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

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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FOX News Showcases DNA Consultants

Thursday, December 03, 2009
Dr. Yates was interviewed by WBRC reporter Jeh Jeh Pruitt of FOX News Alabama at the company offices in Phoenix on October 22. The report was broadcast on affiliate stations in late November. Watch it on MyFoxAlabama.com.


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M. Moore commented on 15-Dec-2009 01:44 PM

I hope there are many more interviews with DNA Consultants. Kudos and Cheers!


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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.
  
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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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Science Is Only for Us Scientists, Don’t You Know

Tuesday, October 06, 2009
That’s the import of a trio of opinions in this week’s Nature magazine. One of them, “Genetics without Borders,” criticizes a “UK government scheme to establish nationality through DNA testing [as] scientifically flawed, ethically dubious and potentially damaging to science.” The “scheme” is a peer-reviewed program of the UK Border Agency to test whether some 100 asylum-seekers are Somali nationals. The testing uses a combination of SNPs, mitochondrial DNA and Y chromosome, plus other forensic means, to determine whether they are actually Somali or not. (That is, within a high degree of probability, since all inductive conclusions are probabilistic.)  

The editors of Nature fulminate against such methods. Yet these are the tools of the trade used by law enforcement officials and academic geneticists, to say nothing of commercial DNA testing companies. “The idea that genetic variability follows national boundaries is absurd,” they scoff. They are not impressed by the work of fellow scientists John Novembre et al., “Genes Mirror the Geography of Europe,” in Nature 456, 98–101; 2008), saying that the idea that genetic variability follows man-made national boundaries is absurd.” What is absurd is the idea that genetic variability is not molded and delineated by language, culture and historical events – the foundation of national boundaries. It seems to escape the opinion makers that Novembre et al. found that genetic patterns echoed linguistic divisions in Europe. This makes eminent sense in that courtship between most males and females is conducted in the same language. That means within the same nationalistic boundaries. 

Random “mating” of an exogamous nature as envisaged by them is not in the nature of humans. It may be a generalization that can be formed of evolution, which is judged in sweeping retrospective, but it is not true of living people at any given time, in any given land or country. Until the 20th century (and perhaps even today) most people marry someone of the same rather narrowly defined ethnicity as themselves. In fact, until the modern period, an Englishman was most likely to marry a woman whose house was situated only an easy walk away. His horizons --- and thus the eligible gene pool – was limited to a 24 mile square specifically labeled his “country.” 

Geneticists are wont to see human genetics in terms of geologic time, whereas the time depth and landscapes of history are more pertinent. The authors end by urging geneticists, “and indeed all scientists,” to nip the government’s “scheme” in the bud before the public finds out about it and an uprising ensues. This call to action seems to combine scientific cant with a patronizing view of the public. 

Lay persons, and sometimes people outside one’s narrow scientific specialty, just cannot be trusted to get anything quite right, can they?

Another day’s blog will address the other two articles in this week’s Nature, which exhibit similar mandarin attitudes. 

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