The Next Revolution In Medicine: Genome Scans For Everyone

Just hold on a minute there, cowboy. by ColdWetDog · 2013-03-01 04:46 · Score: 5, Insightful

Price isn't the only determinant of whether something is a 'routine part of medicine'. For the foreseeable future, there is remarkably little utility that an individual's genome brings to the table. It will become a very important part of medical research, but in terms of an individual's health, not so much.

It will be hyped. It will likely end up like 'full body CT scans" - a bragging tool for the seriously hypochondriac but of no help to the routine patient.

Even the Single Nucleotide Polymorphism (SNP) data which is pretty cheap now (basically what the police use for forensics) helps most people very little. In the context of answering a specific genetic question, perhaps - but not as a routine. When you send someone to a medical geneticist, most of the time and effort revolves around getting the person to understand what you are trying to accomplish and the pros and cons of doing so. Having whole genome sequencing just makes it even harder.

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Faster! Faster! Faster would be better!

Re:Just hold on a minute there, cowboy. by pesho · 2013-03-01 04:49 · Score: 5, Insightful

Price isn't the only determinant of whether something is a 'routine part of medicine'.
yes it is, do you know how much money your doctor can make by adding this to your routine blood work?
Re:Just hold on a minute there, cowboy. by bhcompy · 2013-03-01 04:52 · Score: 1

It will probably be something more along the lines of medical companies using it for data collection and risk assessment. Actuaries formulating rates and risk assessment would kill for this information
Re:Just hold on a minute there, cowboy. by Anonymous Coward · 2013-03-01 04:53 · Score: 0

As a diagnostic tool it would be invaluable. Supposing a patient presents with the symptoms for say Celiac. Assuming a genetic test exists you can sample a drop of blood rather than perform a biopsy of the colon to confirm the diagnosis.
For $1000 I can forgo an invasive, uncomfortable procedure? Sign me up.
Re:Just hold on a minute there, cowboy. by WillAdams · 2013-03-01 04:55 · Score: 1

The interesting thing will be when we can act on a genome as we can any other set of plans or diagrams. Hal Clement's short story ``The Mechanic'' takes an interesting look at this, the protagonist is a genetic engineer able to create new life forms, or to re-grow / repair parts of existing life forms (incl. people).
The scary part will be when insurance companies will be able to use such information to determine who is unprofitable to insure --- for that see the movie _Gattaca_.

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Sphinx of black quartz, judge my vow.
Re:Just hold on a minute there, cowboy. by Anonymous Coward · 2013-03-01 05:03 · Score: 0

That will only be a problem in the US, who are the only ones to not have universal health care.
Re:Just hold on a minute there, cowboy. by ColdWetDog · 2013-03-01 05:11 · Score: 2

First off, insurance companies in the US are already barred from using genetic data for insurability purposes.
Second, straight DNA sequencing doesnt give you the keys to the kingdom. Epigenetic factors like methylation are turning out to be extremely important factors in gene expression. Further, there are a number of classes of RNAs that are likewise critical to organism development.
Basically, the central dogma has been barking up the wrong tree.

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Faster! Faster! Faster would be better!
Re:Just hold on a minute there, cowboy. by drinkypoo · 2013-03-01 05:29 · Score: 4, Interesting

For the foreseeable future, there is remarkably little utility that an individual's genome brings to the table.
That's true as long as you treat humans like poor people treat cars and fix them when they break, but it's not true if you treat humans like rich people treat cars and take them in (or have them taken in) for all their scheduled maintenance.

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"You're right," Fisheye says. "I should have set it on 'whip' or 'chop.'"
Re:Just hold on a minute there, cowboy. by K.+S.+Kyosuke · 2013-03-01 05:31 · Score: 2

As a diagnostic tool it would be invaluable. Supposing a patient presents with the symptoms for say Celiac. Assuming a genetic test exists you can sample a drop of blood rather than perform a biopsy of the colon to confirm the diagnosis.
Not only that, what happens if you do large-scale sequencing of human population and correlate their medical records with their genetic makeup, and apply some serious machine learning? I smell large health care expenses savings ahead...

