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

Why would you do this?

[BadAnalogyGuy]

If phenotype is not determined by genotype, then why would you put yourself at risk of higher health insurance premiums?

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: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:Why would you do this?

[Anonymous Coward]

Several mistakes in the question. One is that with the GINA legislature passed, no DTC genomic tests are allwed to be used by insurance companies. Here goes one vulnerability.

Second vulnerability WAS that most people believed that nobody can legally submit saliva-sample by using some else's name (and credit card).

Francis Collins provided a precious example that he could legally avoid exposing his identity, and still get insights by the (similar) SNP tests by pioneering DeCodeMe (Iceland), 23andMe and Navigenics (Silicon Valley).

Third, while e.g. George Church is on the web with his video that "your genome is NOT your destiny" - some red flags e.g. for colorectal cancer, etc. already sent people for check-up (and to snip in the bud such diseases) who otherwise normally would not go for colonoscopy at the age of 38. (Most often, the threshold was believed to be 50).

Fourth, Francis Collins was quite positive about DTC genomic testing on several counts. One was its accuracy - while different vendors interrogate a different number of polymorphisms, the industry is quite consistent. Naturally, the higher is the number of reference-points, the more likely that their "flagging" should be taken seriously. Second, Francis started with a slide projecting the US health-care expenditure growing at an alarming and very clearly unsustainable rate of the GDP - and the only practical solution appears to be "genome-based prevention" of some of he most outrageously expensive diseases (Alzheiers' and Parkinson's in the lead).

Francis concluded with a slide that "Personalized Genomics is Here to Stay" - and not a single soul at the jam-packed Consumer Gentics Conference disagreed.

More analysis at my news column "hologenomics" [dotcom, "newsw"].

Pellionisz, HolGenTech_at_gmail.com

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:Why would you do this?

[freedom_india]

Try saying that to AIG and State Farm.
StateFarm recently was in the news for rejecting coverage of someone whose DNA tests were known to it.
Hitler would have loved this.
It would have given the SS and Gestapo valid, legal reasons that were sought in this conference.

Re:Why would you do this?

[number11]

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

Which prohibits use of such information as the sole reason for discrimination. So if they see the information and deny you coverage because not only do you have bad genetics, but you're unattractive too, they're in the clear. It also does not appear to have criminal penalties for violation. What financial penalties there are appear to be at the option of the government (think worst case scenario, with Dick Cheney making the decision).

I would suggest that to expect compliance by a large insurance company, you need penalties like mandatory jail time for the officers, or fines that will actually hurt, like $10M for the first offense, doubled for each subsequent case.

Re:Why would you do this?

[mrrudge]

I don't think you gave an adequate answer either, addressing only the financial side of an information gathering process which could very well lead to an extended and more fulfilling life. I think this is symptomatic of having a healthcare system which cares more about money than health.

You seem to be advocating a position whereby saving money is more important than knowing more about the specific body you have, and any potential problems you may have with it in the future.

If you look at it from the position of someone in their fifties with incredibly painful, terminal bowel cancer, I think they'd probably swap quite a lot of money to have had the information earlier that eating certain foods would extend their life considerably. *

* As an example only, I have no idea about the correlation of foods to cancer.

Re:Why would you do this?

[Moridin42]

I know its tempting to think of hypotheticals such as your cancer sufferer. Unfortunately in the current climate, it isn't a choice between "hmm, I know I'm prone to x disease let me take y preventative action" and "let me blow off knowing anything about my genetics." If I look at it from the position of your example, testing won't do any good whatsoever. He already has the condition. I might wish to have the option to swap money for having this information in the past. Fantasies are nice, sometimes very nice, but they are by definition not reality.

The gp is being pragmatic, not idealistic. The question you must ask, given the current climate and behavior of the healthcare industry, would I want to know about my dna if that information is also likely to land in the hands of others. It is somewhat similar to playing the lottery, hitting the roulette tables, or dropping some coins into a slot machine. Gambling. Yes, you can learn something about yourself. But you do so at the risk of letting other people learn the same information. The healthcare industry can take two routes, basically, to pay for the cases that come up. A) Healthy people overpay to cover the costs of the sick people or B) the company can charge you more when you're healthy to cover the costs of when you're sick. In the absence of information as to the at-risk, A is the only viable option. Start digging up such information and B suddenly becomes possible.

Yes, I know those cases aren't spot on. But I'm not writing a detailed analysis of any particular industry here.

Re:Why would you do this?

[mrrudge]

Pragmatic only if you happen live in a country which has a health service who's main objective is to make money.

