Maybe the Nature editors should have read their own writings as the “roadmap for regulation” (19 Feb 2015) states correctly about gene methylation Continue reading Hope dies last
Maybe the Nature editors should have read their own writings as the “roadmap for regulation” (19 Feb 2015) states correctly about gene methylation Continue reading Hope dies last
There are different strategies to improve the aerodynamics of road cycling. At 50 km/h about 90% is being spend to overcome aerodynamic drag of the riders silhouette. Barry et al. now sent a rider into a wind tunnel and discriminated basically 9 different positions that I am summarizing here in a cartoon including front area and estimated Watt count. Continue reading The optimal cycling position
When I moved from the theological seminar to the medical faculty of Marburg University, I expected to move from a rather liberal but largely closed belief system to a rational environment where belief does not play a central role. It took me only a few years to recognize my misunderstanding. Medicine represents an even more closed belief system („peer review“) than I encountered in theology. There are so many assumptions in daily medical practice that have never been formally tested.
It is commonly assumed that genetic testing is ready for widespread use. But is it true? The authoritative Stanford Encyclopedia of Philosophy has in an excellent contribution about the ethics of belief that there is a „cluster of questions at the intersection of epistemology, philosophy of mind, psychology, and ethics“. And even more
Contemporary analytic philosophers of mind generally use the term “belief” to refer to the attitude we have, roughly, whenever we take something to be the case or regard it as true. To believe something, in this sense, needn’t involve actively reflecting on it: Of the vast number of things ordinary adults believe, only a few can be at the fore of the mind at any single time … Forming beliefs is thus one of the most basic and important features of the mind, and the concept of belief plays a crucial role in both philosophy of mind and epistemology.
Do you want to know your full genome sequence? And do you want it to be published on the internet? Or do you think this is private information that should stay within your body cells where it had been encrypted since the origin of humans? Before we look at any belief surrounding genetic testing, we may have to take a small side-step. Yes, of course, we are dealing here in the first instance with a large industry that has strong commercial interest in genetic testing. Equipment companies selling chemistry and scanners want to increase their sales figures. Insurance companies need data for their policy calculations. Doctors and hospitals want to maximize their income by customer retention. Universities want to increase their attraction by showcasing fancy technology. Even patient advocacy groups are not neutral as they act in the presumed interests of their members. While any of these interests may be good or bad, it is worth to note that the discussion is driven by commercial interests and not ethical convictions.
Having said that, we probably all agree that genetic testing is a research method: useful, interesting and promising to classify, prevent, predict, or treat disease ,. But even after many years it is still a research method of unclear scope, unclear benefit and unclear risks. Should genetic testing really been applied outside of supervised research just because of the economic pressure surrounding it?
I can not see so much benefit of DTC genetic testing right now while there are disturbing case studies how „ordinary humans“ are getting confused when genetic testing is done outside of a research setting. These reports show not only a crude misunderstanding of the predictive value of single nucleotide variants but also a plethora of adverse reactions on nagging questions that are posed but never answered. Some users complained about mix up of samples making even some the claimed success stories finding unknown family members („hey, bro“ ) questionable.
In the pre-internet age, there would have been an intense scientific discussion when a certain method is being ready for prime time. Such a method would have been limited to experts who know something about constraints of a research method, who know how to find additional information in the library or run further lab experiments when the knowledge is being limited. They could consult colleagues from other fields and eventually put these pieces into context. But only a few critical minds could do that, most of them with an academic training over many years.
This landscape has changed, radically changed. The majority of research papers is now being published online. There are no more fences, only a few toll gates, but no gatekeepers. While the church lost most of their authority during the age of enlightment, universities lost their primacy with the advent of the internet. Of course scientists are trying to get back in the discussion by submitting guidelines. I fear, however, that the public perception sees this a bit like in the famous Feynman quote being “as useful .. as ornithology is to birds.“ It is only when an agency like the FDA U.S. Food and Drug Administration issues a warning, that genetic testing is being brought to a (preliminary) end.
