Tag Archive for 'regulation'

Cracking non-coding variation, carrying cystic fibrosis, and more Alzheimer’s prediction

Daniel and Luke attended the Biology of Genomes conference at Cold Spring Harbour last week. The talks did not have a huge amount of direct relevance to personal genomics, but did show some real quantum leaps in understanding the function of the non-coding DNA that makes up most of our genomes. Understanding mutations that lie outside of coding DNA is largely a prerequisite for transitioning to whole-genome sequencing for personal genomics, as most of the variation that drives genetic differences between people appears to lie there. As we’ve said before, one of the powerful aspects of sequencing is that it allows you to get at the aspects of your DNA that are unique to you, but that is only really useful (and a lot cooler) if we know what this unique variation does. Biology of Genomes showed us that that dream is closer now than it has ever been before.

For a (somewhat technical) account of some of the conference talks, you can read Luke’s blog posts over at Genetic Inference (along with a signficiantly less technical post about chipmunks and wood cabins), and Matthew Herper has a lay-friendly post on his Forbes blog. As has become standard, Twitter was an important way of disseminating knowledge live during talks, and Keith Bradnam and EpiExperts wrote about this aspect. [LJ]

Since GNZ started, Luke has actually been holding back writing about his many and varied genomics woes, and his resulting quest for bodily health, mostly for lack of time. However, one part of this has leaked out somewhat: he has recently given an interview to fellow blogger Elaine Westwick about being one of the two cystic fibrosis carriers in Genomes Unzipped. Read the interview at Elaine’s blog The Stuff of Life. [LJ]

On a similar subject to our recent post about calculating Alzheimer’s risk, over at Genomics Law Report Dan has written a detailed post about the regulatory challenges ahead for both direct-to-consumer and clinical tests for Alzheimer’s. [LJ]

Last chance to submit comments to the FDA about DTC genetics

Today is the last day to submit comments to the FDA about the future of regulation of direct-to-consumer genetic testing, and, by extension, the future of personal genomics. I would strongly urge anyone reading this blog to submit a comment; the FDA needs to hear the full diversity of opinions and facts on this subject to make an informed decision.

Have you or your family taken a DTC genetic test, and can explain your experiences, either positive or negative? Are you a scientist working on human genetics and have thoughts about the scientific merits of the tests? Are you a clinician, and have insights into how individual’s having direct access to their own genetic information will effect your practice? Are you an ethicist, social scientist or public health professional with opinions about the rights of individuals to access their genetic data, or the impacts such access will have on society or public health? Write a hundred words or so and submit them to the FDA.

You can submit comments via this form; remember, today is the last day before comments close. You can see the comments that have already been submitted here.

For more coverage on this round of comments, see posts by Dan, Daniel and Razib. You may also like to reread our consensus statement about the FDA’s recent investigations.

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:
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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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Friday Links

Two exciting-looking new science blogging collectives have been announced this week. The Public Library of Science launched a new blogging collective, including personal genomics blogger Misha Angrist, and the Guardian newspaper has launched its Guardian Science Blogs network, including Dr Evan Harris, ex-MP for Oxford West and long time supporter of the role of science in public policy. I’m pretty excited about these new blogs, but it does stand to increase my RSS load significantly. [LJ]

In this month’s issue of European Journal of Human Genetics, Yang, Visscher and Wray contribute to the discussion around the aetiology of common complex diseases.  They demonstrate that the existence of a large number of sporadic cases (instances where a patient has no first, second, or third-degree relatives with the disease) is not incompatible with a polygenic model of disease.  A little less hot-off-the-press are two opinion pieces on genetic testing regulation from the August issue of Nature.  Arthur Beaudet argues that stringent government regulation should be applied to genotyping/sequencing, and interpretation should be the exclusive domain of the medical profession.  Gail Javitt takes a different view, arguing that genetic tests to be treated in the same way as other medical tests and that the level of regulation imposed should be determined by medical relevance of the outcome. [KIM]

Finally, Procreation News; our very own Daniel MacArthur and Ilana Fisher have recently given birth to a baby boy (the picture to the left may be a little out of date). Daniel made the announcement on Twitter, and also had this to say:

After careful inspection, I’ve decided that my six-day-old son is the most remarkable human being to have ever lived.