I live in a country which has a nationalised health service ( it's not great, and getting worse ), it's subsidised by taxes on things which generally cause inhealth ( cigarettes, Etc. ) and the very idea of gambling with information which could seriously affect the most important thing in your life is horrific, to me you're saying that you'd avoid the prostate check ( * ) because they might find that you have prostate cancer ?

Your genetic disposition can surely be statistically approximated by looking at your family history, life expectancy as an average of your grandparents + a margin for increased nutrition and sanitation ? Probable cause of future death ( barring accident ) is likely to be one of the subset of deaths experienced by your recent family ? Is this information used to change your insurance premium ? ( I'm asking, I have no idea. )

Anyway, it sounds like a horrible situation to be in, the hypothetical cancer sufferer of course won't benefit from that information now, but could have if they'd known twenty years ago, which is the very real situation that we are all in now, we will all die of something, and more information about what the causes are likely to be now gives individuals more tools with which to manage that.

Re:Why would you do this?

[izomiac]

The degree to which genotype determines phenotype lies in how you define phenotype. If you say phenotype is the risk of a disease, then your environment is going to play a huge role. If you say phenotype is the type and amount of protein your cells produce, then the two are practically interchangable (depending somewhat on gene regulation, but that's arguably genotype as well).

One of the more common misconceptions is that certain genes cause certain diseases. This isn't quite right. BRCA1, for example, plays a role in double stranded break repair in DNA. It's a high fidelity repair system, so it's preferable to another system your cells have that is far more error prone. The "BRCA1 mutation" generally means that one of your two copies of the BRCA1 gene is nonfunctional, or at least has reduced functionality. This means that you can't repair your DNA quite as well. That phenotype is 100%. Now, that doesn't guarantee that a woman will get breast cancer, but it does make it a bit more likely. (Cancer of any form requires several random mutations, error-prone DNA repair mechanisms can introduce these mutations over time if you're unlucky.)

The thing is, though, for BRCA1 there often isn't a point in testing. The advised treatment for women with or without the gene are pretty much the same, with the possible exception of avoiding routine x-rays if you have BRCA1, and maybe starting mammograms sooner. OTOH, BRCA1 only accounts for something like 20% of familial breast cancers. So if you have a family history of breast cancer, then you're not in the clear if you don't have the gene unless you know that your family's breast cancer is caused by BRCA1. Either way, you'd want to have mammograms earlier and such just due to the family history, so there's no real difference.

Re:Why would you do this?

[Moridin42]

I'm not an actuary for health care provider, so I don't know if they have access to family histories, targeted life expectancies or any of that. So, I can't answer that question. Although knowing the answer would be useful. Since, I agree that at least some of the information from genetic testing can be replicated/approximated from other information sources. And if such information is already used, there is less risk to genetic testing because of it.

If you suspect that you currently have a condition, get tested. Different question than examining the probabilities of suffering from a condition in the future (especially with the variation in the results noted from the article as well as subjective language like 'low' 'moderate' or 'high' risk for a condition), based on genetics. Ideally, I'd like to know. But health care here certainly isn't ideal. I'm not certain I want to know, given the imperfect conditions, currently. Isn't ideal in your country either, it would seem. The imperfections are different, but present.

I am not in favor of nationalized health care because political solutions tend to be horribly crafted, at least here. And they also tend not to go away, even when they deteriorate and perform ever more poorly. I dislike the current state of health care in the US because it tends to be inefficient for many of the same reasons that nationalized health care isn't. When consumers don't bear the whole costs of their choices, they overconsume. And yet, as they overconsume, costs rise, calculations change and premiums rise. So what you don't pay directly to the care provider, you (more than) make up in periodic payments to your insurer. And that causes the consumer to think things like "I pay so much already, I may as well go consume even more health care" .. it is a .. not optimal cycle. I can think of some alternative systems. But there are glaring issues with them, too, and I can't really figure out a good way to transition anyway. If I could, I'd make a case to someone somewhere. And I'd even forego paying taxes, so I, too, could be a cabinet member!

Re:Why would you do this?

[mc moss]

But thats the problem. They all gave him different risk calculations. One company give him low risk while another gave him high risk. So which one do you believe?

Re:Why would you do this?

[Carewolf]

Why would this affect insurance? This not a condition known before signing the insurance, as such the insurance has to accept the loss and carry the costs. The entire point of health insurance is to protect from new disease, which included new discovered diseases you could not have known you had when signing the insurance. If they just raises the premium for that, the might as well raise the premium if you get HIV from infected donor blood, or any other condition that is just raises the risk of other conditions.

Better yet: Get public health insurance, then you are covered no matter what.