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Ezekiel 23:20
Re:Just hold on a minute there, cowboy. by Artraze · 2013-03-01 05:38 · Score: 2

> Price isn't the only determinant of whether something is a 'routine part of medicine'. For the foreseeable future,
> there is remarkably little utility that an individual's genome brings to the table.
Technically, yes, it's not so much price and it is value, but realistically price is still a major factor in that calculation.
As it stands, there are quite a few diseases that we can identify just looking at the genome. For many, sure, there are other tests, but if genome screening was, say, cheaper than two of those, then it would be a significant and valuable first stop for both diagnostic and preventative medicine.
(And of course, the cheaper it becomes, the more analysis can be done and the more useful it becomes.)
Re:Just hold on a minute there, cowboy. by Grave · 2013-03-01 06:01 · Score: 2

Along with making the entire insurance industry freak out. If you can know, from birth, the statistical likelihood of ending up with a disease, that suddenly does some interesting things to health care premium calculations. Does the requirement that you cannot be denied coverage due to pre-existing conditions have any restriction over individual premiums?
Re:Just hold on a minute there, cowboy. by CptNerd · 2013-03-01 06:08 · Score: 1

Right, in every other "enlightened, caring" country, government bureaucrats will determine that everyone gets one, and they will get to use that information for the purposes of better government. And we know that will work out well, as it always has before...

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By the taping of my glasses, something geeky this way passes
Re:Just hold on a minute there, cowboy. by K.+S.+Kyosuke · 2013-03-01 06:30 · Score: 1

I'm not sure that, emotions put aside, this should make anyone freak out. What if it turns out that many, if not most (or all) of us have some disposition towards a particular averse medical condition (every one of us a different one, of course), we just don't know it? If we end up knowing what each and every one of us can expect in the future, health-wise, how does not decrease overall medical expenses of our society? Isn't prevention and early treatment the most cost-effective way of handling most medical conditions?

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Ezekiel 23:20
Re:Just hold on a minute there, cowboy. by Fwipp · 2013-03-01 06:48 · Score: 2

Because if I have a 40% chance of getting leukemia, my insurance premiums will be through the roof. So even if I never got leukemia, I would have spent significantly more than Jane down the street.
(Really, this just continues to argue against private insurance and health care. But having expected/mandatory genetic tests will punish some individuals for things they have no control over.)
Re:Just hold on a minute there, cowboy. by ceoyoyo · 2013-03-01 06:53 · Score: 1

Good thing you're not in charge of treating patients.
First, the assumption that a genetic test exists for a given disease is an incredibly poor one. Genetics isn't that simple. There are a very few diseases where a simple genetic change means you've got the disease. Guess what? Those all have tests already. Most of the time genes only increase your chance of developing a disease, and that influence may be spread thinly over tens, hundreds or thousands of genes, all interacting.
Secondly, you can't confirm a diagnosis, except in a few rare cases, with genetics. Oh hey, you have a some genes that increase your likelihood of having Celiac disease by a few percent, sometimes. Let's skip the biopsy and just cut out that troublesome bit of bowel!
Genetic sequencing is a horrible diagnostic tool, and probably will be into the foreseeable future.
Re:Just hold on a minute there, cowboy. by ceoyoyo · 2013-03-01 06:59 · Score: 1

Yes, in that case you get exactly what the OP suggested - paranoid rich person status symbols like the full body CT (which does more harm than good, by the way - it's a classic example of why screening tests are so limited).
You can already get tested for various "important" genetic factors and you'll get back a report saying you have the "gene for X," which increases your probability of getting some disease by some small percentage or fraction thereof. Which is where the rich paranoid starts throwing money at more quacks and crackpots.
Re:Just hold on a minute there, cowboy. by Anonymous Coward · 2013-03-01 07:11 · Score: 0

Eventually they might be able to peg certain genetic markers to individual metabolic differences within the human population. Why would that be useful? Some drugs that might be useful for some individuals may be toxic to others. (Believe it or not, people break down different chemicals in different ways or at different rates.) Also dosages for various drugs could be altered in a more accurate manner depending on long it's likely to stay in a person's system. (Not just a generic guideline by weight or sex anymore.) So by pre-screening, doctors prescribing medication would be able offer the strongest or most effective medications when needed with much less worry about adverse effects.
Of course the FDA will have to alter how drug screening studies are done in order to get the kind of data that would make this procedure actually useful. Some banned drugs might also be worth reviewing, provided this process is effective enough at preventing medications from getting to those individuals that would react badly to them.
Re:Just hold on a minute there, cowboy. by Anonymous Coward · 2013-03-01 07:18 · Score: 0

Why try you cant fix stupid with these people. There is way to many of them that keeps them all gigged up.
It is a lot like going back to a bar twenty years later to find the same five people sitting on the same stools as when you left.
Very sad really.
Re:Just hold on a minute there, cowboy. by confusednoise · 2013-03-01 08:41 · Score: 1

Well, no offense but clearly you're not in charge of treating patients either. There are a number of misstatements in your post.

