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review of scientific and news articles on dna testing and popular genetics

Fifteenth Anniversary of New Genome Sequencing

Monday, November 21, 2011

At a time when it seemed that American science had bitten off more than it could chew with the Human Genome Project, Craig Venter and his innovative company published "A New Strategy for Genome Sequencing." Appearing in the journal Nature in 1996, the Venter multi-center approach bypassed laborious gene mapping and allowed the HGP to meet its goal of full sequence information on the human genome in 2000.

"In the race to sequence the human genome," write the editors of Nature's DNA Technologies Milestones, "research groups had to choose between the random whole genome shotgun sequencing approach or the more ordered map-based sequencing approach." The choice of randomness versus order was present from 1982, but the Venter strategy was resisted for many years. Finally, in 1996 it was accepted and given an equal emphasis with the more orthodox approach.

After a standoff between the two groups of scientists, "a showdown ensued, with the biotechnology firm Celera Genomics wielding whole-genome shotgun sequencing and the International Human Genome Sequencing Consortium wielding map-based sequencing. Yet when the dust settled, it was a draw -- both groups published their initial drafts of the human genome concurrently in 2001."

The maverick technology helped make high throughput genomic sequencing at commercial labs an economy reality and gave birth to a range of new DNA tests within the reach of ordinary consumers like you and me. Today, fifteen years later, those interested in autosomal ancestry testing and personal genomics have biologist and entrepreneur Craig Venter and his irascible persistence as a scientific pioneer to thank.




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Should the DNA Marketspace Be Regulated by the Government?

Tuesday, March 08, 2011

In a paper to be delivered at the American Marketing Association's meeting in Washington in June, Elizabeth C. Hirschman estimates that the number of people who have purchased a DNA test now exceeds 1.5 million. Her work suggests that the value of the market (excluding paternity testing) in 2011 will reach nearly $150 million in sales. That seems like too big an industry to escape government oversight, and it's true that several scientists have targeted the direct-to-the-consumer DNA testing business for criticism, particularly personal genomics companies like 23andme.

Before another academic grant gets written to send out another industry questionnaire, however, marketing professionals and public policy analysts ought to have a look at Hirschman's new case study, destined, we think, to become a classic. "Altruistic Economics and Consumer Cooperatives in the DNA Marketspace" sketches a vibrant picture of DNA test takers busy following up on their results in social networking sites like DNA Communities and even joining in the design process for product improvements by the leaders in the industry. No unhappy campers there!

The proof of the pudding is in the eating. Rather than mount yet another policy making roundtable, would-be regulators should just order some of the DNA tests available from today's leading companies and judge for themselves how accurate or valuable or harmful they are. That makes a lot more sense than writing another food review for a restaurant they do not intend to patronize, or for a cuisine that is not to their taste.

The AMA's Marketing and Public Policy Conference is the premier national and international event for marketing academics, public policy makers, and marketing practitioners interested in social and public policy.

Another point made by the paper is that "The industry has completed the introduction, early growth stages and consolidation phase of its life cycle . . . . It is a mature field facing few new technology thresholds, and it is still very much confined to the United States, Canada and England." That having been said, it may be too late to regulate the industry. It seems to be doing fine all by itself. Like the pharmaceutical and computer industries, the DNA marketspace is an American phenomenon we should all just basically let thrive and be proud of.

Altruistic Economics and Consumer Cooperatives in the DNA Marketspace

 

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US, EU Move to Regulate Direct-to-Consumer Genetic Testing

Sunday, November 28, 2010

Discussion is accelerating in the United States and European Union to regulate private genomic testing that provides consumers medical information, according to Science magazine and the European Journal of Human Genetics. No mention is made in the reams of white papers about ancestry testing, but some of the pitfalls and bureaucratic morasses in the thinking about true genetic/medical testing are fairly ominous, if not silly.