Re:Why would you do this?

[Ihlosi]

And yet, as they overconsume, costs rise, calculations change and premiums rise. So what you don't pay directly to the care provider, you (more than) make up in periodic payments to your insurer. And that causes the consumer to think things like "I pay so much already, I may as well go consume even more health care" .. it is a .. not optimal cycle.

I'm sure people are really keen on overconsuming chemotherapies, colonoscopies, root canals, hip and knee replacements, brain surgery, appendectomies, tonsillectomies, mastectomies, etc.

Re:Why would you do this?

[Ihlosi]

Why would this affect insurance?

Because private insurance companies are free to deny coverage to "unacceptable risks" or jack up your rates sky-high.

This not a condition known before signing the insurance, as such the insurance has to accept the loss and carry the costs.

That may be true, but don't even think of switching to a different insurance contract. You'll basically be locked into the one you have now (or locked out of getting any if you didn't have one before), and the insurance company is going to pull every sleazy trick up their sleeve to get rid of you. Have fun ... and don't get sick.

Re:Why would you do this?

[Moridin42]

Right.. because those are the only procedures in health care. Those are the only reasons you'd ever go visit an MD. Never any wasteful, trivial visits. Oh wait..

Re:Why would you do this?

[Faerunner]

It's not the colonoscopies they're looking for, it's the "I have the sniffles again this week and I NEED an antibiotic, doc! Don't worry, my insurance will cover it!"

Re:Why would you do this?

[Anonymous Coward]

If they used your genetics to make any sort of case against coverage, they would violate this law. They can't use it along with other information any more than by itself.

Re:Why would you do this?

[bitt3n]

A) Healthy people overpay to cover the costs of the sick people or B) the company can charge you more when you're healthy to cover the costs of when you're sick.

or C) people get genetic tests under false names, find out they're going to be really sick, and then get the ultra-deluxe insurance they wouldn't have purchased otherwise, thus driving up rates for everybody, and forcing everybody to get genetic testing before deciding whether they want to pay for insurance.

Re:Why would you do this?

[Anonymous Coward]

And this is a stain on your health record that will last the rest of your life. Nice going.

Which will be a nice long life since you found out that you were more at risk and were able to keep that cancer in check sooner. So - damn you genetic screening!

Re:Why would you do this?

[tnk1]

Aside from how the health care is provided, I think the real question here is "how would the insurance companies get their hands on my DNA reports in the first place?" If you just plain got tested on your own dime, then that information should be between you and the testing company.

If you were tested as instructed by a doctor for an actual condition, that your insurance then had to pay for, you would expect that they could get their hands on it because they paid for it. Even then, it may be overreaching on their part for them to demand the entire result set of the tests if they didn't relate to the procedure that they are paying for.

If these tests do make it possible for third parties to get your information, then they are probably a poor idea, and not just because of insurance rates. You don't want the government or other companies getting their hands on this. What happens if your girlfriend/boyfriend breaks off your engagement because she found that your genome showed signs that meant that your children might be something other than "perfect"? Or you find yourself under "unofficial" police scrutiny because you are found to be extremely susceptible to genetically-triggered psychological disorders in certain situations? There is a wide variety of potential abuse of this information, just like there would be for any medical record you have.

Re:Why would you do this?

[Ihlosi]

It's not the colonoscopies they're looking for, it's the "I have the sniffles again this week and I NEED an antibiotic, doc! Don't worry, my insurance will cover it!"

That's where copayments and the point about covering only treatments that are both medically necessary and effective comes in. Treating a common cold with an antibiotic is neither, so if you wanted that antibiotic anyway (which your doctor should advise against, see the whole issue of resistances, plus you're messing up your digestive system as a side effect), you can pay the twenty bucks or so out of your own pocket.

And doctors aren't supposed to prescribe whatever the patient wants. They'd put drug dealers out of business if they did.

Re:Why would you do this?

[Faerunner]

And doctors aren't supposed to prescribe whatever the patient wants.

Exactly.

Re:Why would you do this?

[L0VECHILD]

your insurance carrier catches wind of your DNA results and jacks up your premiums so now you can't afford health insurance

What kind of healthcare system would penalize someone for ensuring they are living the healthiest lifestyle possible? The US healthcare system needs reform.

Re:Why would you do this?

[sexconker]

I went to the doctor to get a prescription for an asthma inhaler one morning (after a bad random attack with no rescue inhaler). She threw antibiotics (azithromycin?)at me as well, claiming I might have a mild upper respiratory infection.