Actually there are 3500 genes that are directly linked to recessive disease and no, not even close to all of those have an existing test. There are also an additional 3500 or so diseases that are suspected to be genetic illnesses but for which the exact gene is not yet know.. Further, the problem with most existing tests is that they are single gene, and each single gene test costs usually at least $1000 - $3000 to administer. The way it mostly works now is that you have a physician or medical geneticist looking at the patient and guessing which single gene test(s) to order. If it comes back negative, the physician makes another try using another gene test. This in turn leads to what is commonly called the 'diagnostic odyssey' where a patient can go years without a diagnosis and can easily go through 20-30k of test.

Contrast that with whole genome testing where for a relatively low cost you can look at all the genes in the genome. This has huge benefits, not the least of which is that genes which wouldn't have normally come to mind for a physician (in the case of very rare diseases for instance) will be interrogated and a mutation can show up.

Disclaimer: I'm in the field working on whole genome sequencing and reduced gene panel sequencing as a diagnostic tool.
Re:Just hold on a minute there, cowboy. by Anonymous Coward · 2013-03-01 09:26 · Score: 1

The short-sighted folks who maintain views such as this miss a key point. While I'm no fan of this particular company's solution, the ubiquitous sequencing of humans by the medical establishment has the potential to provide researchers ACCESS TO THE VERY DATA THAT WILL PROVIDE THE INFORMATION THAT WILL MAKE GENOME SEQUENCING MORE MEDICALLY RELEVANT. If you stop the process before it gets started in earnest, then what these folks are pouting about becomes a self-fulfilling prophecy. We will not be able to extract much actionable medical knowledge from genomes because we won't have the sample numbers to conduct that statistics that will make it possible. Right now the old farts of the clinical establishment are laying down all the groundwork to make what should be a 10 year transition to personalized genomic medicine into a 50+ year one. They are further enabled by biomedical ethicists who must justify their existence by warning about the dangers of something or another... Those concerns about insurance discrimination, etc, can readily be addressed--and largely have been--through appropriate laws.
Re:Just hold on a minute there, cowboy. by Anonymous Coward · 2013-03-01 09:38 · Score: 0

The short-sighted folks who maintain views such as this miss a key point. While I'm no fan of this particular company's solution, the ubiquitous sequencing of humans by the medical establishment has the potential to provide researchers ACCESS TO THE VERY DATA THAT WILL PROVIDE THE INFORMATION THAT WILL MAKE GENOME SEQUENCING MORE MEDICALLY RELEVANT. If you stop the process before it gets started in earnest, then what these folks are pouting about becomes a self-fulfilling prophecy. We will not be able to extract much actionable medical knowledge from genomes because we won't have the sample numbers to conduct that statistics that will make it possible. Right now the old farts of the clinical establishment are laying down all the groundwork to make what should be a 10 year transition to personalized genomic medicine into a 50+ year one. They are further enabled by biomedical ethicists who must justify their existence by warning about the dangers of something or another... Those concerns about insurance discrimination, etc, can readily be addressed--and largely have been--through appropriate laws.
Re:Just hold on a minute there, cowboy. by Anonymous Coward · 2013-03-01 09:52 · Score: 0

We should be getting paid to have our individual genome identified and used for marketing purposes.
Re:Just hold on a minute there, cowboy. by Anonymous Coward · 2013-03-01 10:38 · Score: 0

If God had left us the blueprints to the human genome, then these tests might be useful today. But unfortunately he didn't, the problem is we don't know what most of the genes do and how they interact with each other, which makes genomic testing pretty useless today, aside from a handful of conditions where we can identify markers that indicate increased risk (but generally not guarantees) of getting diseases, and for some recessive genetic diseases which may impact your decisions regard having children if your chosen partner also happens to share the same recessive gene. Right now we have a lot of reverse engineering of the human genome to do before these tests will be truly useful.
That's the difference between humans and cars, cars are simple and we know how the are supposed to work, humans are complex and we only have a rudimentary understanding of how they work.
Re:Just hold on a minute there, cowboy. by Anonymous Coward · 2013-03-01 11:17 · Score: 0

Well, hopefully once genomic sequencing leads to actual cures for genetic conditions, then we'll have made it past that vulnerable stage where we were fearful of being denied coverage for something we had no control over.
All in all, the fact that widespread sequencing will lead to more cures is something that will outweigh the temporary risk during the transition period.
Re:Just hold on a minute there, cowboy. by rmcd · 2013-03-01 11:30 · Score: 1