Due to double blinding, neither we nor Daniel know whether he has an actual or placebo baby, so we can’t yet assess the significance of this claim. Watch this space! [LJ]

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

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?  

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Regulation of personal genomics: what next?

(Dan Vorhaus’ comment on a previous post recaps a number of key issues discussed during Regulation Week here at Genomes Unzipped, so I’ve promoted it to be the final post of the week – and the final post, for the moment, on the regulation of the direct-to-consumer genetic testing industry. These are questions we all – and especially the FDA – need to consider carefully over the next few weeks. Next week we’ll be getting back to the science, at least until the next regulatory scuffle emerges. DM)

1) Wait and Talk. On the topic of “don’t knock it until we see it,” while I think Jeff and Kate’s point is well-taken, I would also suggest that it is incumbent upon the regulated community – which includes companies, investors, customers and even clinicians – to speak up about what does and does not make sense when it comes to a regulatory solution. The FDA’s public conversation was part of that process, but that was (a) not directed specifically at the regulation of DTC testing and (b) should mark the beginning, not the end, of the dialogue. There are still a number of options on the table, and not all of them are equal. Waiting passively for regulators to act may not be the best strategy.

2) Line-Drawing. It’s clear that whatever regulatory system emerges – and this applies to the much broader category of lab-developed tests (LDTs), as well as to DTCs – the issue that Caroline, Misha and so many others have identified is going to be one of, if not the, most difficult to solve: what counts as a medical interpretation worthy of heightened regulatory scrutiny?

Regulating all genomic interpretations is incompatible with providing broad access to genomic information, since only a handful of people can interpret the raw data on their own (and I’m certainly not one of them). But determining where to draw that line, particularly given the interconnectedness of gene-trait associations and the rapid rate of change in the science (both discussed in this comments thread), is going to be fiendishly difficult. The key will be to come up with some standard-setting body that strikes the proper balance between involving stakeholders (this is an issue that should not be determined by the FDA – or any other agency – acting on its own) and minimizing the number of voices so that the body is nimble enough to respond to changes in the science. I’m not sure there are any perfect solutions here.

2a) Useful to Whom? A sub-point here is whether that line-drawing incorporates (i) analytical validity, (ii) clinical validity and/or (iii) clinical utility. I think that there is widespread agreement on (i), a general agreement that (ii) is important, although no clear agreement on how to assess it, and very little agreement about whether (iii) is appropriate. The issue of clinical utility gets at one of the core tensions here: is my genomic information useful when I say it is useful, or only when my doctor (or some standard-setting body) says it is useful?

3) What is special about DTC? When it comes to the regulation of DTC genetic tests – as a subset of all other genetic tests – I think we (and regulators) need to be much clearer than at present in explaining where, exactly, the concern lies. Is it that individuals are being misled by untrustworthy businesses? If so, then the Federal Trade Commission (or possibly the FDA acting in a similar role; the Genomics and Personalized Medicine Act would have the two agencies work together) has a clear role to play. Is it that genetic tests are not appropriately evaluated beyond analytical validity? If so, then it’s not clear that DTC tests should be regulated differently than the broader category of LDTs. Or is that individuals cannot be trusted to appropriately handle certain types of genetic information and interpretations? If so, then it may be that certain types of information simply cannot be presented directly to consumers, although then we return immediately to the line-drawing problem discussed above.

It is insufficient to know that the FDA intends to regulate DTC genetic tests (as they clearly do); what is needed is a clearer explanation as to whether, why and how DTC genetic tests are to be regulated differently from other types of tests.