The next time I went in (many months later), I was sick as shit, getting a respiratory infection.
I had a busy week of work ahead of me, so I go in and ask for antibiotics. (Normally, I'd take a few sick days and tough it out and wait for the weekend.)
The same doctor tells me that I'm probably at the start of an upper respiratory infection. She says "I don't like to hand out antibiotics unless they're necessary. There's a lot of stuff in the media now about using too much antibiotics.".
She tells me to come in in a day or two if I'm worse, and she might give me some then.

Fucking copay and time wasted. No way in hell was I going to go back (yes, I was much worse the very next day) after that. Why is it that my primary care provider (a guy who is not an idiot) is the one I never see?

I don't really have a point.
Just consider the idiot doctors as well, the prescription barrier to many common medications (I know people who buy penicillin for horses/aquariums to use for themselves), etc.

Re:Why would you do this?

[sexconker]

Except that they have and have gotten away with it.
Oops.

Re:Why would you do this?

[Anonymous Coward]

What happens if your girlfriend/boyfriend breaks off your engagement because she found that your genome showed signs that meant that your children might be something other than "perfect"?

She goes out the door ass-first. If I'm feeling kind, I'll open the door first. If someone's willingness to stay with me depends on my genetic profile, they're not the sort of person I want to be with.

Re:Why would you do this?

[Ihlosi]

What kind of healthcare system would penalize someone for ensuring they are living the healthiest lifestyle possible?

One that is run for profit? In such a system, it doesn't matter how healthy your lifestyle is. All that matters is how large and calculable your risk is. If your genes say that you're an unacceptable risk, you can live as healthy as you want and sill not get any insurance (or a rate that pretty much says 'We don't want to insure you.').

Re:Why would you do this?

[PCM2]

You missed the part where this is America and you have no health insurance with which to combat said cancer. You go bankrupt in the first year and succumb swiftly thereafter.

Francis Collins and "cdesign proponentism"

[Anonymous Coward]

Francis Collins also believes that Jesus rode dinosaurs. He was once a respected scientist, but then he took a short step off a long intellectual pier. Why should I give his advice any consideration?

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.

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

Fair enough, I was wrong. He doesn't think Jesus rode dinosaurs. He thinks God spoke to him in the form of a tripartite waterfall.

That's what tenure is good for, I guess. It can make the difference between being appointed to the National Institutes of Health, or being sent to a padded room. Oh, wait, that's not tenure at all... it's religion.

Re:Francis Collins and "cdesign proponentism"

[Bigjeff5]

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

Do you mind if I borrow that for my sig? I imagine you saying that in a sort of angry condescending tone, and I love it.

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

Do you believe in a god? Please repeat after me:

"I talk to an invisible man in the sky. He created the Earth and he dosen't know why"

Repeat 40,000 times until you're fallen into a vacuous blank-stared trance, the kind the Mormons have. Now you are at the height of suggestability. This is God speaking, and I order you to ruin or kill all infidels and blasphemers. It is your holy duty to make the pilgrimage to Iran and beat up as many riot police as you can find.

Now hold on for a sexond while I make a deal with Allah to get you those 72 virgins.

Re:Francis Collins and "cdesign proponentism"

[ColdWetDog]

Be sure to keep the "God Bless" part. Cover all your bases, as it were.

Re:Francis Collins and "cdesign proponentism"

[spiffmastercow]

Francis Collins also believes that Jesus rode dinosaurs. He was once a respected scientist, but then he took a short step off a long intellectual pier. Why should I give his advice any consideration?

Because you don't want to commit an ad hominim fallacy?

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

It's not an ad-hominem fallacy when someone deliberately calls their own judgment into question. Read the links and see if you think they're the work of a rational human being.

Re:Francis Collins and "cdesign proponentism"

[Daniel Dvorkin]

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"

[Anonymous Coward]

The mockery of religion seems to lie in one of two camps.

1: Religion is stupid.

Arguable. People may argue that the belief in a improbably and unprovable entity is ridiculous and credulous, however such a belief, provided that it causes no harm, does not matter. Contempt towards another person's beliefs shows not enlightenment, but prejudice. An attitude of disbelief yet acceptance towards the moderate or liberal religious believers is acceptable, however mockery or contempt is not. For hardcore theists, do as you like.

2: Religion causes harm.

Once again, arguable. People point out the Inquisition or religious terrorists as examples of the inherent harm of religions. I argue that this is not the fault of religions but of zealots. Religion may in fact inspire far more zealots, however once you decry something for the bad it causes while ignoring the good is the point where you jail the innocent in order to capture the guilty. Further, a person who desires to can twist anything into a reason for causing undue harm to others. Perhaps I could be an atheist who is also a hedonist. Due to the lack of a negative afterlife, I could go out and rape and murder without abandon in order to satisfy my desires. Is this the fault of atheism? Doubtful. This is the fault of an individual.