The autonomous individual falls back mainly to the information channel he can easily use: the internet search engine. The belief of an individual about the usefulness of genetic testing is influenced by quick google searches showing some bystander comments in an online forum. There is an endless skimming of newsfeeds, magazines and scientific papers. Everything is done at high speed but at the uppermost surface. It reminds me a bit about the 2010 EDGE question „How is the internet changing the way you think“ :
Playwright Richard Foreman asks about the replacement of complex inner density with a new kind of self-evolving under the pressure of information overload and the technology of the “instantly available”. Is it a new self? Are we becoming Pancake People — spread wide and thin as we connect with that vast network of information accessed by the mere touch of a button.
Technology analyst Nicholas Carr wrote the most notable of many magazine and newspaper pieces asking “Is Google Making Us Stupid”. Has the use of the Web made it impossible for us to read long pieces of writing?
…
Social software guru Clay Shirky notes that people are reading more than ever but the return of reading has not brought about the return of the cultural icons we’d been emptily praising all these years. …
Frank Schirrmacher, [former ]Feuilleton Editor and Co-Publisher of Frankfurter Allgemeine Zeitung, has noticed that we are apparently now in a situation where modern technology is changing the way people behave, people talk, people react, people think, and people remember. Are we turning into a new species — informavores? — he asks.
The belief about benefits of DTC genetic testing is certainly not influenced by any European or American Scientific Society Ethics Committee. It is influenced by those brief sometimes adequate, sometimes inadequate information pieces in the internet , TV, radio or newspaper snippets.
When it comes to any direct action (blood drawing, selection of a specific laboratory, test system employed, readout and interpretation of results) the patient belief’ is further shaped by the doctors belief system. A detailed description of the attitude towards genetic testing, in particular in the relationship between doctor and patient, would be an enormous enterprise, needing a large cluster of experts at the intersection of epistemology, philosophy of mind, psychology, and ethics, as well as social scientists, biologists, among others. And who will even judge what is a correct assumption? Is a certain genetic variant really a pathogenetic variant? Even the most advanced attempts so far, just lists bullet points only.
Believe it or not, genetic testing for health related outcomes is still a research method.
References
 http://plato.stanford.edu/entries/belief
 http://www.pnas.org/content/104/21/8685.full
 http://jama.jamanetwork.com/article.aspx?articleid=1840236
 http://www.nature.com/ng/journal/v34/n4/abs/ng0803-347.html
 http://www.nytimes.com/2013/12/31/science/i-had-my-dna-picture-taken-with-varying-results.html?ref=science&_r=0
 http://www.theguardian.com/science/2013/jun/08/genome-sequenced
 http://www.bloomberg.com/news/2012-02-15/harvard-mapping-my-dna-turns-scary-as-threatening-gene-emerges.html
 http://www.spiegel.de/spiegel/print/d-57223342.html
 http://www.spiegel.de/wissenschaft/mensch/23andme-gentest-firma-vertauscht-dna-ergebnisse-ihrer-kunden-a-699436.html

 http://www.fda.gov/ICECI/EnforcementActions/WarningLetters/2013/ucm376296.htm
 http://edge.org/annual-question/how-is-the-internet-changing-the-way-you-think
 http://www.nature.com/nature/journal/v508/n7497/full/nature13127.html
Jane Kaye from Oxford was speaking on the 15th Oct 2014 in Coimbra during the ChipMe meeting about the question “How to cope withe unexpected – incidental findings”.
The talk basically refers to a new EJHG paper dealing with UK10K issues. The UK10K research project Continue reading How to cope with the unexpected – incidental findings
A new study published in PNAS finds evidence for non-random mating
Spouses are more genetically similar than two individuals chosen at random … our unadjusted GAM result of 0.045 suggests that a 1-SD increase in genetic similarity increases the probability of marriage by roughly 15%. This association is confounded, in part, by intraethnic marriage among whites but we continue to observe GAM even after a se- ries of models designed to eliminate this source of assortative mating.