I believe the Obama health-care law prohibits the use of genetic information in setting health-care premiums. I think life insurers can use the information if they get it, but not health insurers.
Re:Just hold on a minute there, cowboy. by Guppy · 2013-03-01 12:26 · Score: 1

yes it is, do you know how much money your doctor can make by adding this to your routine blood work?
If you're seeing an independent family doctor? Not much, and maybe nothing. He/She can charge you for the blood draw (if done at the office), and can charge you for a follow-up office visit to discuss results, if you come back for that. But your family doc doesn't receive any share of the test fee or ensuing referrals, as that would be considered an kickback (illegal).
Note that there are some situations where the kickback prohibition on tests can be bypassed, however. If your doc's office does the testing right there, they can charge you for it (probably doesn't apply to sequencing, at least not yet). If you have a test performed at a physician-owned hospital, your doctor can also profit personally (this tends to be more of a problem when seeing high-end specialists).
More common is the situation where the hospital owns the physician (that is, the physician's practice) -- technically the doc has liberty to refer you elsewhere, but there may be pressure from management to stay in-system. But this situations would tend to apply more to tests that might be actually performed at a hospital, like a CT scan or an Echocardiogram; if your doc send you to an outside lab service like Quest or LabCorp, he won't see any of that money.
Re:Just hold on a minute there, cowboy. by Rutulian · 2013-03-01 12:43 · Score: 1

Did you happen to notice the statement,

The following is a list of genetic disorders and if known, causal type of mutation and the chromosome involved.
(emphasis added)
Yes, there are a lot of genetic disorders, but no, there are not many we can identify by simply looking at the genome.
Re:Just hold on a minute there, cowboy. by drinkypoo · 2013-03-01 13:45 · Score: 1

If God had left us the blueprints to the human genome, then these tests might be useful today.
If I sequence your genome today then as the information becomes more useful I can find out information about you then without having to call you in. So the question then becomes, how long until it becomes so cheap that we can replace enough tests with it that it provides an obvious cost benefit?

--
"You're right," Fisheye says. "I should have set it on 'whip' or 'chop.'"
Re:Just hold on a minute there, cowboy. by Anonymous Coward · 2013-03-01 16:47 · Score: 0

I saw a documentary about this subject.
Re:Just hold on a minute there, cowboy. by TheSeatOfMyPants · 2013-03-01 16:52 · Score: 1

Nothing: my doctor's paid the same whether she orders a test, refers me to specialists, or tells me to take ibuprofen, as my HMO (Kaiser) is also the sole employer/owner of the lab, pharmacy, and staff.

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Now mostly at Usenet:comp.misc & SoylentNews.org (it's made of people!)

will make a mockery of preexisting conditions by Trepidity · 2013-03-01 04:54 · Score: 2

Either:

1. Using this data for insurance purposes will be banned, which turns "preexisting condition" into a criterion that can only be applied with eyes closed;

or 2. Huge numbers of people will be uninsurable, because the likelihood of their future illnesses will be known before they try to buy insurance.

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10 PRINT CHR$(205.5+RND(1)); : GOTO 10

Re:will make a mockery of preexisting conditions by ADRA · 2013-03-01 05:00 · Score: 5, Insightful

It works great for countries where health is 'free' (through taxes), and their main goal is to make people healthy, not to extract maximum funds from your pocket. It's too bad that you don't live there.

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Bye!
Re:will make a mockery of preexisting conditions by compro01 · 2013-03-01 05:07 · Score: 1

1 is already in place, at least theoretically, in the form of the Genetic Information Nondiscrimination Act.

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upon the advice of my lawyer, i have no sig at this time
Re:will make a mockery of preexisting conditions by P-niiice · 2013-03-01 05:08 · Score: 1

Mike Huckabee recently compared insuring someone with a pre-existing condition to insuring a house that is already burned down or a car that is already totaled. So I'm sure he'd be all for excluding people based on genetics.
Re:will make a mockery of preexisting conditions by gmanterry · 2013-03-01 05:12 · Score: 1, Interesting

Don't forget that when Obamacare kicks in the government will hold all your health records. Now, don't you think that they will submit your DNA info to at least the FBI if not all local law enforcement departments? I do.

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Since when is "public safety" the root password to the Constitution?
Re:will make a mockery of preexisting conditions by Anonymous Coward · 2013-03-01 05:17 · Score: 0

There are a lot of laws that prohibit discrimination, but percentages show something else. As long the data is there, accessible to someone, it will be seen, and you will be judged by it. Look at the internet right now. You have a work life, and a private life. But can't do anything serious in your private life anymore, because it will stay on the internet, and if they see pics of you drunk, you won't get the raise, promotion, job etc, no matter it happened only for the third time in 30 years.
Re:will make a mockery of preexisting conditions by Anonymous Coward · 2013-03-01 05:22 · Score: 0

So. And just what are you hiding? Been up to stuff you don't want people knowing about have you?
Re:will make a mockery of preexisting conditions by Trepidity · 2013-03-01 05:30 · Score: 2

From an actuarial point of view, it's a reasonable comparison. The difference is that people are born in one body with a lot of things that they can't really do anything about. Sort of like being born in a burnt-down house without any possibility to move to a new one.
A conclusion could be that insurance for healthcare makes no sense. How do I insure against the possibility of being born with a genetically caused condition? I'd have to buy insurance before I was born.