Others speak of how religious belief causes a decline in scientific advancement. Again, this is cause by zealots not by moderates. The proper understanding of the universe, I believe, should be that irregardless of the existence or nonexistence of God, the universe is run by fundamental rules. We, as humans, should learn to understand said rules. For theists, this is to grow in wonder at how God created the universe so perfectly. For atheists, this is to grow in wonder at how the universe runs by such perfect rules. The attitudes of those who say that scientific advancement or a growing understanding of the world is unnecessary because "God did it" is the same attitude as those who say "Things are fine as is/Things seem to work let's just leave it at that." The first is something hardcore theists would say. The second is something a Luddite would say. In both examples, they stifle scientific advancement.

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?

Re:Francis Collins and "cdesign proponentism"

[artor3]

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."

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"

[fractoid]

Funny, I read the whole thing (including the 'God Bless' at the end) in Ned Flanders' voice. It makes it even more disturbing. ;)

Sigs and religion aside, it's not surprising that this first wave of DIY genetic screening tests is somewhat iffy. It's a lot more complex than things like pregnancy tests, and they've only been around for a relatively short amount of time. Sorta like the difference between detecting a particular file on your computer vs. testing for a particular few bytes in that file being one of several values, except the computer's made out of goo.

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:Francis Collins and "cdesign proponentism"

[Daniel Dvorkin]

[sigh] I know exactly what "sic" means, and if you carefully read my post and the post I responded to, you'll see why I used it.

Your example of the chef doesn't really hold up. You're the only one qualified to decide if you like the way his food tastes; there are no issues of fact to debate. A closer analogy would be one of food safety -- no matter how tasty the food that comes out of the kitchen, would you be comfortable eating at a restaurant where the head chef had gone on record stating that he thought health and safety inspections were a waste of time?

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

Religion is neither.

It is a distraction to life. A sense of community of distraction, a pre-modern-day Playstation 2 - who has the best life? Who will go to God for goodness. Karma... Love... Money..

Religion is old school populace dominance....

Re:Francis Collins and "cdesign proponentism"

[wellingj]

Um... I'm not a hard core believer in Jesus as my savior and all that, but I'm pretty sure his main contention was that we should be good to one another.

Misinterpretation for personal benefit has really messed up organized religion.

Re:Francis Collins and "cdesign proponentism"

[Saysys]

If you ever do honestly question the existence of God just pray with an open mind to know whether God is real and the spirit of God will make itself evident to you.

Personal hurt is easily solved by the personal love God has for each person.

Re:Francis Collins and "cdesign proponentism"

[Ethanol-fueled]

I like the Greek gods. They became intoxicated, had affairs...they were imperfect.

Jesus Christ was a pretty cool dude, but he was too perfect. Like Dostoevsky's Idiot, it was only a matter of time until he was thrown to the sidelines muttering and babbling to himself while the Grand Inquisitors siezed power.

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.

Re:Francis Collins and "cdesign proponentism"

[Ethanol-fueled]

HAIL SATAN.

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

Um... I'm not a hard core believer in Jesus as my savior and all that, but I'm pretty sure his main contention was that we should be good to one another.

Um... you need to spend some time with a Bible, then post.

Re:Francis Collins and "cdesign proponentism"

[socrplayr813]

I tried that when I was young and found nothing. I felt much better after learning the truth. Life is much more pleasant living with my own, appropriate set of values, rather than the arbitrary BS that people tried to cram down my throat (granted, my values aren't much different from theirs, but now I don't have to put up with them). It also adds some comedic value when the odd extra-religious person looks at me funny and tries to avoid telling me that I'm going to hell for not believing.

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

Y'see, you're going for specific religion there whereas I'm just saying the concept of religion isn't wrong

Now, I don't hate any abstract concept. I don't hate the internet. I do dislike specific websites but that doesn't mean I hate all websites. Just because Hitler was around doesn't mean humanity, Germans, or even the Hitler family is inherently flawed. I won't condemn religion, although I may condemn some religions or religion wannabes. Unless you show that the concept of religion, not in fact specific religions or religious beliefs, is somehow less abstract than love or democracy, religion also holds the same rights those do as well.

You may hate specific religions and hey, that's your right. Like I said, I do too. Some are stranger than others. But to say that the structure of all religions is inherently wrong and harmful is a bit extreme.

