Archive for the 'Opinion' Category

Why publish science in peer-reviewed journals?

The recent announcement of a new journal sponsored by the Howard Hughes Medical Institute, the Max Planck Society, and the Wellcome Trust generated a bit of discussion about the issues in the scientific publishing process it is designed to address—arbitrary editorial decisions, slow and unhelpful peer review, and so on. Left unanswered, however, is a more fundamental question: why do we publish scientific articles in peer-reviewed journals to begin with? What value does the existence of these journals add? In this post, I will argue that cutting journals out of scientific publishing to a large extent would be unconditionally a good thing, and that the only thing keeping this from happening is the absence of a “killer app”.

Google Scholar in 2015?

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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.

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My Genome Online – A Challenge To You

[Editor's Note: This guest post is contributed by Blaine Bettinger. Blaine is the author of The Genetic Genealogist, a blog that examines the intersection of genetics and ancestry, and a patent attorney at Bond, Schoeneck & King in Syracuse, NY.]

As you may have heard, I recently made my 23andMe and Family Tree DNA autosomal testing results available for download online at “mygenotype,” and dedicated the information to the public domain (if dedicating DNA sequence to the public domain is even possible – I’m currently doing some research in this area and expect to write more in the future). [Editor's Note: see additional comments on personal genomics data in the public domain at the end of this post.]

At “mygenotype” you can download the following:

My Family Tree DNA Results:

  1. Affymetrix Autosomal DNA Results (2010)
  2. Affymetrix X-Chromosome DNA Results (2010)
  3. Illumina Autosomal DNA Results (2011)
  4. Illumina X-Chromosome DNA Results (2011)

My 23andMe Results:

  1. V2 Results (2008)
  2. V3 Results (2010)
  3. Y-DNA Results (2010)
  4. mtDNA Results (2010)

You can also find my SNPedia Promethease reports:

In addition to my genome, Razib Khan of Gene Expression has a spreadsheet of approximately 48 other genomes that are available for download online.

A Challenge To YOU

Now that the information is out there, available to anyone who might be interested, it remains to be seen who might be interested in the information.

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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.

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.

Are synthetic associations a man-made phenomenon?

Early last year David Goldstein and colleagues published a provocative paper claiming that many GWAS associations are driven not by common variants of modest effect (the canonical common disease – common variant hypothesis underpinning GWAS) but instead by a local cluster of lower frequency  variants that have much bigger effects on disease risk. They dubbed this hypothesized phenomenon “synthetic association” and the term quickly became a genetics buzzword. The paper was widely discussed in both the specialist and mainstream media, and caused quite a stir among academic statistical geneticists.

That debate has been re-opened today by a set of Perspectives in PLoS Biology: a rebuttal by us (Carl & Jeff) and our colleagues at Sanger, a rebuttal by Naomi Wray, Shaun Purcell and Peter Visscher, a rebuttal to the rebuttals by David Goldstein and an editorial by Robert Shields to tie it all together.

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Getting Serious About Personal Genomics’ Risks

When we launched Genomes Unzipped three months ago, we promised a focus on the “budding industry of personal genomics.” Recent developments, however, have demonstrated that this emerging field is susceptible to critics who may be more focused on generating controversy than in engaging in a thoughtful discussion about the balance of risks and benefits in personal genomics. The University of California Berkeley’s short-lived proposal to provide a voluntary and educational genetic testing program for its incoming freshman class highlight this concern.

Over at the Genomics Law Report, in Getting Serious About Personal Genomics’ Risks, I review the Berkeley example and argue that we must carefully examine where and why we restrict the ability of individuals to participate in personal genomics. The failure to do so threatens not only the future of personal genomics but the autonomy of the individuals involved.

For more, please see the complete post at the Genomics Law Report.

Excessive regulation of DTC genomics will come at a cost

Caroline and I have an opinion piece in this week’s New Scientist arguing that regulators should consider the benefits of personal genomics (in terms of increasing genetic literacy and innovation) before imposing excessive regulation on the direct-to-consumer genetic testing industry. Here’s the take-home message:

We don’t yet know what role personal genomics will play in the future of medicine. However, we do know that it has great potential for innovation and education, and we must ensure that neither excessive regulation nor medical paternalism get in the way.

Unfortunately due to space restrictions several sections of our argument were cut – for instance, we spent some time arguing against the idea of arbitrary divisions of tests into “medical” and “non-medical” categories, with the former requiring supervision of a medical professional to receive results. Here’s the original wording:

Unlike many commentators, including the HGC, we do not support an unsustainable division of tests into separate categories, one for health-related tests that require counselling from a medical professional and another for everything else with no such requirement. It is hard to justify the argument that results suggesting a mildly elevated predisposition to obesity require a professional intermediary to provide support, while those indicating unexpected paternity do not.

In general, we would argue that people should be free to access their own genetic data unless there is good reason to believe that doing so will cause them real harm – and as long as the information is accurate and transparent. Companies should ensure that customers have access to expert advice if they want it, but medical supervision should not be a requirement for access to your own genome.

In a similar vein, if you missed the editorial on DTC genetics in last week’s Economist, you should go read it now. The final two paragraphs warrant quoting in full:

But three things argue against wholesale regulation. First, the level of interference needs to be based on the level of risk a test represents. The government does not need to be involved if someone decides to trace his ancestry or discover what type of earwax he has. Second, the laws on fraud should be sufficient to deal with the snake-oil salesmen who promise to predict, say, whether a child might be a sporting champion. And third, science is changing very fast. Fairly soon, a customer’s whole genome will be sequenced, not merely the parts thought to be medically relevant that the testing companies now concentrate on, and he will then be able to crank the results through open-source interpretation software downloadable from anywhere on the planet. That will create problems, but the only way to stop that happening would be to make it illegal for someone to have his genome sequenced—and nobody is seriously suggesting that illiberal restriction.

Instead, then, of reacting in a hostile fashion to the trend for people to take genetic tests, governments should be asking themselves how they can make best use of this new source of information. Restricting access to tests that inform people about bad reactions to drugs could do harm. The real question is not who controls access, but how to minimise the risks and maximise the rewards of a useful revolution.

It’s great to see these issues getting sensible discussion in the wider media; let’s hope the FDA is paying attention.

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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Should you trust a genome scan?

(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 my response to one of Mary’s questions: How does she know if she can trust the results, and should she be scared of what she might find out? A summary is also posted on the Newsweek website along with answers from Thomas Goetz, Hank Greely, Robert Green and Misha Angrist.

Genomes Unzipped is well-represented in Mary’s project: Jeff Barrett wrote about risk predictions yesterday, and tomorrow our resident legal expert Dan Vorhaus will be discussing the present and future state of regulation of the DTC genetic industry.)

The results you receive from genetic testing companies rely on two critical steps: firstly, the generation of your raw genetic data; and secondly, the interpretation of that data into information about your ancestry, family and disease risk.

For reputable genetic testing companies – and I would count the four major personal genomics companies (23andMe, deCODEme, Navigenics and Pathway Genomics) in this category – the first step is generally extremely accurate. These companies rely on the same technology used by academic researchers studying the genetic basis of human disease, applied in carefully quality-controlled labs, so their error rate is typically very low. As an illustration, I recently had an opportunity to compare the raw genetic data provided by two companies to Times journalist Mark Henderson, and found an error rate per company of around one in every 14,000 data points: that’s far better than most routine clinical tests.
Continue reading ‘Should you trust a genome scan?’


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