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10 PRINT CHR$(205.5+RND(1)); : GOTO 10
Re:will make a mockery of preexisting conditions by K.+S.+Kyosuke · 2013-03-01 05:36 · Score: 1

Mike Huckabee recently compared insuring someone with a pre-existing condition to insuring a house that is already burned down or a car that is already totaled.
Actually, It would be more like insuring a house with insufficient compliance to fire safety regulations. You'd be asked to take precautions as a condition for being provided with the insurance (get your house fixed), or you'd pay some extra insurance premium, or both.

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Ezekiel 23:20
Re:will make a mockery of preexisting conditions by moeinvt · 2013-03-01 06:34 · Score: 1

It's a fair comparison in many cases. If you go to buy "insurance" and your pre-existing condition is lung cancer, the house has burned down and the car is totaled.
Insurance is based on pooling risk for unexpected and unlikely events. Calling something an "insurance" policy when dealing with costs related to events which have already occurred is ludicrous. It's also stupid to use "insurance" to cover the costs of routine physicals, contraceptives or pregnancies. That's not "insurance", it's pre-payment and subsidy for costs which are totally expected.
Why not adjust health insurance premiums and coverage to match the individual's risk profile? Why not use genetic information as well? If genetic science ever gets so precise that we can predict future health problems with 100% certainty, then "insuring" against them is foolishness.
Re:will make a mockery of preexisting conditions by moeinvt · 2013-03-01 06:51 · Score: 1

Or
3. Their insurance premiums are adjusted based on their risk factors.
I'm not on the cutting edge of genetic science, but I don't think it's nearly advanced enough to make accurate predictions on an individual basis. Certainly no more accurate than predicting that obese people and smokers are at increased risk for certain conditions.
IMO, it's only logical to charge people different premiums and to make insurance policies highly specialized for the individual.
If my risk of getting a brain tumor is 50% and yours is 5%, it makes no sense to charge us the same premium on a policy which covers brain tumors. It should be my option to pay a higher premium, or buy a policy that doesn't cover brain tumors.
The government has wrecked the U.S. healthcare system with their ridiculous mandates, price controls and and cost-shifting which prevent something as sensible as making premiums a function of risk.
Re:will make a mockery of preexisting conditions by Trepidity · 2013-03-01 06:56 · Score: 2

I disagree. I think if some people have the misfortune to be born with worse genes, they shouldn't have the double misfortune of also having a significant financial burden piled on top of other burdens such as needing to get surgery. I wasn't born with a congenital heart defect, for example, but that was pure luck, not something I "deserve", and I'm perfectly happy to pay my fair share towards treating those who were less fortunate in their birth.

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10 PRINT CHR$(205.5+RND(1)); : GOTO 10
Re:will make a mockery of preexisting conditions by Anonymous Coward · 2013-03-01 07:04 · Score: 0

The Genetic Information Nondiscrimination Act, or GINA, explicitly prohibits insurance companies or employers from using genetic information as a basis for insurance or hiring decisions. Family history, even of heritable mendelian conditions such as Huntington's Chorea, is also covered under GINA. The act does not cover life insurance, or long term care insurance, however. GINA passed in 2008 with unanimous support. You can read more here: http://www.genome.gov/24519851
Re:will make a mockery of preexisting conditions by Anonymous Coward · 2013-03-01 09:41 · Score: 0

So. And just what are you hiding?
If I were to answer that question honestly, I wouldn't be hiding anything very well, now would I?
And what's it to YOU what I've been up to, anyway, creep?
Re:will make a mockery of preexisting conditions by Anonymous Coward · 2013-03-01 10:33 · Score: 0

or 2. Huge numbers of people will be uninsurable, because the likelihood of their future illnesses will be known before they try to buy insurance.
Hey Trepidity, this is your boss. I have decided to cut your salary to $50,000/year. Any objections?
What? Well, if you quit, you also lose your group health insurance..... ....thought so, thanks for staying on!
Re:will make a mockery of preexisting conditions by Kjella · 2013-03-01 11:35 · Score: 1

It's a fair comparison in many cases. If you go to buy "insurance" and your pre-existing condition is lung cancer, the house has burned down and the car is totaled.
My pre-existing condition is to have a mild case of asthma - occasionally I take some very weak meds for it and I've completed two half-marathons so I'm not exactly a wheezing geezer, but my insurance in case of accident or disease (on top of universal health care) specifically exempts anything and everything lung-related. It's more like they refuse to insure any chassis damage if it has a dented fender.