"Although there has been speculation about the potential psychosocial harms of testing [that is, genomic medical testing], such as an increase in anxiety or encouragement of fatalistic behavior, there are, to date, few studies addressing these concerns," writes the reporters for Policy Forum in the Oct. 8 issue of Science. "The limited evidence tends to be reassuring, even for risk information associated with relatively serious ailments...however, the scope for potential harm from unnecessary or unproven treatment after genetic risk assessment is an important unstudied question" (pp. 181f.).

We commend scientists and physicians for finding a new field of study divorced from reality but have to wonder what they will do about ancestry testing once they have conquered and tamed Frankenstein's elder monster. We suggest the following guidelines:

  • Labeling on Internet sites and Zen Shopping Carts that explicitly states, "The claims for this ancestry product have not been evaluated by the U.S. Government Accountability Office (GAO), U.S. Federal Trade Commission (FTC), House Energy and Commerce Committee, Food and Drug Administration, National Institutes for Health or Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA 98195 USA."
  • Predictive ancestry information may be hazardous to your progeny.
  • No animal has been harmed in the production or clinical evaluation of this ancestry test.
  • If you discover you have ancestry you did not expect, take a deep breath. Then take a healthy dose of skepticism, followed by two aspirins and a glass of water.
We're waiting for the next gambit from the genius bar in Washington!
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Mad Hatter's Tea Party at American Colleges

Wednesday, June 16, 2010

To Do DNA or Not to Do DNA?

Much Ado about Nothing

American education is in such a state of decline and confusion that the following new program, with all its pros and cons, seems tantamount to a mad hatter's tea party. We reproduce a description of it from Nature in all its carefully nuanced and agonizing detail. We suggest that rather than fretting over whether DNA testing companies might use predatory marketing on teenagers or students be pressured into making purchases and be psychologically damaged by DNA results, the school authorities worry about real threats like the fast food poisons served up in the cafeteria franchises on their campuses. Or overpriced and watered down textbooks. Or alcohol in dorms. Or date rape. Or just about anything else.

A DNA education

Nature 465: 845-46 16 June 2010

Taking personal genetic testing into the classroom brings ethical and legal sensitivities to the fore. Although personalized genetic testing is still very new and controversial, its increasing use in health care seems inevitable — a trend that makes it essential to give consumers and physicians a better education in the technology's strengths and weaknesses.

That was the rationale behind an announcement made last month by the College of Letters and Science at the University of California, Berkeley. This year, instead of sending its incoming students a book for later discussion in class, the college will send them a kit to swab their DNA. If they so choose, students can send in their sample to be analysed for three common gene variants that indicate how an individual metabolizes alcohol, lactose (found in dairy products) and folic acid, a vitamin common in leafy green vegetables.The impulse behind Berkeley's announcement was commendable.

But officials there were too hasty in designing the programme, as evidenced by the firestorm of criticism it triggered and the changes the university has instituted in response. For example, each student's kit will now include not just details of the measures being taken to safeguard and anonymize the data and descriptions of the genes to be tested, as originally planned, but also information about the ethical and legal issues surrounding genetic testing. In addition, the university has modified a contest that accompanies the programme: the prize will no longer be a full genetic test conducted by a commercial testing company, which could be perceived as an endorsement of such firms, but will instead be cash.

Finally, organizers have decided to hold off revealing the tests' results until just before a lecture at which the benefits and limits of genetic testing, as well as the three chosen genes, will be discussed in detail. They will also give an accompanying lecture on the ethical and social dimensions of genetic testing. And students will be able to seek private counselling about their results if they wish.

Although it was wise of Berkeley to make these improvements, concerns remain. The university contends, for example, that there will be no pressure on students to participate in the genetic testing. Not only will they be told it is entirely optional, but students — or in the case of those under 18 years of age, their parents — will sign an informed consent document. Moreover, faculty members will never learn which students participated and which did not. But critics still worry about indirect pressure: the very fact that the kits are being sent to all of the college's incoming students could give them the impression that their participation is expected, in which case their choice may not feel so free.

