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Comment Re:Open Source Personal Analysis Tool (Score 1) 96

At this point, SNP genotyping is pretty much obsolete for health-related uses because you can now get a full genome sequence for about $1,000 from just a few drop of saliva - well the raw data, at least - a custom interpretation for a suspected genetic condition might easily run you $20K. SNP genotyping can still be useful for detecting losses or duplications of large parts of a chromosome ("structural" variations) - but mainly because the analysis software is more mature.

I am aware of the difference between the cost of data and the cost of healthcare resulting from said data, but the poster was explicitly asking about the relevance of "open source" raw data so that he could do the interpretation himself. I am also explicitly mentioning arrays, because this is the cheapest technology and the one used by 23andme. Nevertheless, this kind of technology (and yes, the genome too!) has not made a very meaningful impact in clinical practice, with the obvious exception of clinical genetics. Now, you probably already know that today it's much easier to get a diagnosis of some rare muscular dystrophy or some weird anomaly of metabolism thanks to genome sequencing. However, with the exception of some genetic conditions (BRCA1/2, Lynch syndrome, Cystic fibrosis), clinical genetics are only useful for a small percentage of the population. That is exactly what I am saying: there is great progress for a small percentage of the population with rare, high-penetrance, devastating diseases, but there is not meaningful genetic test for type 2 diabetes, hypertension, cardiovascular disease, COPD and other frequent conditions. I already explained the reason above but you can also read more about it elsewhere (for example:, frequent diseas)

Based on the presentations at the American Society for Human Genetics (ASHG) in Baltimore last month, many of the major healthcare organization in the USA are making plans to implement genetic testing for adverse reactions to these drugs. It may be a few more years before it all actually gets rolled out universally (there are currently a number of large pilot studies ongoing) - and it may just be full genome sequencing rather than SNP genotyping - but this is coming. It's a question of "when" rather than "if".

I agree, which is why I said that this kind of application is more mature and that's why I called it an "exception". I already occasionally ask for DPYD or UGT1A1 genotyping for my patients, so certainly this is not a very remote scenario. Nevertheless, some kind of HARD data will have to justify the expense: reduction of hospitalisations, chemotherapy mortality or something similar. Just showing that universal genotyping predicts ... genotype is not enough. There has to be a meaningful clinical advantage for a significant number of patients.

There were quite a few people who found out through 23andMe that they were carriers for dangerous BRCA variants. 23andMe almost certainly saved some people from dying of breast cancer. Personally, I'd say that not dying of breast cancer is useful.

Well, that is an interesting byproduct of chance and certainly these people were lucky. However, you are certainly aware that SNP genotyping is NOT a valid test for BRCA variants for many different reasons. So, I would counter argue that some people were also falsely reassured by a negative result of a suboptimal test.
If people need to know their BRCA status, they need a proper test (=sequencing with sufficient depth at an accredited lab), a proper interpretation of variants (especially class 2-3!) and discussion of the family tree by a medical geneticist. I understand that cheap DIY healthcare is appreciated in the US, but you can't seriously consider 23andme results as sufficient in this context.

Comment Re:Open Source Personal Analysis Tool (Score 1) 96

The data is quite simple. At the most basic level it's just a photo of bright spots on a chip, as read by the machine. Knowing that spot A corresponds to variant A and spot B to variant B, an algorithm then decides ("calls"), depending on the relative brightness whether the person has variants AA, AB or BB (or impossible to tell). This is the only real processing and there IS open source software for that (packages for R, most famously CRLMM).

So, the whole point is getting the variant calls, ie what sort of nucleotide the person has at specific positions, for example rs314159 --- yes I chose that based on pi, but it does exist. If you have the variant calls, you can then try to decide, based on available literature, what this means for your health.

The not-so-obvious reason why SNP genotyping has not yet made it to the clinic is that polymorphisms (the stuff that genotyping arrays discover) are either frequent or associated with significant effect, but rarely both. Some rare variants (for example BRCA1/2) have important consequences and some variants are very frequent (for example, for hair color) but don't have important health consequences. This is the result of natural selection: bad genetics tend to get thrown away and become rare.

Simply put, most of the information associated with frequent polymorphisms only modifies risk by a relatively weak amount (relative risk 1.2-2, for example) and may also depend on other polymorphisms or entire haplotypes (a whole bloc of DNA) or even the environment. The resulting information is NOT of sufficient quality to dictate anything beyond things that we already know, ie don't smoke, eat healthy, moderate exercise etc. There are a few exceptions, for example in pharmacogenetics, where some people react differently to drugs, especially important or highly toxic drugs (clopidogrel, 5-fluorouracil, irinotecan etc). In these cases, there is some interest in genotyping and the FDA does mention cases where it could matter. Nevertheless, genetic testing for pharmacogenetics is not universally performed and is not generally required.

In the end, at the current state of affairs, the information provided by 23andme is most useful for ancestry but not particularly useful for health-related decisions. Which is why the FDA stopped them in the past.

Anyway, don't underestimate the interest 23andme has in farming your data (like Google). Even anonymized data without phenotype correlations can be scientifically very interesting. This is not necessarily a problem, but is likely to be the case with all similar genotyping offers.

Comment Re:Wake me up when they stop using 28nm (Score 2) 76

What is the likelihood that, in three years' time, they have made any significant innovations on the hardware front whatsoever, aside from stacking memory modules on top of one another?

To me this looks like an attempt to continue to milk yesterday's fabrication processes and throw in a few minor bones (like improved VCE, new API support) while not really improving in areas that count, like power efficiency, performance per compute core, cost per compute core, and overall performance per dollar.

