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Get ready for PGD, the acronym for preimplantation genetic diagnosis. We don’t really talk about “test tube babies” anymore. It’s “IVF,” and as American as apple pie (OK, perhaps as Israeli as falafel). Here’s the Ngrams result:

It’s just not that big of a deal anymore. But take a look at the order articles in The New York Times. There was a day that peopel were very worried about what “test tube babies” entailed. The end of the world as we know it? If that happened I don’t see anymore complaining.

The Globe & Mail in Canada has a very long piece on PGD, Unnatural selection: Is evolving reproductive technology ushering in a new age of eugenics? I do think it is ushering in a new age of eugenics, though it doesn’t go by that name. Many of the issues I’ve brought up on this weblog, such as the incentive for governments which fund national healthcare to take a deep interest in sifting through the range of future taxpayers and consumers of services, are explored. My basic instinct here is much more libertarian than most people. As a practical matter I’m rather close to a maximalist in terms of the amount of latitude I think parents should be given in selecting the nature of their offspring. But, I’m not a libertarian in an absolute philosophical sense, and I think a broader discussion in a society where the state and majority have coercive power over individuals is warranted.

There are two minor technical angles that I do want to bring up though:

- PGD seems to be ideally tailored already for people who marry their cousins. It would be relatively good at screening for the many recessive diseases which are common in the children of cousins. Also, it might even be able to reduce the fraction of runs of homozygosity through judicious selection. So, in the near future Muslim nations might be major consumers of PGD (Muslims as a whole are moderately anti-abortion, but they take a much more pragmatic line on these issues than the Roman Catholic church).

- PGD for trait selection runs into some statistical genetic difficulties. But, I wonder if perhaps PGD for decreased mutational load might be useful? With high coverage full genome scans could not one ascertain with good precision which genes have been subject to inherited or de novo deleterious mutations? It is generally assumed that loci where there is a major deleterious mutation masked by a normal functional copy still induce some fitness drag on the individual. The range in outcomes in siblings may be part of the natural variation in the mutational load. Parents may be tempted to lop off the asymmetrical-faced end of this.

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If anyone works at, or knows someone who works at, Genzyme Oncology in San Antonio, can you contact me? I have a few questions. Any of these methods will work:

• Category: Science • Tags: Biotech 
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Direct-to-Consumer Genetic Tests Neither Accurate in Their Predictions nor Beneficial to Individuals, Study Suggests:

Direct-to-consumer (DTC) genetic tests give inaccurate predictions of disease risks and many European geneticists believe that some of them should be banned, the annual conference of the European Society of Human Genetics heard May 31….

Here’s the abstract for the talk which argued that DTC companies don’t give the best disease risk estimates:

Objective: Direct-to-consumer (DTC) companies predict risks of common complex diseases on the basis of genetic markers. Given the low number of markers involved and their small effect sizes, it is unclear whether high-risk groups can be identified. We investigated the risk distributions generated by two DTC companies for 8 diseases.

Methods: We simulated genotype data for 100,000 individuals based on published genotype frequencies. Predicted risks were obtained using the formulas and risk data provided by the companies.

Results: The table presents observed and trimmed ranges of predicted risks. The two companies used different formulas to calculate risks. One company predicted risks higher than 100% for 5 out of 8 diseases, which for AMD concerned 1 in 200 individuals. Observed ranges were smaller for the second company, except for Type 1 Diabetes. Predicted risks higher than 50% were frequently observed for company 1, but were exceptions for company 2. When predicted risks of company 1 were calculated using the formulas of company 2, observed ranges were substantially smaller.

Since I don’t put much stock in the small effect disease risk predictions currently, I am not surprised. But I’d be curious to look at the guts of their results. This was presented at conference, so some caution has to enter into the picture. The main issue I’d always want to emphasize with critiques of the lack of efficacy of DTC is that they need to be evaluated against the baseline of the limits to the efficacy of medical professionals and medicine in general. Genomics and DNA doesn’t make something magical, whether for good or ill.