A telling contrast in approach has been provided by Stanford University in Palo Alto, California, which announced a similar course designed for medical students shortly after Berkeley announced its programme. Recognizing the potential for controversy from the outset, Stanford officials first appointed a task force of basic scientists, clinicians, legal professionals, genetic counsellors, ethicists and students who spent a year designing precautions against coercion and conflicts of interest by the institution, and working out access to counselling.

The result is a well-thought-out programme — which also includes a research component designed to test a commonly held belief: do students truly learn better when the information presented to them is of personal relevance?

That said, the Berkeley and Stanford programmes are both still experimental. No one has all the answers to the issues they raise, which is why designing such curricula will involve constant refinement and evolution. It is shortsighted for critics to oppose such endeavours on the grounds that experts don't yet know how to interpret genetic information or how to integrate it into medical care. That is changing rapidly — and these two programmes are only the beginning of a long conversation that needs to happen on campuses worldwide.

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VIEWPOINT: Personalized Genomic Information

Wednesday, February 03, 2010

Preparing for the Future of Genetic Medicine

Alan E. Guttmacher et al.

Nature Reviews Genetics 11, 161-65 (February 2010)

Four experts with different insights into the field of genomic medicine answer questions about the prospects for using this type of information. The issues range from scientific to ethical and logistical.

 

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Book Review: The Language of Life by Francis S. Collins

Wednesday, February 03, 2010
Nature 463/298-299 (21 January 2010)

Abdallah S. Daar in reviewing this new book by NIH director Francis Collins maintains that “we have entered the era of rapid, inexpensive genetic testing and genome sequencing” and must simply come to terms with the phenomenon of personal genomics and consumer genetics. In the next decade, he predicts, the cost of sequencing a human genome will drop to a few hundred dollars. The cost for the Human Genome Project was about $3 billion over 13 years.

The Language of Life:  DNA and the Revolution in Personalized Medicine

By Francis S. Collins

Harper/Profile. 2010. 368 pp/288 pp.

$26.99.

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Does deCODE's Bankruptcy Signal False Promise of Genetic Medicine?

Sunday, December 06, 2009
Future Shock or Future Letdown?

New York Times reporter and DNA author Nicholas Wade raised an interesting question in his report on the bankruptcy last month of Iceland's deCODE Genetics, which attempted to make it possible for an ordinary consumer to buy the latest applicable information on the connection between their personal genes and their personal disease risk. The article was titled "A Genetics Company Fails, Its Research Too Complex."

In the November 17 edition in the Science and Technology section, Wade wrote:  "The company's demise suggests that the medical promise of the human genome may take much longer to be fulfilled than its sponsors had hoped." But there may be more to the story. "The discovery that major diseases do not have any simple genetic pattern of causation has dealt a serious setback to the gene-hunting field as a whole," he added.

Signs of the deflation of the field of "gene hunting" over the past 10 years since the Human Genome Project was completed and the second phase of the HGP was announced as focusing on the "conquest" of disease are:

  • Discovery that genes are not found in continuous sequences or segments or even on the same chromosome.
  • Realization no DNA can be considered "junk DNA" and even "non-coding" loci have at least place-holder functions and hence their values are not neutral.
  • Greater respect for the role of environment in inheritance, including the nano-environments within the cell where DNA is stored and replicates.
  • Jumping the gun on numerous claims concerning genome-wide association studies in scientific journals like Nature and Science, and subsequent retractions by editors and authors.
  • Ever increasing sample sizes with ever increasing lack of robustness for the data and clarity for conclusions.
  • A push for extending genetic surveys to rare and under-represented populations, with few surprises in the analysis of the implications for medical research or consequent benefit for public health.
  • Diminishing returns on research investment (ROI) on nearly every front.
  • Not a single viable gene therapy product ever introduced.
  • Realization that only very rare genes are discoverable and selection usually takes care of them and extinguishes them over time; hence the bulk of medical research funds goes toward the rarest of cases and not widespread disease such as cancer or diabetes.
Harvard biology professor Richard Lewontin maintained as long ago as the 1960s, and continued to warn even on the eve of the completion of HGP I in 2000, that gene hunting was essentially a scientific fetish with little true power or efficacy. In 1992, he wrote "The Dream of the Human Genome" as a review article in response to The Code of Codes:  Scientific and Social Issues in the Human Genome Project, edited by Daniel J. Kevles and Leroy Hood, and seven other recently published books on the subject of genetics and medicine. The essay was reprinted in Lewontin's own book It Ain't Necessarily So (second edition, New York Review, 2001). 

