Pre-Pregnancy Genetic Testing

Posted on September 27, 2010 by

A California company called Counsyl Inc. is the latest contender in the effort to push genetic testing into the consumer mainstream.

See this story, by Michael Totty for the WSJ: A Genetic Test for Prospective Parents

Proponents of universal prepregnancy genetic screening make a bold claim: If these tests were widely available, they could significantly reduce, and possibly eliminate, hereditary diseases. Parents who discovered that they carried the genes that would put their children at risk for these diseases could pursue other alternatives—adoption or in vitro fertilization, for example. Widespread screening also could reduce infant mortality; 20% to 30% of infant deaths are caused by genetic illnesses.
…
Counsyl, based in Redwood City, Calif., has devised a single test that covers more than 100 genetic disorders, including Tay-Sachs, cystic fibrosis and spinal muscular atrophy. The saliva-based test costs about $350….

A few points worth noting:

1) Counsyl is no fly-by-night operation. According to the WSJ story, their lab “received regulatory approval in the U.S. in the spring of 2009.”

2) The pricing for Counsyl’s test (even if customers choose not to submit an insurance claim) is well within reach for millions of concerned middle-class parents. In terms of finding a market for genetic tests, this seems like a bit of a breakthrough.

3) As with most genetic tests (and many other kinds of tests), the big question for consumers remains: what should I do with this new knowledge? The company’s FAQ says that their tests “are intended to be easily understood by non-scientists”, and that they offer free genetic counselling by phone or email. But that won’t necessarily tell parents what they should do — IVF? adoption? take a chance? — in the face of new information about the risks they face.

Posted in embryos, ethics, genetic testing, IVF, risk | Leave a comment

No Decision About GM Salmon

Posted on September 25, 2010 by

Given the controversy over AquaBounty’s GM salmon, I can only assume this headline is sarcastic:

By Kim Carollo, for ABC News, Surprise: FDA Panel Unable to Reach Conclusion on Genetically Modified Salmon

After two days of hearings, several members of an 11-member advisory panel of the U.S. Food and Drug Administration found that there are not yet sufficient data to determine that a genetic modification that enables salmon to grow twice as quickly is safe for the affected fish or for consumers.

The panel, made up of outside experts, did not vote or make a recommendation on whether to approve these fish for human consumption….

Most of what’s in the story (other than the non-decision itself) is not new, and will be familiar to everyone who has been following this story.

It’s worth mentioning that this story gives just a hint at the complexity of the FDA’s decision-making process, which includes at least the following:

  • The Commissioner (currently Dr. Margaret A. Hamburg);
  • The panel of outside experts, charged with making a recommendation to the Commissioner;
  • Staff scientists (who produced the report submitted to the panel)
  • Scientists for AquaBounty, who generated data to submit to the FDA;

And then, of course, there’s the public commentary process — a process which critics have said was inadequate, in this case.

As I’ve noted elsewhere, there’s plenty of criticism out there regarding the effectiveness of the FDA in general (see How Good (or Bad) is the FDA?). One of the key worries has been about political and corporate interference. Understanding the key contributors to a regulatory decision — including the key pieces of the FDA’s own process — is crucial to figuring out a) just how good (or bad) the FDA is at its job, and b) how to make the process better.

Posted in ethics, GMO, regulation | 3 Comments

Allowing / Permitting / Forbidding GMO Labels

Posted on September 20, 2010 by

OK, so the FDA seems unlikely to require the probably-soon-to-be-approved GM salmon to be labelled. See this story by Lyndsey Layton, for the Washington Post: FDA rules won’t require labeling of genetically modified salmon

…As the Food and Drug Administration considers whether to approve genetically modified salmon, one thing seems certain: Shoppers staring at fillets in the seafood department will find it tough to pick out the conventional fish from the one created with genes from another species.

Despite a growing public demand for more information about how food is produced, that won’t happen with the salmon because of idiosyncracies embedded in federal regulations.

The FDA says it cannot require a label on the genetically modified food once it determines that the altered fish is not “materially” different from other salmon – something agency scientists have said is true….

But apparently the FDA “not requiring” labelling is easily mistaken for “not permitting” labelling. See, for instance, this story from Raw Story: FDA won’t allow food to be labeled free of genetic modification: report. As far as I can tell, the Raw Story just gets it wrong. According to the Washington Post story (which Raw Story cites)…

The agency allows manufacturers to label their products as not genetically engineered as long as those labels are accurate and do not imply that the products are therefore more healthful.

Now, it’s true that the FDA doesn’t permit misleading forms of labelling. And so (for example) the Washington Post story points out that the FDA has reprimanded food companies that have been sloppy in their use of various sorts of “GM-Free” labels. But that’s only fair. I am strongly in favour of permitting clear and accurate voluntary labelling, but that labelling must be done in such a way that it actually informs consumers — all kinds of consumers — rather than confusing them further.

Posted in Uncategorized | 3 Comments

GM Rice and Intellectual Property

Posted on September 15, 2010 by

Are GM crops aimed at helping farmers, or corporate shareholders? Generalizing in that regard is probably a mistake.

See, for instance, this story from The Sydney Morning Herald, Group produces GM rice

A team of Australian scientists has genetically modified rice to improve its tolerance to salt, offering hope of increased global production.

And work is already underway to transfer the technology to wheat and barley, other staple foods for billions of people around the world….

One interesting aspect of this project is the issue of intellectual property protection — in particular, because there is none. Notice that the story cited above doesn’t mention the word “patent,” which I thought a bit odd. Patents — an important form of intellectual property protection — are often thought essential to the research-and-development process. So, I contacted the Australian Centre for Plant Functional Genomics and got clarification. According to the ACPFG, there is no legal protection for this technology: it’s being developed as a public good.