This comes somewhat unexpected. Unfortunately, the authors missed in their discussion what Carole Ober published about HLA and mate choice in humans
Hutterite mate choice is influenced by HLA haplotypes, with an avoidance of spouses with haplotypes that are the same as one’s own.
So I am a bit confused – more similar in general but still different at the HLA locus??
Reminds me to the old joke, that your male genome is more similar to a male chimpanzee (on a per base statistic) than to your wife.
I am currently writing a piece on genetic testing, basically arguing that genetic testing is still a research method and whole genome sequencing nothing for prime time as basically now summarized also in JAMA:
In this exploratory study of 12 volunteer adults, the use of WGS was associated with incomplete coverage of inherited disease genes, low reproducibility of detection of genetic variation with the highest potential clinical effects, and uncertainty about clinically reportable findings. In certain cases, WGS will identify clinically actionable genetic variants warranting early medical intervention. These issues should be considered when determining the role of WGS in clinical medicine.
Maybe the judgment of any scientific method was largely limited to experts about 20 years ago. You had to know something about research, you had to go to a library, you had to find the relevant information and eventually put it into the right context. Only a few people and only a few journalists could do that. (and only the latter would even publish their opinion).
This has completely changed with so many research papers now being published online. There is no more gate, no more gatekeeper. It means, however, that research papers are frequently misinterpreted – from patient advocacy groups to companies to medical doctors. I would wish that research papers would carry a “For research use only!” label as printed on many bottles with enzymes, antibodies and alike (Medical information is otherwise still restricted in Germany to physicians, pharmacies and medical staff). Given that rather muddle-headed situation in genetic testing, I think the new JAMA paper is a welcome recommendation for everybody!
incomplete … low reproducibility .. uncertainty
yea, yea.
Vitamin D level is an activity or lifestyle marker, although this has been largely neglected in the medical literature, maybe except Gannage 2000, Hyppönen 2007, Sohl 2013 and Choi 213. A new paper by de Rui in PLoS now shows that
serum 25OHD levels were significantly higher in individuals who engaged in outdoor pastimes … compared to those who did not. In particular, subjects regularly practicing gardening or cycling had higher serum 25OHD levels than those who did not, whereas 25OHD levels differed little between subjects who did or did not undertake indoor activities.
While these are good news for older cyclists Continue reading Cycling is good for you (and vitamin D is an activity marker)
Responsezahlen sind für Epidemiologen entscheidend, wenn es um Repräsentativität und Verallgemeinerung von Schlussfolgerungen geht. Denn mit sinkender Response verändern sich nicht nur massiv Risikokonstellationen, auch werden Krankheitshäufigkeiten falsch geschätzt. Mit niedriger Response sind üblicherweise mehr Kranke in dem Untersuchungskollektiv (weil sie mehr Zeit haben und sich vielleicht auch mehr von einer Studie erwarten). Es fehlen dann aber die gesunden Probanden, an denen man protektive Faktoren studieren könnte. Mit niedriger Response sind gewöhnlich auch Frauen überrepräsentiert, oft auch Arbeitslose und bildungsfernere Schichten. Die einzelnen Faktoren haben zwar keine direkte Beziehung, in Kombination verzerren sie aber Studienergebnisse bis zur Unkenntlichkeit. In der Literatur ist dies auch als selection bias bekannt. Leider gibt es keine guten statistisches Verfahren, um für den selection bias zu korrigieren. Wie sollte das auch gehen? Daten können hier kaum extrapoliert werden. Wann ein solcher Selektionsbias einsetzt, kann man nicht eindeutig sagen. Mit 90% Teilnehmerate ist man auf der sicheren Seite, unter 50% wird es kritisch und irgendwann dann sinnlos. 75% Response sind in der Epidemiologie Standard, in der Marktforschung begnügt man sich auch mit weniger. Der Qualitätsmaßstab in der Epidemiologie liegt aber wegen der Relevanz deutlich höher. In der Vorbereitung
Continue reading Warum die Teilnehmerzahlen so niedrig sind in deutschen Studien
The UCSC Genome Bioinformatics Group ( who is running one of my favorite websites ) just announced
After 15.4 years of CPU run-time in 9,905,594 individual ‘jobs’ and 99 cluster runs for lastz pair-wise alignment…we are excited to announce the release of a 100 species alignment on the hg19/GRCh37 human Genome Browser.
