Renowned Geneticist Analyzes Consumer DNA Tests

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."

Comments

Re:Francis Collins and "cdesign proponentism"

[JoshuaZ]

First, of all that's not accurate. Collins is pretty strongly against creationism in most of its forms, including classical young earth creationism and intelligent design. He is a variant of a theistic evolutionist with perhaps more of a notion of direct intervention by God than most theistic evolutionists. So describing him as you did is inaccurate.

Even if Collins views were not more moderate than you portray them, it wouldn't make his expertise any less. To use another example, I think that Noam Chomsky has a very strange ideas in his head about politics and how the media work. That doesn't mean I'm going to pay less attention to him when he talks about linguistics. Someone can have bad ideas in one area and still be an expert in another. Given his background, Collins clearly knows what he is talking about and is qualified to evaluate the products in question.

Re:Francis Collins and "cdesign proponentism"

[ShakaUVM]

>>Francis Collins also believes that Jesus rode dinosaurs.

I've actually read his book, and he actually is pro-evolution, and thinks Christians shouldn't tie their belief in God to belief in evolution.

So, in other words, you're completely fucking wrong, you idiot retard.

God bless.

sequence once

[jmilloy]

Sounds like there's room in the market for just the risk analysis. No reason to have the dirty work done three times - just sequence once and get a whole range of opinions, or focus on certain areas for detailed analysis. maybe this already exists.

Re:sequence once

[jd]

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:Why would you do this?

[JoshuaZ]

Genotype doesn't completely determine phenotype but it does provide some input. Genotype with environmental effects and stochastic elements determines phenotype (broadly speaking, I'm oversimplifying slightly since how one classifies epigenetic factors is complicated). Moreover, genotype is a major factor. So if I know information about the genotype I can prepare a lot. If for example I have an allele that is connected to increase risk of colon cancer, I know to have colonoscopies more often. If I'm a female with a bad BRCA1 allele I know that I should have my breasts checked much more regularly. Etc. 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?"

Re:Deep sequencing

[tpjunkie]

And if they drop a couple of Gs in the sequencing, god only knows what kind of results you'll get back

Re:Deep sequencing

[jd]

They might also give results at the drop of an 'AT.

Re:Why would you do this?

[Martin Blank]

In the United States, discrimination on the basis of genetic information or the requesting, requiring, or purchasing of genetic information by any health care plan is prohibited by the Genetic Information Nondiscrimination Act of 2008, passed by Congress in April 2008 and signed by President Bush the following month. Similarly, employers may not discriminate on the basis of genetic data, nor may they generally request nor require an employee to undergo genetic testing (there are a few very limited exceptions).

Basically, you can learn about your genome without worry that your insurance premiums will change, because with very limited exceptions, the insurers will never have access to it.

Re:Francis Collins and "cdesign proponentism"

[Man On Pink Corner]

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?

[PCM2]

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"

[Paradise Pete]

[sigh] I know exactly what "sic" means

You changed the spelling, and keeping the original spelling is the central point of using sic, so that the reader knows the error was in the original and not introduced by the quoter.