They explicitly mentioned 50% more perf-per-watt with respect to the R9-290X. In the end, if you get the performance you want and a reasonable power consumption, what do you care if it's made in 28nm or 22nm or whatever? Process technology is only relevant if it enables these targets.

Comment Lipid formulations of cancer drugs exist (Score 3, Informative) 39

Lipid formulations of cancer drugs already exist, notably liposomal doxorubicin. Usually these result in better intracellular delivery and less toxicity. The problem is that making stable lipid formulations is quite hard and the resulting product quite expensive. If this, apparently simple, method can create liposomal carboplatin (or whatever other drug), it could allow cheaper and more diverse liposomal anti-cancer drugs. That would be nice. Especially carboplatiin (and cisplatin) are extremely important for many, many different chemotherapy protocols.

Comment Re:Almost impossible (Score 1) 324

Ebanking often depends on two-factor authentication. Furthermore, this is exactly the kind of situation that would rapidly generate enormous publicity. Do you think that people losing thousands or millions are not going to notice? A firmware trojan in that situation would be very short-lived. Everything is possible, of course, but I would be more inclined to think industrial espionage or three-letter agencies, where this kind of "weapon" is likely to be used with discretion and over a long time.

Comment Almost impossible (Score 1) 324

Firmware is usually not signed. Furthermore, I am not even sure that most drives support reading the firmware. Overwriting with a "fresh" firmware might also be impossible, since I assume it happens through vendor extensions of said firmware. A malicious version could be able to thus protect itself.

In the end, such an elaborate scheme is probably directed towards very high value targets. I don't think this is the kind of trojan that runs out in the wild. I could be mistaken, though.

Like you, I do wish it becomes more secure in the future. If anyone has a list of vulnerable targets (brands, models etc), I would be interested to know.

Comment BitDefender renewal (Score 1) 467

I would just like to mention a rather dubious automatic yearly renewal I got with BitDefender. Although I normally wouldn't mind being given a reminder, in that case I only discovered the item in my VISA card statement. Annoyingly, they didn't even apply the discount that was running at their website at that moment, so I was charged something like $89 for a product that was selling $49 or so.

Anyway, be sure to check this if you are running or planning on buying BitDefender.

Comment Fundamentally not secure (Score 2) 186

I had the same thoughts when I tried installing CM on an old Android device. In the end, the platform was never meant to be secure or really open to user scrutiny. I suppose with a considerable amount of effort you could achieve some sense of security by inspecting all major components, but if you are inclined to invest a considerable amount of effort, then you probably want much better security and are looking at the wrong place. Phones/tablets are fundamentally insecure, and this is probably by design.

Comment Re:Quarterly forecast (Score 2) 153

I don't really think that is true. Just read Science and Nature on a regular basis. Lots and lots of new insights and discoveries by mostly US centers. It can and should be better - we're on a Red Queen type journey and much of our problems can be solved either by dropping us back into the Bronze age or moving forward understanding our world and how to live in it. Standing around staring at the scenery isn't going to get society very far.

Although I don't doubt for a second that US centers produce first-tier research, I am also inclined to believe that publishing in Nature is far easier when you come from a big US center. So, it is, in a way, a self-sustaining situation. Friends who have been to famous US centers (Dana-Farber, NIH, MIT), find it far more difficult to publish when they come back to Europe, and that is even after having established connections around the world.

With respect to TFA, I would just like to add two parallel phenomena that possibly contribute to the apparent "lack" of funding for young scientistis:
- Research is becoming exorbitantly expensive, therefore grants are more likely to be big and only distributed to the people at the top. Funding twenty young researchers with 100k is unfortunately much less productive than funding a big consortium with 2M because the barrier of entry (equipment, regulatory overhead etc) is very high.
- The PhD "inflation" means that today a scientist is considered senior/lab head after one and maybe two post-docs. It used to be that after the PhD someone would get a tenure-track job and the associated funds. Today this step occurs at a later age. Naturally, researchers under 35 are seen as "beginners" while a hollywood star or athlete is seen as a veteran at age 35. Such is life for the modern scientist...

Comment Time to buy vinyl? (Score 3, Insightful) 169

This economy baffles me. I rent a house, lease a car, subscribe to a Adobe software, pay-per-view TV, stream music, and play online-DRM games and god knows what else. The day I stop having income, I don't own a thing. I am not by any means going back to the age of carrying chunks of gold on my person, but I get the impression property is quickly being replaced by service in too many aspects of our living. Although practical and convenient, this can only amplify the financial insecurity of the middle/lower classes.

Well, if the shit hits the fan, I can always listen to my vinyl collection.

Comment Re:Not really missing vinyl (Score 1) 433

I'd generally agree about the quality of the speaker, but even in pure mathematical terms a piano is a very complex instrument with hundreds of moving parts and multiple configurations (pedals, chords etc). In fact you can connect most electric pianos to a hifi of your choice, but I don't think it's enough. I would try this, but I don't have a high-end speaker handy ;-)

Comment Re:Not really missing vinyl (Score 3, Insightful) 433

If it were that simple, we could also completely emulate any instrument like a piano or a violin. Electric pianos can do wonders (I own one) but they can't copy the real thing (which I also own). The point is that a turntable is, in that sense, a complex transformation, like an instrument. You may like it or hate it, but it isn't that simple to emulate.

That being said,I'm sure people have mentioned the simple pleasure of actually owning stuff (instead of a virtual license to some bits on some server). Vinyl has that.

"Of course power tools and alcohol don't mix. Everyone knows power tools aren't soluble in alcohol..." -- Crazy Nigel