4) Transparency First. Finally, I can only echo Daniel’s comment that, no matter what, there is a need for greater transparency. By this I think we both mean a more proactive approach to data collection (i.e., what genetic tests are available, how they are marketed, how they are used by individuals and what impact – positive or negative – they have on end users, both with respect to and apart from influencing medical decisions) and greater regulatory openness. Without such transparency it is difficult to see how any government entity can expect to craft a regulatory framework that strikes the proper balance between the protection of the public and the preservation of innovation and long-term growth in the area of genetic testing and personalized medicine.

Is industry best practice in DTC genetics good enough?

(It looks like this has become Regulation Week here on Genomes Unzipped; Daniel’s initial post sparked a ferocious comments thread, and follow-up posts from Caroline, Dan V and Jeff and Kate continue to add fuel to the discussion. We have one more post on regulation to come to round off the week, before next week returning to our regular, more balanced schedule of posts.)

It’s becoming clear that the arguments with regards to direct-to-consumer (DTC) genetics here aren’t really about regulation per se; I doubt anyone wants to see companies be allowed to make any claims they wish without requiring accuracy or consumer protection. So what exactly are we arguing about?

There are a set of arguments that essentially come down to how one trusts the FDA to act rationally and in everyone’s best interests: some people point to recent statements from FDA officials as evidence that they will apply overly strict regulation, or regulation that requires implausible amounts of money and effort to comply with; others point to the American government’s strong tradition of supporting business, and assume that cooler heads will prevail when it actually comes to making policy. These are arguments about the FDA specifically, and the American legal and legislative system in general, that only one of the Genomes Unzipped contributors has a strong background in.

Beyond specific questions about the actions of the FDA, discussions in the comments here and elsewhere appear have brough up two differing viewpoints about what DTC regulation should look like. One viewpoint (e.g. Daniel MacArthur’s) proposes a Trade Standards/consumer protection type regulatory mechanism; ensuring technical accuracy, associations and health claims based on well-supported scientific evidence, and a lack of misleading or confusing claims or presentation. The other suggests that we need to go further, and proposes something more akin to the regulation of medical practice; some combination of proven clinical utility, proven lack of significant clinical harm, direct supervision by a trained medical professional and high standards of informed consent.

Continue reading ‘Is industry best practice in DTC genetics good enough?’

If you’re predicting disease, you should be regulated

Last week’s Congressional hearings on the direct-to-consumer genetics industry (featuring a provocative GAO report based on covertly recorded phone calls made to major DTC companies) have spurred plenty of discussion, including Daniel MacArthur’s post here at Genomes Unzipped and Dan Vorhaus’ post at Genomics Law Report.

But we disagree with some other Genomes Unzipped members about the regulatory future of the industry, and in particular we believe that medical interpretation of genetic data should be regulated.

Continue reading ‘If you’re predicting disease, you should be regulated’

Personal genomics: a voyage of exploration

The last few months have seen the brave new world of personal genomics thrown into a state of turmoil, as the might of US federal regulators turns on this fledgling industry. There is no question that some level of regulation would be welcomed, to iron out the irregularities and squeeze out the fraudsters. But hidden somewhere in amongst the hype and the scaremongering are some real gems that we should not abandon lightly. Take note, please, Mr Regulator.

Some of the recent crop of consumer genomics companies are true innovators, pioneers attempting to navigate the treacherous complexities of modern human genetics. Their attempts at presenting complicated genomic and risk information in an accessible form have been exemplary. Is the information useful? For the most part, no. Is it harmful? Again, so far the answer is a resounding no. So what’s the problem? Speaking to numerous individuals who have had their genomes scanned reveals that most are notably under-whelmed by the experience – they didn’t learn much of direct use, and they haven’t changed their lifestyles. But individuals are free to chose to purchase these tests, or not, and to decide for themselves whether it is worth parting with their hard-earned cash.

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