Of course, this is /. and the most vocal ones here are often supporters of atheism, as if it were some form of enlightenment. Maybe it is, maybe it isn't. I'm more of an agnostic myself in that I neither deny nor affirm any specific God or gods. I simply leave myself open to the possibility that it just might be true. To willfully blind yourself to the possibility of a being existing outside the scope of our knowledge is, in my mind, unscientific. The other extreme, blind faith in some form of deity is just as bad if not worse. Blind faith leads to stagnation. It's only in questioning God that people can grow to know him/her/it. A compromise, in my mind, is that a deity or deities could exist. But irregardless of their existence or nonexistence, until they affect the world somehow, we can treat them as an unnecessary factor.

Let me confirm this though. I'm not supporting Francis Collins or his view on God. I just have to say, pulling out one or two, frankly whacky people and declaring "This is what religion does" is a showing of your own ignorance. Religion has its costs and its benefits. There's the good and the bad just as in everything else in life.

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

> Misinterpretation for personal benefit has really messed up organized religion.

And now it appears to be working on organized atheism, too...

Re:Francis Collins and "cdesign proponentism"

[Belial6]

Maybe Jesus was all happy hugs and kisses, but his dad, the guy that the Jesus worshipers believe is the real power, and the one with the ultimate say in all things, demands his followers be prepared to wage war, kill those that are different, rape, pillage, plunder, and murder their own children as human sacrifices.

Claims of Jesus's endorsement of piece and love doesn't give much comfort when he is only the SON of God. It's not like there would be any chance of him gaining the throne. It's documented how usurpers are handled after all.

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

His advice may merit consideration because Francis Collins accomplished more in the time it took me to write this sentence than you have, or will, in your entire life.

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

Speaking as an atheist and a working geneticist, Francis's scientific credibility is without question. I could learn that he worships Kermit the Frog and it wouldn't make the scientific discoveries he's made any less valid.

Re:Francis Collins and "cdesign proponentism"

[Saysys]

Love and faith go hand in hand.

I, personally, do not think I could look at my wife and child without seeing how much the creator of all existence loves me.

I do not believe God sends people to hell, simply that we spend our eternity exactly the distance form God that we chose to be in life.

Distance from God being a function poorly influenced by church attendance and strongly influenced by your loving relationship with God.

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

As an exercise, substitute "belief in the Tooth Fairy" for each instance of the word "religion" in your post. Then, explain why this substitution was, or was not, appropriate.

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

I, personally, do not think I could look at my wife and child without seeing how much the creator of all existence loves me.

Wait until your wife or child comes down with a case of guinea worms, then talk to me about the work of a loving God.

Your point of view is at once naive, provincial, and myopic. You hold it only because modern secular society gives you the leisure to do so.

Re:Francis Collins and "cdesign proponentism"

[ShakaUVM]

Do you mind if I borrow that for my sig? I imagine you saying that in a sort of angry condescending tone, and I love it.

Sure, no problem.

Remember, Jesus tells us to love the stupid person, but hate the stupidity.

Re:Francis Collins and "cdesign proponentism"

[Bigjeff5]

Muchos Gracias.

Re:Francis Collins and "cdesign proponentism"

[socrplayr813]

I, personally, do not think I could look at anything and believe that there is a creator of all existence. My distance from your God is infinite because I do not believe He exists. I have no relationship with your God or any other god because, again, I do not believe that they exist.

I could go into detail exactly what I think about religion and its followers, but I will do my best to avoid insulting you. I respect your right to believe what you wish; please do the same for me.

Re:Francis Collins and "cdesign proponentism"

[Saysys]

God loves us enough not to end our existence despite the evils that we perpetrate or fall into. It may feel, some times, like everything would be better where we not to exist. But God's love is so great that he allows us to exist despite the pain of life.

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

Murder their own children? Abraham was prevented from actually sacrificing Isaac, and G-d abhors human sacrifice, such as the practice of the Canaanites sacrificing their children in the fires of their idol Moloch. The L-rd's anger toward human sacrifices is one important reason among many why Jews don't believe in the Christian demigod who the Christians think was killed as a human sacrifice. FYI.

Re:Francis Collins and "cdesign proponentism"

[Anonymous Coward]

Your post is the very reason why moderation on slashdot is voting, not moderation.

"[God]... and specific plans for humanity that simply are not compatible with the rational worldview we (should) demand of our scientists."

A pure scientist doesn't care about the world view. Your stance is a religious one, based on the faith in his science and the scientific theory.

btw, you don't speak for me, so don't use "we." You speak for yourself and maybe your tribe/clan.