It's also stupid to use "insurance" to cover the costs of routine physicals, contraceptives or pregnancies. That's not "insurance", it's pre-payment and subsidy for costs which are totally expected.
I bet there's a lot of women who'd disagree with you that the pregnancy was not at all expected, lol. If it's completely routine check-ups I agree, but even for rather mundane consultations there's a level of "insurance" involved, it lowers the threshold of actually going to the doctor if you're sick. I talk to a friend in the US, he's pretty pissed because he blew $750 in health costs on essentially nothing... but next time maybe it isn't a false alarm, but I'm not so sure he'll go.
There's a lot of myths on universal healthcare in the US, the biggest one is that it's all free so go nuts. Trust me, doctors are good at telling the people who are frivolously wasting their time to stop and they still have to pay their copay. They also don't hand you things unless you have a real, medical need for them. The whole process is generally slow and annoying enough that nobody with a real need would "lose" things. And people don't generally act more reckless and get themselves ill or injured just because healthcare will pick up the bill, most people value their health and those that don't you probably find among your coworkers in your risk pool too.
Doctors are - if you take away all that insurance crap - actually not bad at prioritizing medical needs. They know doctors and procedures and medications are all limited resources and mostly make a genuine effort to make sure those who it the most gets it, and with a more sane legal climate you also don't have to overtreat patients or risk crazy malpractice lawsuits. Slightly off topic but it's very hard to match economic and medical incentives, I was at a seminar recently about a doctor who for about $2400 in gravel and volunteer work reduced the cost of femur fractures by about $400000. But the county paid, the state hospital saved so the economic incentive for the county was to let it happen.

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Live today, because you never know what tomorrow brings
Re:will make a mockery of preexisting conditions by nedlohs · 2013-03-02 14:57 · Score: 1

As any rational person should.
If you live in a high crime neighborhood your home and contents insurance will cost more (in terms of cost per amount covered) than that of someone living in a low crime area.
If you have a higher chance of running up large health bills than your health insurance should be more expensive.
The obvious conclusion is that health care is unsuitable for an primarily insurance model and some other method of allocating health care resources (and allocating resources towards health care) should be used by society.

Doubt it by ceoyoyo · 2013-03-01 04:55 · Score: 2

Very few diseases are due to simple genetic factors, and those already have dedicated tests. Genotyping may eventually become a big part of medicine, but not until there is a LOT more research done into how to use it, a lot more data available, and a lot better techniques for using it.

Re:Doubt it by K.+S.+Kyosuke · 2013-03-01 05:38 · Score: 1

but not until there is a LOT more research done into how to use it, a lot more data available, and a lot better techniques for using it.
Item #2 is what this is about. Items #1 and #3 (uh, redundancy?) are what you get by working with #2.

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Ezekiel 23:20
Re:Doubt it by Maximum+Prophet · 2013-03-01 06:01 · Score: 1

Very few diseases are due to simple genetic factors, and those already have dedicated tests. Genotyping may eventually become a big part of medicine, but not until there is a LOT more research done into how to use it, a lot more data available, and a lot better techniques for using it.
Right now, the genetic tests still cost $1000's, any may not be covered by insurance. (At least for what I might have)

A sub $1000 test for *everything* could save some people a lot of money.

The trick is getting the insurance companies to use genetic testing to help people instead of simply excluding the high risk patients. (The most recent bill in congress banned health insurance exclusion, but not life or long term care)

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All ideas^H^H^H^H^Hprocesses in this post are Patent Pending. (as well as the process of patenting all postings)
Re:Doubt it by Anonymous Coward · 2013-03-01 06:52 · Score: 0

A huge number of diseases are due to simple genetic factors - the diseases which come under the umbrella term of cancer. If the cost of this can drop to the point where the sequencing of cancerous tissues becomes routine, then chemotherapeutic agents can be targeted at the faulty pathway or protein and treatment regimes can be tailored to the exact type of cancer, and I expect this would be greatly beneficial to a huge number of people.
I imagine the data which could be extracted by mining a national database of genomes tied to medical histories (anonymised, I would hope) would also be incredibly useful for correlating genes to their functions and effects - on longevity, susceptibility to disease, etc. Although, of course there would be privacy issues here.
Re:Doubt it by ceoyoyo · 2013-03-01 07:04 · Score: 1

No, this story is about using genotyping to treat or diagnose people. Cheap genotyping will definitely help with #2, but it's not going to be useful for treating or diagnosing people for some time. With current trends, by the time that happens actually sequencing your genome will be essentially free.
#1 and #3 are not redundant. A genome is large and complicated. How to analyze it is a major area of research (#3). Even if you have tools to do that effectively you STILL have a big jump to make to link it back to anything that's useful for the individual in the clinic (#1).
Re:Doubt it by Anonymous Coward · 2013-03-01 07:20 · Score: 0

