Renowned Geneticist Analyzes Consumer DNA Tests 97
pdragon04 sends in the hardly surprising news that direct-to-consumer genetic testing isn't predicting diseases as well as they claim. "...[Francis] Collins, who played a central role in the Human Genome Project and is rumored to be the next head of the National Institutes of Health, announced at the Consumer Genetics Conference in Boston last week that he had had his genome analyzed [using a made-up name] by the big three of direct-to-consumer genetic testing: 23andMe, Navigenics, and DecodeMe. Collins said that sequence-wise, the tests 'appear to be highly accurate': there were almost no differences in the genotype information generated in the three different analyses. But there were significant differences in the numbers of genetic variations used to calculate disease risk, as well as the final risk score. ... For example, one company used 5 single nucleotide polymorphisms, or SNPs, to calculate risk for a particular disease, pronouncing Collins at low risk. Another used 10 SNPs, placing him at high risk, and the third used 15, concluding that he is at average risk."
Re:sequence once (Score:5, Insightful)
To judge from the complaints that frequently get posted to the GENEALOGY-DNA mailing list, even the experienced big-name DNA corps screw up on even testing a few dozen STRs. The chances of fouling up somewhere along the entire genome seems extremely high. Thus, redundant testing seems a really good idea - at least until they improve their methods.
On the other hand, there probably IS a huge market for risk analysis. The DNA analysis market is pretty much glutted, but there's not much out there for DNA analysis for the average person at the moment.
It is worth bearing in mind that the sorts of studies done might not pick up all of the secondary genetic data needed - markers whose presence doesn't alter the probability of a condition UNLESS the primary marker is also present. Simply doing a gigantic "diff" isn't going to pick those up, as their presence isn't always important.
Then, there are conditions with multiple genetic triggers. Chronic fatigue has seven, according to a BBC report a while back, each of which produces a different condition with essentially identical symptoms but which respond to different treatments. (Unless there's genetic overlap, I would assume this means there are 5040 potential conditions that could be produced from these markers.)
Then, on top of all that, some conditions may occur but be too mild to notice. There are claims that autism is far more common than currently thought and certainly, the UK diagnoses it twice as often as the US (implying that either closer examination DOES yield more positives, or that us British are just strange). There's also a claim that many, if not most, people have some degree of synaesthesia. But is it useful to know that there's a very high risk of being normal?
(Ok, ok, Slashdotters might want to know if there's a genetic danger of becoming normal, but ASIDE from that...)
It would seem to me that conditions such as autism and synaesthesia follow something close to a Poisson distribution, with the vast bulk of people at close to no effect. Even if they're absolutely guaranteed the effect, they'll never notice.
Unless studies into risk go far, far beyond the horribly basic and naive results you get at the moment, the results are useless. And that kind of massive data-crunching analysis is something that Beowulf clusters and BOINC clients are going to be very good at... ...provided an answer even exists. If the severity isn't present in the DNA, then the risk is useless.
Re:Francis Collins and "cdesign proponentism" (Score:3, Insightful)
Because you don't want to commit an ad hominim fallacy?
I'll see your "ad hominem [sic] fallacy" and raise you a "credibility of the witness."
In the ideal world of the philosophers, where all parties are equally able to evaluate all the arguments raised, attacks on character are indeed fallacious. 2+2=4, and it doesn't matter if the person telling you that is someone you like, someone you despise, or someone you don't know from Adam. But in the real world, nobody knows everything. Most of the time, most people who are debating any subject don't know nearly enough about it to decide if what they're being told is true. So we fall back on acknowledged experts, because we have to; none of us have time to become experts on every subject that might possibly be of interest. Our evaluation of how credible a particular expert seems to be is how we decide which statements we will accept as fact.
The vast majority of people considering personal genetic testing aren't going to know enough about the science involved to be able to decide, on a purely logical basis, whether they're getting their money's worth. Many of these people will think, quite reasonably, that a prominent geneticist will have more insight than they themselves will. But if the geneticist does things which call his scientific judgement into question, then this information whould be included in evaluating the worth of his statements on the subject.
Whether or not this principle applies to the debate at hand is left as an exercise to the reader.
Re:Francis Collins and "cdesign proponentism" (Score:3, Insightful)
I'll see your "ad hominem [sic] fallacy" and raise you a "credibility of the witness."
If you don't know what "sic" means, don't use it.
Also, the expert's beliefs in some other field do not affect his skill in his specialty. A fantastic chef might have appalling taste in wine, but that won't stop me from eating at his restaurant, because all I care about is the skill in question.
Re:Francis Collins and "cdesign proponentism" (Score:5, Insightful)
Religion isn't bad. Extremists are bad. Zealots are bad. Idiots are bad. Religion may bring about these things, or those with these may be attracted to religion, however that isn't the fault of the religion itself. If a country began to kill and oppress in the name of democracy would you say democracy was bad? If a man began to kidnap and rape people in the name of love would love be bad?
Two points:
1) Zealots have little power in the absence of a moderate base. The difference in influence between a Pat Robertson and a Jim Jones is quantitative, not qualitative.
2) Democracy and love are rather abstract concepts compared to the notion of a specific God who wants me to hate and persecute specific classes of people. That's the problem with the faith of someone like Francis Collins... his apologetics are all hand-wavy and woo-woo-driven, but the actual God he's evangelizing for has specific traits, specific likes and dislikes... and specific plans for humanity that simply are not compatible with the rational worldview we (should) demand of our scientists.
Re:Why would you do this? (Score:5, Insightful)
Your comment is sort of like saying "why should I learn about my family medical history if knowing about it can make my insurance premium go up?"
I don't think his comment was "sort of" anything. I think that was exactly what he was asking and I don't think you gave an adequate answer.
So let's see... you find out from your DNA screening not that you actually have any condition, but that you need more tests, more careful screening, regular check-ups, etc, because you're at high risk. Unfortunately, your insurance carrier catches wind of your DNA results and jacks up your premiums so now you can't afford health insurance, and ergo you can't afford to pay for any of these regular tests you've been told you need. And this is a stain on your health record that will last the rest of your life. Nice going.
Re:Francis Collins and "cdesign proponentism" (Score:3, Insightful)
Misinterpretation for personal benefit has really messed up organized religion.
Re:Deep sequencing (Score:3, Insightful)
You've GATA me there. I'm out of puns.
This practice is common (Score:3, Insightful)
Heritability (Score:2, Insightful)
One item in the article that surprised me: the companies aren't offering information to their clients about diseases they are carriers for. For instance, it would add value to their service if clients knew they carried the gene for cystic fibrosis (a common genetic test).
It's either a huge oversight by the 'big three', or they think that their clients are so focused on themselves as to not really care about what diseases their children could inherit.