Your world view does not account for a world of tolerance and separation, which occurs intrinsically in a physical world.

"but the actual God he's evangelizing for has specific traits, specific likes and dislikes..."

So he's accountable to (his) God. So what? Anything he says is subject to scientific proof. For a person who puts faith in science, you have very little trust in the very system you deem necessary for a rational worldview.

The reason your silly claims fall apart is because your world has simply results and proof, no standards besides that of empty observation. It's based on hate of religion, that god is in teh way, distrust of the religious establishment, which does not reconcile with the trust you place in the science which is run by the very people who, of these scientists, have for centuries been religious and areligious.

iow, your science is founded and continuous to flourish based on scientists who also happen to be religious. And to claim to have a rational world in the absence of ethics and morals, which science has done little to nothing to advance, is silly.

Your rational is in absence of emotion, which is no way to live. The Human Genome Project spent billions setting up ethic departments, and little to nothing has been done for a generation to advance this beyond a religious debate, mainly because the science side of the ethics debate has no foundation.

This was proved, ironically, by the Bush clone ban, which pushed research that is deemed more acceptable for treatment by the mass of our population than the limited left that it would have served and the right which would have been forced to chose between religion and ethics, and fatality or disability. Religion was the foundation of that argument, religion was right in that argument, and yet it continues today, whether through ignorance, promoting a liberal rational worldview, that such staving of treatments was wrong.

Your science is not in the absence of culture, politics, or life. Your rational world is not rational at all if it misses the point of life and death.

btw, I'm an areligious scientist. I don't believe in God. But people like Collins are and can be professionals. It's really you, who don't think people can do that sort of mental separation, which seems to be irrational, dismissing out of hand because someone may or does believe.

While you reap the benefits of the person who aided your cause. How fascist.

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.

Deep sequencing

[SUB7IME]

If I'm going to drop a couple Gs on getting a genome-based risk assessment, they had damn well better deep-sequence that shit.

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:Deep sequencing

[Miseph]

And if you get it on the cheap, they might even give you results at the drop of a C.

Re:Deep sequencing

[jd]

You've GATA me there. I'm out of puns.

Re:Deep sequencing

[Atmchicago]

It's time to launch a full-scale, nucleotide-based, pun-ishing ATTAC!!

Re:Deep sequencing

[Miseph]

You killed it. Now go sit in the punalty box.

So the conclusion is....?

[some1somewhere]

So which service produces, in his expert opinion, the better overall results/conclusions/advice?

I RTFA and fail to see what the pros/cons of each service is, and which one he recommends.

I know that would be a boon to whichever company is producing the better results, but who cares? If he is suppsoed to be independent, what does it matter if he gives his honest opinion?

Re:So the conclusion is....?

[Anonymous Coward]

Conclusion is DTC genetic testing has room for improvement?

Re:So the conclusion is....?

[BrokenHalo]

I RTFA and fail to see what the pros/cons of each service is, and which one he recommends.

That's because he can't recommend any on the basis of the results or methodology of the testing.

SNPs can be a useful tool, but because (by definition) they are single nucleotides, you need a lot of them to be able to validate a pattern. From the submission, he mentions 3 labs using 5, 10 and 15 SNPs and claiming to be able to draw inferrences from these. My understanding (FWIW) is that a mere 5 polymorphisms are not really sufficient to draw useful conclusions in this way, and 15 might still be on the low side, given that there is little in the way of firm proof of association with known disease conditions.

If you want to pursue this kind of testing, one can only suggest that the more SNPs the lab tests for, the more credibility you can expect it to have. And the more you can expect it to cost.

Re:So the conclusion is....?

[some1somewhere]

Problem is, he doesn't specify which labs use more SNPs or "more useful" SNPs (which as you mentioned, should provide better/more accurate results).

The point of experiments and tests should be to draw some conclusion (even if the conclusion is that all fail) but clearly some services are performing better than others and are turning out more accurate. Why does he not state, in his professional and unbiased opinion, which one is better?

Re:So the conclusion is....?

[dondelelcaro]

Problem is, he doesn't specify which labs use more SNPs or "more useful" SNPs (which as you mentioned, should provide better/more accurate results).

Primarily because it's not known yet for a large number of diseases.

The point of experiments and tests should be to draw some conclusion (even if the conclusion is that all fail) but clearly some services are performing better than others and are turning out more accurate. Why does he not state, in his professional and unbiased opinion, which one is better?

Because most of the diseases that people actually care about haven't yet been completely characterized there's no way for anyone to even determine how well they are performing. The studies that are going into this (Genome-wide association studies) are still in their relative infancy and we've only been able to find the causative alleles in a few genes for a few diseases at this point in time.