I think it is time to elevate gene hunting to the danger of something beyond a harmless fetish for the members of a narrow profession or scientific sect. Its waste and failures have taken on the proportions of a national form of folly and collective denial. While huge expense and sensational efforts continue to be thrown away on the molecular biology revolution, the need to renovate our neglected infrastructure and reform political mechanisms goes unanswered. Resources that might be better allocated keep dwindling. The supposedly most advanced society in history turns a blind eye on such relatively easy measures of public health as universal health care and uncontaminated chemical-free food and water supplies. While geneticists continue to cackle about inch-sized strides in their progress toward scaling the distant peaks of genetic medicine we are slipping into the abyss of logical disconnects. 



Comments

naturopathic physician commented on 06-Dec-2009 02:34 PM

The area of personalized genomics for health intervention has not really panned out. For example, the BRCA 1 and BRCA2 genes were hailed with great fanfare a few years ago as causal agents of breast cancer. But the true percentage of BRCA 1 and 2 mutations contributing to breast cancer are between 5 and 10%, leaving an astounding 90-95% of breast cancer due to other environmental factors. It is those factors that bear looking into, not the "faulty" genes.

The available personalized SNP (single nucleotide polymorphism) panels that are available today for use without a physicians input, are leading people into unproven territory as the true associations between these SNPs and the disease they purport to contribute , is not supported by science.


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Iceland's deCODE Defunct

Saturday, November 28, 2009
Icelandic genomics firm goes bankrupt

Nature 462/401 
23 November 2009

In a report by Erika Check Hayden, the journal Nature gloated that the innovative personal genomics company deCODE Genetics went out of business, leaving the disposition of valuable genetic data unclear. "After struggling financially for years, the genomics company deCODE, based in Reykjavik, Iceland, filed for bankruptcy on 16 November," wrote Hayden, who follows the genealogy-and-genetics business beat for Nature. "The question now is whether other companies looking to commercialize genomics will follow the same path." 

DNAPrint of Sarasota, Fla., went down that path last February without even an obit in scientific journals.

But according to Kari Stefansson, deCODE's CEO, the fate of the data never was in play since it belonged to individuals who had their DNA tested at their own expense with the service lab of deCODE. The lab, Islensk Erfdagreining, continues to operate today "under the same data and privacy protections as ever, rooted in the Icelandic community and within a tried and tested regulatory environment," wrote Stefansson in a comment on the online report by Nature. 

Such an accidentally-on-purpose misunderstanding is more than sloppy science journalism or bad science. It reveals the fundamental hostility of academic geneticists and related disciplines to commercializing or even popularizing DNA. Geneticists should stop thinking they are doing God's work. They should give up the illusion that the great generality of humankind can only understand, profit from and benefit from their work if they, the scientific intelligentsia, condescend to allow it and specify the conditions and goals of its use. 

Those on the payrolls of governments and public institutions have received so much money they think now they can be governors -- governors of the applications of their research.
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Officious or Official Regulation?

Thursday, October 22, 2009
Council of Europe adopts protocol on genetic testing for health purposes

In a report so-titled by Laurence Lwoff in the European Journal of Human Genetics (2009) 17, 1374–1377, first published online in July, it was noted that the Council of Europe has weighed in on one of the most controversial areas of DNA testing, whole-genome sequencing and SNP testing to find genetic predisposition to disease for individual customers. Recent editorials in Nature have called for similar measures in the United States, which is home to 23&me and other companies offering such services.

