Author Archive for Daniel MacArthur

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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]

Using 23andMe to confirm identical twinnery, and a chance to tell the FDA what you think about DTC genetics

Over at Daily Kos, Michael Convente shares a fascinating story of using 23andMe data to pin down the precise relationship he has with his twin brother Matt. When Mike and Matt were born, the obstetrician told their mother that the presence of two separate placentas indicated that the brothers were non-identical (fraternal) twins – yet their incredibly similar appearance while growing up (see photo on left) suggested otherwise. Testing with 23andMe confirmed what the brothers had always suspected: that they are in fact identical twins. This is a useful reminder of the non-medical value of accessible genetic information: when it comes to unravelling these kinds of family mysteries, direct access to large-scale genetic data can be a powerful tool. [DM]

Readers who care about access to genetic information (i.e. all of you) and who are concerned about the potential effects of regulation on this access and on innovation in the field in general will soon have an opportunity to make their voices heard. Thanks to the efforts of Dan Vorhaus and others, the FDA has agreed to reopen the opportunity for public submissions while it deliberates on its next move following the agency-sponsored meeting on direct-to-consumer genetics last month. The submissions docket is apparently due to reopen today, and will remain open to submissions until the 2nd of May – so you all have a month to get your opinions in there. You’ll hear more from us about the process of submitting to the docket over the next week or so. [DM]

On a related note, genetic counsellor Christine Patch and academic (and Unzipped guest blogger) Barbara Prainsack have penned a response to the above-mentioned FDA meeting for BioNews. Patch and Prainsack provide a welcome note of nuance to the discussion; their final two paragraphs are worth quoting in full:
Continue reading ‘Using 23andMe to confirm identical twinnery, and a chance to tell the FDA what you think about DTC genetics’

‘Disguised’ heritability, changes ahead to marketing of personal genomics, deciphering developmental disorders

Even though genome-wide association studies (GWAS) have identified many loci associated with complex disease, much disease heritability is still unexplained, or “missing”. But what if rather than being missing, some of the heritability was “disguised”. This is the term put forward by Chris Spencer and collegues to describe the proportion of heritability that we miss because SNPs (imperfectly) correlated to the causal variant (“tag SNPs”) are used to estimate explained heritability rather than causal variants themselves. Reassuringly, their simulations show that for the vast majority of loci detected via GWAS the risk estimated from the best tag SNP is very close to the truth. They also show that, occasionally, fine mapping of GWAS loci will identify causal variants with considerably higher risk and this is more likely if the true effect of the locus is large. The figure above, taken from their paper, shows that for estimated relative risks in the range 1.2–1.3, there is approximately a 38% chance that the true relative risk exceeds 1.4 and a 10% chance that it is over 2. The consequence of all of this for personal genomics is that disease risk could be much greater than currently thought for those individuals who, for a given disease, carry a large number of common risk variants. [CAA]

Continue reading ‘‘Disguised’ heritability, changes ahead to marketing of personal genomics, deciphering developmental disorders’

People Have A Right To Access Their Own Genetic Information

This week has seen another FDA meeting seeking guidance on how to regulate direct-to-consumer (DTC) genetic tests in the US. The meeting itself has been covered by GNZ bloggers Daniel at Genetic Future and Dan at Genomics Law Report, and its apparent outcome has sparked furious debate elsewhere. The discussion among the “independent” panel convened at the meeting appeared to converge on the proposal that all health-related genomic tests should be ordered and reported through physicians. However, the outcomes of the meeting in terms of FDA policy remain unclear, and one FDA official has indicated that decisions about the availability of genetic tests will be made on a test-by-test basis.

There is no doubt that the appropriate regulation of personal genomics tests is a complex issue, and there is a diversity of opinion about how best to achieve it within GNZ (as there is throughout the genomics community). However, there are several points we agree on:

  • Individuals have a fundamental right to access information about themselves, including genetic information. While it is important to also consider the accuracy, interpretation, validity and utility of tests, this underlying principle should guide policy.
  • There is currently no evidence that DTC genetic tests pose a danger to consumers. A recent study of over 2,000 participants in DTC testing concluded that “testing did not result in any measurable short-term changes in psychological health”. In the absence of any evidence of harm there is no justification for restricting individual autonomy.
  • DNA does not have magical powers, and does not require special treatment simply by virtue of being DNA. Genetic exceptionalism – the idea that genetics must be treated as special under the law – is an inappropriate basis for policy-making. Tests should be regulated appropriately based on their predictive power, utility and potential for harm, all of which are related concepts.
  • As DNA sequencing becomes cheaper, the line between medical and non-medical testing will continue to blur. Excessive regulation of health-related genetic tests could also unncessarily hinder the ability of people to access their entire genome sequences for other purposes (such as genetic genealogy).
  • Most clinicians do not have the appropriate knowledge to interpret genomic tests, particularly in healthy individuals. This point is almost universally agreed, even by the FDA, and has certainly been the experience of some of the GNZ members upon taking our genetic results to doctors. Physicians in general are therefore a strange choice for ‘guardians of the genome’.
  • Most early adopters of DTC genetic tests are sufficiently well-informed to understand the implications of a genomic test and interpret the results correctly. Putting a general physician between these informed individuals and their own genomes is paternalistic and unnecessary.

While the outcome of the FDA’s deliberations remain uncertain, it is clear that there will be intensive lobbying against any attempt at excessive legislation. In the worst case scenario, the fledgling and innovative personal genomics market could be crushed by the FDA. However, there is still plenty of room for a measured approach that enforces test accuracy, punishes false claims and promotes informed choices by consumers, without reducing the ability of responsible companies to continue to operate and innovate.

We urge others in the genomics community to make their voices heard on these issues. Let the FDA – and, if you’re based in the USA, your political representatives – know that regulation of genetic testing should be based on evidence, not fear, and that any attempt to unreasonably restrict your access to your own genetic information is unacceptable.


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