This new Conservation track shows multiple alignments of 100 species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package. This adds 40 more species to the existing 60 species track on the mm10 mouse browser. For more information about the 100 species Conservation track, please see its description page.
Quite some time passed already since my last post (to be exact, more than 5 years) but now there are good news. The FDA issued a warning letter on the 22nd
… The Food and Drug Administration (FDA) is sending you this letter because you are marketing the 23andMe Saliva Collection Kit and Personal Genome Service (PGS) without marketing clearance or approval in violation of the Federal Food, Drug and Cosmetic Act (the FD&C Act) … However, even after these many interactions with 23andMe, we still do not have any assurance that the firm has analytically or clinically validated the PGS for its intended uses … Therefore, 23andMe must immediately discontinue marketing the PGS until such time as it receives FDA marketing authorization for the device …
The response is quite flimsy. Yes, there may be negative side effects of genetic testing and of course tests need to validated first. Slate may be correct that the FDA’s battle with 23andMe won’t mean anything in the long run but now at least, we are set back to science, yea, yea.
There has been so much written about Frederick Sanger (see nobelprize.org or Sanger Centre itself) while I like most what he wrote himself in Annual Reviews 1988:
These prefatory chapters are usually accounts of biochemists’ experiences in research, teaching, and administration. In my case the last two are easily dealt with as I have done hardly any and have indeed actively tried to avoid both teaching and administrative work. This was partly because I thought I would be no good at them, but also out of selfishness. I do not enjoy them, whereas I find research most enjoyable and rewarding.
Sydney Brenner, another British nobel laureate (2002) thinks:
A Fred Sanger would not survive today’s world of science. With continuous reporting and appraisals, some committee would note that he published little of import between insulin in 1952 and his first paper on RNA sequencing in 1967 with another long gap until DNA sequencing in 1977. He would be labeled as unproductive, and his modest personal support would be denied. We no longer have a culture that allows individuals to embark on long-term—and what would be considered today extremely risky—projects.
Sanger remains one of my heroes – the only scientist from whom I possess an autograph, bought a decade ago on Ebay.
I have been attending yesterday an interesting talk of Stephen Quake. Yes, this was a Leica sponsored event, but not about photography, it was about single cell genomics. I was always interested in that field and quite impressed by the Quake approach. These biology-baptized mathematicians and physicists can easily compete with whole research centers and a 100fold head count.
The commercial spin-off is fluidigm.com while his main research is not only sequencing of the fastest moving bacterium but also an estimate of mutations in his own haploid (sperm) genomes, single cell expression along with single cell methylation patterns.
One of the really exciting questions is the mismatch of single cell RNA and protein content where I need to go for some papers that I wasn’t aware off. Another excellent idea is the clustering of single cell expression profiles. This is already leading to new classes of cells and a probably much more valid approach than using random? surface markers as immunologists usually do, yea, yea.
Do you know what bp;dr means? Here is the solution:
behind paywall; didn’t read
The very first use is being quoted to @NeuroPolarbear. I am using it in emails too but maybe it should be added also to bibliographic references of printed papers, yes, yea.
Most people think that you can google for everything you want to know. What an overestimate!! There are so many relationships that will probably never turn out in any graph search ( at least I believe so ). And here is a nice example as I recently heard of a patient with an allergy AGAINST dimethindene maleate ( Fenistil (R), an antihistmaine used TO TREAT allergy. So whenever you enter “fenistil allergy” you get 119.000 hits. Although you get that result in 0,23s it will take you 23y to wade through the results. Hint: You could google for “leroy dimethindene” and you will find that there are only 2 patients so far in the literature plus the one that I know.