So far, no regulatory proposals have been aimed at genetic ancestry testing, only medical and health-related screening. One of the warnings often raised in the public discussion on genetic testing for health purposes, however, is that results may confuse and unnecessarily alarm consumers--a criticism that could apply equally to ancestry services.  Another is that commercial research scientists and business operators may jump the gun with findings and peddle bad science, although critics admit that the state of knowledge on nearly every topic of interest to geneticists and medical researchers is in a constant state of flux. A finding about a gene for Alzheimer's will be trumpeted in the pages of a major journal one week only to be updated or withdrawn in the next. 
 
This being the case, one wonders when discoveries will ever be fit to be commercialized or made available to the public. Should science only serve scientists?

We have always maintained that the would-be regulators underestimate moderately educated people's ability to understand emerging science. They overestimate commercial companies' disregard for professional practices and responsible communications. Most of the measures under discussion will have the effect of denying people access to valuable information. Regulation will also hamper growth in a direct-to-the-consumer business with unimaginable promise for society at large. A home paternity test purchased at the corner drugstore may make all the difference in the life of a family. Discovery of varied ancestry through a DNA test can be an important factor in furthering a consumer's interest in other peoples and countries, in history, and ultimately in tolerance of others. DNA testing can help bring peace of mind but it can also help bring peace in the world. 

Many, if not most, of the innovative contributions to society by science have come from non-specialists. The scientific establishment is not oriented toward practical applications of knowledge. The Croatian inventor and engineer Nikola Tesla dropped out of college and never received any formal training. Driven entirely by his natural aptitude for learning, he patented some of the most important contributions to the birth of commercial electricity, including alternating  current (AC) electric power systems and the AC motor. His inventions helped usher in the Second Industrial Revolution. So far from being overpowered by the profit motive, he died penniless at the age of 86 in 1943. No government program or university gave him any support or assistance. Whatever else the Council of Europe deliberated about, we hope they were not cynical or self-important enough to discount the possibility there may be many more popular scientists like Tesla in Europe's future. Science and technology are increasingly becoming a way of life for millions of people around the world who do not happen to have an advanced degree. It is a positive sign that consumers are so eager to take responsibility for their own health they will use the latest innovations from genomics to gain knowledge and control. Scientists should be glad they have such an impact. They should not squander the respect they enjoy in our eyes with pedantic discussions about fixing something that is not broken.  

Isolated populations as treasure troves in genetic epidemiology:  the case of the Basques

Paolo Garagnani et al. (2009) in European Journal of Human Genetics 17: 1490-1494.

The Basques living on the western border between Spain and France are a unique population. "Basques" often comes up as a match in people's DNA Fingerprint results, often because (as is widely believed, at least) a people resembling Basques helped repopulate the British Isles after the last Ice Age. But Basques are not an isolate. This article proves they blend gradually into their closest neighboring populations in Spain and France so they are not a candidate population, as say the Finns are, for the study of disease associations. "Basques do not show the genetic properties expected in population isolates," according to the authors. On the contrary, as many previous studies suggest, the Basques have so much diversity among themselves they were probably the source of population diffusions in prehistory, not a backwater trap for inbreeding.
  
Comments

Anonymous commented on 22-Oct-2009 11:28 PM

This is most perplexing and sounds medieval. Does the Council of Europe think we are all children? Are they truly concerned that their citizens may become confused and alarmed? What planet are they living on currently? I suppose they are unaware (or have forgotten) that Darwin had a background in religion (how alarming). This is 2009 and the world is an alarming place. One gets rather used to it though after a number of years. There must be some other reason than this for their suggested protocol. Something truly alarming.


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Putting the Test to a Test

Thursday, October 08, 2009

In the last blog post, we responded to the call of Nature (the journal, that is) in “Genetics without Borders.” In this, we examine the second of three editorials in this week’s issue concerning regulation of DNA testing companies:  Putting DNA to the Test.” 