Wrong. Genetic factors play into every disease. The biggest thing affecting your ability to slough off an infection is your immune system, and its functioning is almost always genetic. There are people who are genetically immune to HIV. The same with non-infecttuous diseases like cancer and heart disease. Ever wonder why one guy can smoke two packs a day for sixty years and die at 92 (like my great-uncle) while a nonsmoker will get lung cancer at 40? Ever notice that half the members of some families have heart attacks in their forties?
The fact is, if half your grandparents died or cancer at age fifty and the other half died of heart disease at age forty, don't count too much on collecting Social Security.
It seems like every day I see articles like this.

Wait 'til the insurance companies get this ... by gstoddart · 2013-03-01 04:57 · Score: 2, Funny

Of course, one of the immediate things people will need to worry about is misuse of this. One can easily see the insurance companies making everybody take one of these, and then refusing you coverage based on your genetics.

These kinds of things can have unintended consequences pretty quickly, and the privacy and legal implications of these kinds of tests cheap and routine haven't all been worked out.

I can certainly see all sorts of potential for abuse of this. I wouldn't be eager to sign up for this, but, I do tend to the tinfoil hat end of the spectrum on these things.

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Lost at C:>. Found at C.

Re:Wait 'til the insurance companies get this ... by compro01 · 2013-03-01 05:09 · Score: 2

One can easily see the insurance companies making everybody take one of these, and then refusing you coverage based on your genetics./quote>
That base is already covered, at least in theory. The Genetic Information Nondiscrimination Act was passed in 2008 to deal with that.

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upon the advice of my lawyer, i have no sig at this time
Re:Wait 'til the insurance companies get this ... by bitt3n · 2013-03-01 05:16 · Score: 1

One can easily see the insurance companies making everybody take one of these, and then refusing you coverage based on your genetics.
one can easily see the individual taking one of these on the sly, then signing up for a full-service insurance plan only if he expects to need it, which then means the company must either do the test on everyone who applies for insurance, or jack up everyone's rate to accommodate such self selection.

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how many pairs of boxer shorts should you own?
Re:Wait 'til the insurance companies get this ... by Anonymous Coward · 2013-03-01 05:29 · Score: 0

So what? If I drive a slower safer car I get cheaper insurance if am not part of a demographic that doesn't tend to speed and cause horrific accidents I get cheaper insurance. Look at it this way, if the casino knew that you had a 70% chance of winning, they wouldn't take your bet without adjusting the pay ratio in their favor. Ether way the free market will sort it self out. What will happen is that people with poor genes will be discriminated against. These people will have less economic opportunity and die younger, hopeful while having less kids. That will weed out the undesirable genes over a couple generations. So it's really only a temporary problem. The socialized system should cause the opposite to happen up and till the point where they go bankrupt because of too many need extensive treatments or the left decides to go back to eugenics and picks the winning genes. Ether way the market forces will build against Big Government until it collapses because it is unlikely that goverment will do a good job picking the "right" genes.
Re:Wait 'til the insurance companies get this ... by Grave · 2013-03-01 06:10 · Score: 1

So the "free market" approach so beloved by ultra-conservatives would, in fact, accelerate evolution? Fascinating contradiction of traditional beliefs.
Re:Wait 'til the insurance companies get this ... by Anonymous Coward · 2013-03-01 06:31 · Score: 0

Issue has already been addressed. See "GINA", the Genetic Information Non-Discrimination Act:
http://en.wikipedia.org/wiki/Genetic_Information_Nondiscrimination_Act
http://www.genome.gov/24519851
Re:Wait 'til the insurance companies get this ... by mange · 2013-03-01 07:11 · Score: 1

The US Congress has already started regulating some of these misuses. http://en.wikipedia.org/wiki/Genetic_Information_Nondiscrimination_Act
Re:Wait 'til the insurance companies get this ... by gstoddart · 2013-03-01 15:38 · Score: 1

The US Congress has already started regulating some of these misuses.
Sure, but with enough cash and lobbyists, they'll come around -- just like they did for every other industry which asks to be deregulated.
The Freedom of Genetic Information for Commerical Purposes Act will give them whatever they want ... and then the governments will want the data of course, but all hush hush and without a warrant.
Now, if you'll excuse me, my hat needs another layer of tinfoil, and I'm contemplating a design for a matching codpiece.

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Lost at C:>. Found at C.

FTFY by NoNonAlphaCharsHere · 2013-03-01 04:58 · Score: 1

âoeOur goal,â Rothberg declares, âoeis to really transform medicine.â

And by that he means HR and the insurance industry.

