseases tested here. The list is certainly not as useful as it could be – for instance, there are no indications of test price or quality, and whole-genome sequencing companies are shown as not testing for any disease, rather than (effectively) testing for all diseases – but it would be a good starting point for a crowd-sourcing project to produce a more comprehensive database. Hmmm… [DM]

Friday Links: peer review discussions, attacks on newborn screening, and Google+

Joe’s post this week on the need for wholesale reform of the current peer-reviewed journal system caused a stir – following links from BoingBoing, Reddit and Hacker News it’s already our second most popular post ever in terms of traffic, and the comments thread currently sits at 86 comments. It’s (unsurprisingly) a topic that aroused passion among scientists, with strong arguments being made both for and against the current system. [DM]

A paper in Nature this week is that rarest of creatures: a high-impact genomics paper with only two authors. Heng Li and Richard Durbin show that the information contained in a single human genome sequence is sufficient to reveal a surprising amount of information about our recent evolutionary history. For the lay summary, Razib Khan has a typically thorough dissection of the paper and its implications. [DM]

Mary Carmichael has a fantastic piece in Nature (free registration required, annoyingly) about a Minnesotan woman who has devoted her life to attacking newborn screening programs. It’s a suitably balanced article: while the anti-screening activists engage in brazen hyperbole against a system that has unquestionably saved many lives, Carmichael doesn’t shirk away from noting that there have also been abuses of privacy. It’s not a debate that will be going away any time soon. [DM]

Colm O’Dushlaine, a scientist at the Broad Institute, has been analysing his 23andMe data in various ways and documenting his methods and results online. If you’re savvy enough to use the Unix command line you’ll find some useful tips for mining your own data. [DM]

Various Genomes Unzipped members have made the transition to Google’s much-discussed new social media platform, Google Plus. You can find Daniel here, Dan here, Joe here, Luke here and Vince here. [DM]

DTC Genetic Testing and the FDA: is there an end in sight to the regulatory uncertainty?

Disclaimer: Genomes Unzipped received 12 free kits from Lumigenix for review purposes, and Dan Vorhaus has provided legal advice to the company. We plan to release a full review of the Lumigenix service in early July.

Last month three direct-to-consumer (DTC) genetic testing companies opened their mailboxes to find a slightly ominous but entirely expected letter from the FDA. The three recipients (LumigenixAmerican International Biotechnology Services and Precision Quality DNA) received substantively equivalent letters, with the FDA warning each company that its genetic testing service “appears to meet the definition of a device as that term is defined in section 201(h) of the Federal Food Drug and Cosmetic Act,” and that the agency would like to meet with company representatives “to discuss whether the service [they] are promoting requires review by FDA and what information [they] would need to submit in order for [their] product to be legally marketed.”

Translated from bureaucratese, that means that the FDA views these services as ones that may need to be formally reviewed by the agency and either approved or cleared before they can be legally sold. The FDA letter asks each company to describe its service and to explain either (1) why it does not require FDA approval or (2) how the company plans to pursue such approval.

This is a strategy that the FDA has pursued with a growing cadre of DTC service providers. These letters (currently 23 and counting1) represent the only public and company-specific actions the agency has taken to date with respect to DTC genetic testing. While many DTC letter recipients are engaged in dialogue with the FDA, those conversations have occurred beyond the public’s view. Until now.

Continue reading ‘DTC Genetic Testing and the FDA: is there an end in sight to the regulatory uncertainty?’

Interpretome: new online tools for analysing personal genome data

Konrad Karczewski and colleagues from Stanford have put together a very handy set of online tools for analysing personal genomic data. The tools work within your browser (Chrome and FireFox only, so the ~18% of you who continue to use Internet Explorer now have yet another incentive to change), meaning your genetic data never actually leaves your computer. They currently work with raw, unzipped data from 23andMe and Lumigenix. The tools were developed initially for use in Stanford’s pioneering Genomics and Personalized Medicine elective course for graduate and medical students, in which students had the opportunity to explore their own 23andMe or Lumigenix data. Karczewski has some background over at his personal blog.

Once you’ve pointed Interpretome to your raw data file (top right-hand corner) and assigned your ancestry you can start playing with the tools – for instance, you can calculate your type 2 diabetes risk or warfarin dose, or estimate the fraction of your genome inherited from Neandertal (see image above for my result). A caveat: I’m writing this post without carefully checking the output from any of these analyses, so as always in personal genomics, interpret your results with caution.

I suspect one of the more popular suites of tools will be the PCA package, which allow you to place your genetic data in the context of worldwide patterns of genetic variation. Here the authors have pre-calculated the crucial information (the PCA loadings) for each SNP in the 23andMe data-set, allowing them to very quickly calculate your position in a worldwide genetic map containing thousands of individuals. Here’s my 23andMe v3 data (black square) projected onto a genetic map of Europe created with POPRES samples. The picture isn’t quite as pretty as the one in the 2008 Nature paper using the same cohort – the Interpretome team haven’t applied the same extensive filters to remove extraneous features from the data have had to work with the smaller number of SNPs that overlap with the 23andMe v3 chip, and you need to plot PC1 vs PC4 before you start seeing something that resembles a map of Europe – but it’s enough to give you a sense as to where you fit. I was unsurprised to find myself sitting smack in the middle of the British cluster:

Anyway, go and check it out, and send it to your friends. We’re delighted to see such a handy package released free to the public – kudos to everyone involved in putting the website together. We’ll likely be posting a more thorough review of the site once we’ve had time to test the tools out on a range of Genomes Unzipped data-sets.

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:

Continue reading ‘The genome hasn’t failed’

Happy DNA Day! Here’s your Alzheimer’s risk

Friday Links is a roughly weekly collection of interesting genomics-related links scraped from the interwebs by Genomes Unzipped contributors.

Happy DNA Day! Cambridge members of Genomes Unzipped will be celebrating this evening in traditional British style with a beer or two at The Eagle, the pub in which Francis Crick famously interrupted the lunches of fellow customers to announce that he and James Watson had “discovered the secret of life” (actually the structure of deoxyribonucleic acid, but close enough).

Others are rejoicing in their own way. New York-based “brick artist” Nathan Sawaya, for instance, has built a massive sculpture of the the double-helical model out of LEGO bricks (left). [DM]

23andMe announced yesterday that it will now be releasing information on Alzheimer’s disease risk markers in the APOE gene to customers who purchased their recently upgraded v3 test. The APOE markers are famously associated with a major increase in risk for late-onset Alzheimer’s, with individuals carrying two copies of the ε4 version of the gene being around 15 11 times more likely than average to develop the disease. Customers who have been tested on the v3 platform will be able to able to access their APOE status after “unlocking” it; customers on earlier versions of the test will need to upgrade to get access. You can see screenshots of the unlocking and results pages here. [DM]

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