The second presentation covered in the ScienceDaily release is kind of more disturbing to me. Here’s the abstract:

An increasing number of private companies are now offering direct-to-consumer (DTC) genetic testing services. The tests offered range from tests for single gene, highly penetrant disorders to susceptibility tests for genetic variants associated with common complex diseases or with particular non-health-related traits. The aim of this study was to collect information regarding the awareness, experiences and attitudes of European clinical geneticists about genetic tests and test interpretations sold directly to consumers. European clinical institutes where genetic counselling is offered to patients were contacted. One-hundred and thirty-one of the three-hundred eligible respondents (44%) answered a questionnaire. Eighty-six percent (110/128) of the clinical geneticists said they were aware that companies are advertising and selling genetic tests directly-to-consumers. Of the 44% (54/121) of the respondents who had been contacted by patients who underwent DTC testing, almost all respondents (98%, 47/48) did discuss test results with the patients. The following respondents somewhat or strongly agreed that DTC genetic tests should be legally banned for following tests: prenatal gender tests (69%, 77/112); genome scans (63%, 70/112), 54%, athletic performance (54%, 61/113), preconceptional carrier tests (53%, 59/112) and ancestry testing (27%, 30/113). The results indicate that most European clinical geneticists have only limited experience with patients who have accessed direct-to-consumer genetic testing, however, these physicians are entering into patient-physician interactions with patients when requested to do so.

I’m going to calm down, because these results frankly kind of piss me off. 30 out of 113 think ancestry testing should be legally banned? The stuff quoted in ScienceDaily is even more disturbing:

Genome-wide scans by companies are totally unacceptable, as they can derive sensitive information about medically relevant conditions and will also provide lots of information which is difficult to interpret, even for medical professionals,” said another respondent. Presenting the results of such tests directly to individuals is unacceptable, the majority of those surveyed said.

90% of respondents felt that a pre-symptomatic test — predicting if an asymptomatic person had a very high probability of developing a condition — should not be allowed without face-to-face medical supervision; 93% felt the same for a predictive test for a condition that has a penetrance (the proportion of individuals with the mutation who exhibit clinical symptoms) of 50 — 60%; 79% for a carrier test for homozygous monogenic disorders, such as sickle-cell anaemia; and 72% for a predictive test for a condition that increased or decreased a person’s risk of developing it by 4% when compared to the general population.

At the moment, DTC genetic tests reach the market without having undergone any form of regulation. “Better regulation is needed at the level of market introduction of these tests,” says Professor Borry. As in the case of drugs, a procedure should be developed for genetic tests.

I think one of the key issues is that these genetic professionals view DTC genomics in the same category as a pharmaceutical. I view DTC genomics as part of the same family of consumer and social goods as information technology. When viewed in the context of our current medical-industrial infrastructure it seems that on the margin the future opportunities to reduce morbidity through better lifestyle choices and more information via DTC genomics is a no brainer. If there was social science evidence that people who receive false positive results are regularly committing suicide then obviously my preference for loose regulation would need re-examination. That would be like someone jumping off the tenth floor of an office building after a “blue screen of death.”

But from what I’ve seen at places likes Genomes Unzipped and FuturePundit these dystopian visions of mass hysteria don’t end up to panning out. Until that point it seems that the best avenue toward improvement of this technology is to allow the trial and error process of innovation to continue. It is incumbent on those of us “in the know” to evangelize about the limitations and opportunities of this technology (e.g., don’t buy AIBioTech Sports X Factor!). But the reality is that much of medicine is already technology, and not subject to careful professional oversight. Instrumentation necessary for life critical functions are designed and built by engineers and technicians.

The bigger social issue here seems to be the attempt by genetic professionals to regulate the flow of information. Though I’m skeptical of most licensing regimes I’m not totally opposed to them on principle. But they need to be imposed on extreme cases only. You don’t want just any random person offering cut rate surgery or mass prescribing antibiotics to one and all. The individual and social costs of these actions can be very negative and irreversible (i.e., someone dies, or a resistant bacterial strain emerges). But when it comes to information services requiring a “professional” is going to choke the supply and spike up the cost. Additionally, there’s going to be a constant latency in terms of the ability of professionals to actually interpret the swell of data which is going to be coming in their direction. The reality is that the professionals are going to have to rely on advanced analytic software. Obviously my own preference is that such analytic software should be widely available and cheap. If you want to ban sex selective abortions address the problem at the level of abortion, a procedure which most people agree should be under some professional and regulatory supervision already. Don’t deny people the information to prevent a few harms.

If anyone wants to release their genotype into the public domain, email me at contactgnxp -at- Know that some clinical geneticists probably think you’re a public health hazard!

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Josh Roseneau, when he’s taking time off from the evolution-creation wars, is poking around his own genome. Some sage advice:

On DNA Day, 23 and Me had a sale on their personal genomics service. They’d do their standard scan of your genome for free, as long as you paid for a year’s worth of their online subscription service.