In the future, when more is known, it will be relatively simple to produce a kit which actually looks at the exact SNPs which are directly associated with disease, and then we can analyze their effectiveness at predicting the actual presence and onset of disease.

God Damn Us...

[fireheadca]

...and let geneticists sort us out.

"almost" no differences?!

[Anonymous Coward]

sequence-wise, the tests 'appear to be highly accurate': there were almost no differences in the genotype information

Almost no differences? Can't a difference in a single gene do pretty crazy things? Like your-gene-is-alenine-don't-worry-you'll-be-just-fine. That gene-is-a-glutamate-your-eyes-will-number-eight...

Re:"almost" no differences?!

[Anonymous Coward]

8 eyes? I've always wanted a few more! Where can I get that?

Basic probability maths

[locster]

Clearly the statistical analyses' are wrong for at least two of those companies. The prior probability of risk for a given disease is 'average', and if you don't test enough polymorphisms or if the correlations are weak then it remains average. Trouble is you can't make a business case on selling such weak information, so there's an incentive to spice up the summary info they provide.

SPOnGE

[Anonymous Coward]

sales a8d so on, Mr. Raymond's part of GNNA if

This practice is common

[MobyDisk]

The practice of using different numbers of gene sequences is common: the same thing happens if you get an HIV test, or an HPV test, or FLU, or whatever. In that case though, the FDA regulates it to prove that the result is clinically valid. I'm not sure what involvement the FDA has in this.

Re:This practice is common

[Anonymous Coward]

All of the tests you're talking about are ELISA (protein), not gene sequencing (DNA).

Re:This practice is common

[MobyDisk]

Nope. I'm talking about PCR assays.

Assign a company to its result

[Anonymous Coward]

From the description here an hearsay, you can assign the results in the same order than the companies are presented in this post. There is also only one of this company who manually curated experimental evidence, instead of computer text mining scientific conclusions. That is to say that risk assessments are more or less "quality controlled"...

Heritability

[drunken_boxer777]

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.

Re:Heritability

[Anonymous Coward]

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.

Or more likely, they want you to pay extra for that information.:/

Re:Heritability

[FleaPlus]

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).

That's kind of odd, because at least 23andme (haven't checked the others) seems to offer information on whether someone is a cystic fibrosis carrier:

https://www.23andme.com/health/cysticfibrosis/

Cystic Fibrosis (Delta F508 mutation)

Cystic Fibrosis is one of the conditions that 23andMe analyzes. Our service includes the following information:

* Whether or not you are a carrier for the Delta F508 mutation linked to cystic fibrosis.
* Information on i3000001, a marker that influences your carrier status for Cystic Fibrosis.
* Background information on Cystic Fibrosis and a list of counselors, links and support groups in your area.

I've got a DNA Sequencing company too...

[PHPNerd]

DNA Sequencing Report for: John Doe Sequencing: 100% Complete Risk for all diseases: average. Have a good day. :)

SNP Analysis

[LabRat007]

I began performing SNP analysis on genomic DNA for schizophrenic patients back in 2002 in the new Pharmacogenoics group of a large Pharmaceutical company. Our goal was to correlate drug effect to the genetic background of the individual. If we could establish a relationship we could potentially get a few failed drugs to perform "better" when used in patients genetically predisposed for a positive effect and get them into the market.

All of our results required TEAMS of statisticians to figure out if there was any correlation. You couldn't simply look at the data and say ah-ha! they are responding! Everything was very subjective and open to interpretation.

The very best current genetic testing can do is tell you if you're more inclined toward some disease. At our current level of knowledge we have few absolutes when it comes to genes.

statistics created doubt about OJ's blood

[peter303]

The defense lawyers used widely varying statistical numbers from scientific experts to create doubt as to whether OJ Simpson's genes matched blood found at the crime scene. This was one piece of doubt among several others in the case before a jury eager to find any reasonable doubt to acquit.

Genotype as preventive medicine, could be good

[Julie188]

When my youngest was born, we were asked to partake in a study about childhood diabetes by giving a blood sample. Lots of diabetes in my family and she turned up to have a marker for it so she was asked to be part of the study. She never got diabetes but she did wind up having Celiac, a somewhat related issue. We ONLY found out about the Celiac because she was in the study ... she was diagnosed via a blood test when she was (we thought) asymptomatic at the time. Celiac screening isn't (though should be) a routine screening process for kids. It could be good for modern medicine if each person had personal sets of screening tests that are done each year rather than some standards based on the statistical likelihood of the entire population.

Julie
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