This is important, for a couple of reasons. The first is practical. The lack of a patent means that the technology will in principle be available to anyone who wants to use it. If seeds end up being produced (and if the crop passes the relevant regulatory hurdles), they can be planted (and harvested and replanted) by anyone. The lack of patent also means that other scientists can more easily study, replicate, and build on this development.

The second reason the lack of patent protection is important is rhetorical: critics of the genetic modification often claim that GM is only going to help big corporations like Monsanto, whose gene patents are zealously guarded by their well-paid lawyers. And that certainly has been the experience that has dominated the landscape (no pun intended) thus far. But it doesn’t have to be the case. Plenty of research on genetic modification is done by publicly-minded researchers at public institutions. And (especially as the cost of genetic research drops) there’s no reason the result has to be a commercialization deal with a major company.

Posted in genes, GMO, patents | 2 Comments

Oil-Eating Microbes

Posted on August 25, 2010 by

Most people probably don’t know that there are naturally-occurring microbes that make their living by eating naturally-occurring hydrocarbons (hydrocarbons are organic compounds that consist entirely of hydrogen and carbon, and that are found in crude oil). The existence of such microbes are good news, in the context of a major oil spill like the one that recently contaminated the Gulf Coast.

By David Biello, for Scientific American: How Fast Can Microbes Clean Up the Gulf Oil Spill?

These are boom times for oil-eating microbes in the deep waters of the Gulf of Mexico, thanks to BP’s Deepwater Horizon accident that has added some 600 million liters of hydrocarbons to those waters. And now research published online in Science on August 24 shows that an array of new and unclassified oil-eating bacteria are feasting on the newly rich resource of hydrocarbons.

Interestingly, the story makes little mention of biotechnology — basically none at all, except to note that the scientists currently studying the microbes munching away at the Gulf Coast spill are from the Energy Biosciences Institute. The omission is interesting, given that a bunch of work has been done on genetically engineering microbes to boost their oil-eating powers.

Posted in environment, genes, industrial biotechnology, risk | 2 Comments

Imitating Evolution

Posted on August 25, 2010 by

Someone (I can’t recall the source) once said that rather than envy the creative power of nature, we ought to emulate it. Genetic algorithms have, for a couple of decades now, allowed scientists and engineers to harness the power of evolutionary processes to evolve (literally) new solutions to hard problems in silico. A new technology developed by George Church at Harvard seems aimed at allowing scientists to do the same thing in vitro.

Here’s the story, by Arielle Fridson, writing for Bloomberg: Harvard Scientists Speed Up Evolution, Aim to Sell Technology to DuPont

Evolution often plays out over millennia. George Church says he can make it happen in days.

He and his team of researchers at Harvard Medical School in Boston invented a table-top machine that can generate multiple changes in the DNA of bacteria all at once, speeding up the evolutionary process. Aiming to sell the technology for use in chemicals, energy, and the drug industry, they’re talking with DuPont Co. and other companies, members of the team said….

This of course is pretty much the exact opposite of the kind of genetic engineering that makes use of careful insertion of genes with known functions. It allows a kind of generate-and-test procedure: generate a bunch of mutations, and see which ones do what you wanted them to do. This allows for enormous creativity, as the literature on genetic algorithms attests. (Back in grad school, I fiddled with G.A.’s and ecological programming a bit, and got to watch novel — and sometimes radically weird — solutions to hard problems literally evolve.) Along with this creativity also comes risk, when the things evolving are potential pathogens. Church is right to worry (as the Bloomberg story notes he does) about the potential for misuse.

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Berkeley Backs Down on Gene Tests for Students

Posted on August 13, 2010 by

I blogged here a few months ago about UC Berkeley’s plan to do (voluntary) genetic testing on this year’s entire first-year class. (See: Genetic Testing and the College Freshman)

Now the university is backing down. Or rather, the university has been forced to back down by the California Department of Public Health. Here’s the story, by Rob Waters, writing for Bloomberg: UC Berkeley Backs Off Gene-Test Program for Students, Blocked by State

The University of California, Berkeley, won’t tell about 700 students the results of genetic tests performed on their saliva, after the state health department barred the institution from proceeding.

The state Department of Public Health views the tests as providing medical information and must, by law, be processed in certified laboratories, Mark Schlissel, the school’s dean of biological sciences, said today in a conference call. The results now will be analyzed collectively and the project will proceed as a research and educational effort, he said….

Regulatory issues aside, lots of people (mostly ethicists) expressed concern about the idea of testing the entire freshman class. As I noted in my previous blog posting on this topic, there were concerns about whether testing could be truly voluntary, and about whether students would be able to understand, on an individual level, the meaning of their test results.

For the most part, I agree with my colleagues who urged caution. I’m skeptical about such tests doing much good, and I’d rather see such testing done on smaller groups of students in a controlled way than on 1000s all at once. But — just to play devil’s advocate — it’s worth asking just what the risk here is. To put it bluntly, no one has ever died from genetic testing, as far as I know. For that matter, where are the horror stories of people’s lives torn apart by their test results? There is evidence that genetic tests can have interesting implications for family dynamics, in families with hereditary diseases. But aside from that, it’s not clear that anyone’s been hurt by a genetic test like the ones Berkeley was proposing. Compare: when Ralph Nader published Unsafe at Any Speed back in the mid-60s, calling for auto manufacturers to make their cars safer, he was able to point at statistics showing actual deaths — lots of them.

Now, again, I’m not a huge fan of personalized genomics. But if we’re going to debate particular cases, it’s worth putting it on the table: the tests may not be all that useful, but if we’re going to forbid them, we ought to be able to point to some actual dangers.

Posted in ethics, genes, genetic testing, health, risk | 1 Comment