It should be pointed out at the beginning that the wrath of the editors descends in unequal fury on commercial enterprises. They are not as irate at ancestry companies as “personal genomics providers.” They seem to have in mind mostly concerns like 23andme, which promises for $399.00 to sequence your personal genome and give you “access to all health, disease, and trait reports” maintained by its staff, together with “ all ancestry features and raw data download.” To the editors of Nature, this is akin to practicing medicine and genetic counseling on the Internet. Spit into a cup, discover your personal DNA sequences and get an email when a medical article mentions your nucleotide position.

The presumptuous and condescending attitude of the editors is evident in their first paragraph (italics added):  “The availability of affordable, direct-to-consumer genetic tests has mushroomed, leaving regulation lagging behind. Dozens of companies now offer inexpensive (elsewhere: cheap) home kits that allow people to spit into tubes, send the samples for DNA analysis and receive a report that allegedly details their ancestry or their possible susceptibility to a long list of disorders that have been linked — often tenuously — to particular genes. But the value of these tests remains debatable, which is why (bad predication in our grammar book) the industry needs a strong set of quality standards and codes of conduct to protect both its consumers and its own credibility.”

Aside from poor writing (which seems to be a requirement for an advanced degree in the natural sciences), there are numerous examples of logical fallacies in this and the rest of the article. Perhaps Wittgenstein was right. What cannot be put into words cannot be thought. What can only be poorly expressed is poorly thought.

It is unclear whether the regulators would extend the same benevolent protection to the academic researchers who also consume genomics laboratory services. A case can be made that even their understanding is not always perfect and up-to-date. Elsewhere in the same issue of Nature are warnings to fellow scientists who make exaggerated claims about their research. The editors also reprove wayward brethren who seek to dip more than once in the immortalizing waters of the Pierian springs, by submitting their work to multiple journals, often under different guises or false pretenses.

The world of science has so much dirty underwear of its own, it is surprising it wishes to examine that of others. Credibility seems to be in short supply everywhere.

Without dissecting what is a mess of snips to start with, let us draw attention to one scenario the would-be regulators raise. “Customers,” they predict, “will frequently receive results telling them only that they face the ambiguous possibility of a somewhat elevated risk of a little-understood disorder.... If the ambiguous, slightly elevated risk relates to a frightening condition such as breast cancer, some individuals might feel compelled to undertake drastic and perhaps needless measures, such as prophylactic mastectomy [surgical removal of a breast to avoid cancer].”

I read this horrific statement to a friend of mine over the phone, who said she had been in that exact situation. Doctors found a lump in her breast. Knowing that ancestry testing had placed her in a category of predisposition to developing breast cancer, she underwent, after due deliberation, “prophylactic mastectomy." “I was thankful I took the DNA test,” she said, “because it gave me information that helped me evaluate my risks.” She says she is sure that if she had not taken the step she did, she would have breast cancer today.

It is arrogant of scientists to think they must protect people from information. This is the stance of a totalitarian state that controls and censures the information consumed by the populace, or of a state religion such as that which ruled supreme during the Middle Ages. It was attempted with disastrous results in so-called “activist era” of the Federal Trade Commission during the 1960’s and 1970’s under Commissioner Mary Gardiner Jones. An institutional ideology of this sort assumes that consumers require protection from scientific information that they may misinterpret and that may lead to personal or social distress. For example, misplaced information like this might lead historically disadvantaged communities to increase their distrust of the scientific establishment . . . . as though the scientific establishment didn’t do enough in that direction!

Another of the editors’ arguments against releasing genetic information to the populace is that genetic information is always evolving and may not be complete. Quoadusque? we may ask with Cicero. When will it be complete? Or complete enough? And who is to make that judgement?

Instead of mad, speculative and needless worry about consumers who are supposedly ignorant and defenseless, why don’t we let reason and the unimpeded flow of information take their course? Those two forces educated, up to a point, the scientists who are now trying to second guess the public. While it may have taught them a lot of facts, it did little apparently to sharpen their powers of philosophical reflection.

 

 

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