For the price (nearly free up front, and a modest cost for the online community provided), my wife and I jumped on the deal. Since I got the results back two weeks ago, I’ve been exploring not only the services and information provided by 23 and Me, but the various other tools that individuals have started producing to help analyze and investigate this insight into my ubiquitous but invisible DNA.

My genome, for instance, revealed a genetic predisposition towards late-onset Alzheimers. The odds of getting Alzheimers are still quite small, but elevated because of this particular mutation to the APOE4 gene. This wasn’t a total surprise, given my family history, and as a healthy, young guy with a background in biology and biostatistics, it wasn’t hard for me to put that information into a context and move on. Down the road, I’ll probably keep an eye out for new research on Alzheimers medicines and look into tools for early detection, but I’m not going to kill myself if I forget my keys. (Thanks to the federal Genetic Information Nondiscrimination Act and the Affordable Care Act’s prohibition on “pre-existing conditions” – not to mention the inherent uncertainties in translating this genetic result to a specific outcome – I’m not especially worried about discussing that result in public)

We need to demystify DNA. It’s pretty obvious to me that people perceive genetics to be in the domain of magic, when in reality it manifests itself in the banal realities of correlations within the family, which we’re intuitively aware of. But Josh’s post is more than just personal, he reviews the book Biopunk: DIY Scientists Hack the Software of Life:

Most of the biopunks Wohlsen introduces us to aren’t trying to cure diseases or create genetic tests. They surely wouldn’t mind if they changed the world somehow, but their interest in DIY biology is driven more by a sense of personal exploration and a pure fascination with how things work. The goal, one of these biopunks explains, is to “increase the tinkerability” of biology, “simplifying and domesticating” it to make it accessible to anyone who wants to play with it. Groups like the Bay area’s Biocurious aim to create communal molecular biology labs which anyone can join and tinker in; Biocurious will open its lab this summer in Mountain View, not far from Google and the researchers at NASA’s Ames facility.

But I’m also fascinated because this is the future even for people whose aversion to biochemistry is even greater than my own. Just as everyone in the mid- to late 20th century needed some grasp of physics to be able to think sensibly about nuclear energy, nuclear war, and a host of related issues, the 21st century is sure to be dominated by biology. And DIYbio can play a key role in democratizing science, precisely because it’s more focused on what’s neat than on what’s likely to turn up a new Nobel Prize or a new patent and venture funding for a biotech startup. Its openness will be a great strength as a tool for improving science literacy, and biopunks know it.

I obviously support this movement and its intents (I’ve met a few of the people who are prominent in it). But we need to keep perspective here. This will probably be analogous to the free or open source software movement; the base of tinkers will be much larger than corporations and academic institutions, but it isn’t going to expand to cover the majority of the public. But so what? Most us can probably agree that the ad hoc decentralized elements of the software engineering community have done good just by putting pressure on the margins of staid institutions. Similarly, a minority of biology enthusiasts and hobbyists are going to shape the production and consumption of the plethora of new products we’re going to see coming online within the next few decades. There is often someone in the family who you turn to for tech advice. Now there may be someone in the family who you turn to for personal genomics advice. This is the democratization and decentralization of specialization!

When it comes to the mass consciousness aspect I think personal genomics and other consumer biotech will play a large role in demystifying DNA, and in the future making the public more open to the possibilities of bioengineering. Those of us alive today are on the cusp of a new age. I think the medium-term shape of that age is highly sensitive to initial conditions, so we should be both hopefully and vigilant.

• Category: Science • Tags: Biology, Biotech, Personal Genomics 
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Portfolio has a story up, Biotech Decline:

Even the industry’s lobbying group, the Biotechnology Industry Organization, says that 45 percent of publicly traded biotech companies will run out of cash in the next 6 to 12 months. A mere 10 percent of the 370 listed companies have a positive cash flow.

Much of the activity at the J.P. Morgan conference involved companies and investors that still have money shopping for deals. “We are being visited by a number of companies,” said Jay Flatley, CEO of the genomic sequencing company Illumina, based in San Diego.

Illumina recently announced an $18 million development deal with Oxford Nanopore of Britain for its next-generation genetic sequencing technology. Illumina has remained profitable with a healthier-than-average stock price even during the downturn.

Dan MacArthur has more on Illumina & Oxford Nanopore.

• Category: Science • Tags: Biotech 
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"