Not just health by symes · 2013-03-01 04:59 · Score: 4, Funny

It would be neat to have a nice, light and portable genome sequencer for when I next go eating meat in the UK

Re:Not just health by Anonymous Coward · 2013-03-01 05:16 · Score: 0

I'd be more worried about diseases such as mad cow than whether or not the meat is actually beef.
Re:Not just health by Anonymous Coward · 2013-03-01 05:20 · Score: 2, Funny

It would be neat to have a nice, light and portable genome sequencer for when I next go eating meat in the UK
I for one would appreciate some serious commentary on the article versus just horsing around.

Gattaca by Anonymous Coward · 2013-03-01 04:59 · Score: 0

Yes, because that always ends well in sci-fi.

Re:Gattaca by bigsexyjoe · 2013-03-01 08:51 · Score: 1

Because they will not have a justification for not covering your pre-existing condition. When you take them to court, they will simply have to cough up.

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Democracy Now! - your daily, uncensored, corporate-free

Re:thank by hoboroadie · 2013-03-01 05:01 · Score: 1

It's been up 15 minutes, maybe something's down.

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They feared that it could be used to suppress protest or support unpopular rule.

Good idea, but get ready for a shock. by Anonymous Coward · 2013-03-01 05:05 · Score: 0

We've had lots of very useful and not that expensive (Compared to potential benefit) genetic testing for years now. Really, we should be doing some sort of collection and testing of ALL children born. The data would be a benefit to medicine and research of incalculable value. (Imagine an anonymoized database of everyone's genetic information. Imagine what you could mine with that)

Yet we don't. We don't even do simple tests unless we suspect a problem. The reason is a big un-spoken taboo that most doctors know about but nobody really talks about.

And that reason is that infidelity is common. A lot more common than society is comfortable accepting. Every time we've tried blanket paternity tests we've found that something like 10-15% of the men listed on someone's birth certificate are NOT their genetic father.

Re:hoboroadie by Anonymous Coward · 2013-03-01 05:06 · Score: 0

Why can't we post without karma bonus any more? Sorry to waste a mod point by forgetting to post AC.

Not a gnome... by Anonymous Coward · 2013-03-01 05:08 · Score: 0

but I know they walk among us, so I am all for it.

Just beacuse you are a carrier or predisposed by Anonymous Coward · 2013-03-01 05:09 · Score: 0

to a certain gene, what are the percentage chances it will be expressed or you will live long enough to develop symptoms?

Seems like we are quite a bit from being able to tell your genetic fortune and this is more of just an FYI at this point.

Pretty little by schneidafunk · 2013-03-01 05:10 · Score: 1

Consider this is only $1000, which is extremely cheap for a medical procedure, and it is only done once. Compare that to the cost of MRI scans, which run about $3,000 a pop at a hospital, with patients routinely getting multiple scans.

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Some people die at 25 and aren't buried until 75. -Benjamin Franklin

Re:Pretty little by Anonymous Coward · 2013-03-01 05:27 · Score: 0

If everyone does it in the US, it would be 300 million x $1000 = $300 billion, as a one time deal, and you better believe that with the state of american EMRs, most people will have this done multiple times because the results get lost.
Re:Pretty little by RobertLTux · 2013-03-01 05:30 · Score: 1

as long as %my-EChart% supports the results it will be hard to "lose" i know that the E-Chart i use allows you to download your ENTIRE Profile (with test results) and its a nice XML format also.

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Re:Pretty little by Anonymous Coward · 2013-03-01 05:49 · Score: 0

$1000 is the cost of the consumables. The machne is much more expensive. Add staff salaries and you will have quite high basis to calculate your proffit on.
Re:Pretty little by Tarsir · 2013-03-01 06:01 · Score: 2

$1000 is what it will cost the hospital. You'll see a $10,000 charge on your bill.
Re:Pretty little by witherstaff · 2013-03-01 06:25 · Score: 2

Only 10X the cost? The latest Time magazine was devoted to Health Care in the US. Most of it was bringing to light the huge overbillings done for nearly everything. We'd probably see a 25x or 50x cost to this.
Re:Pretty little by davester666 · 2013-03-01 06:29 · Score: 1

This most definitely will NOT cost $1000 in a US hospital. $1000 might be what gov't run healthcare plans pay for it. Other insurance companies would pay more (maybe $1500). Individuals get to pay the rack rate, maybe $3000-$4000.

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Sleep your way to a whiter smile...date a dentist!
Re:Pretty little by Westwood0720 · 2013-03-01 07:40 · Score: 1

No different than my medflight that was billed for $67,000.
Re:Pretty little by ChumpusRex2003 · 2013-03-01 07:46 · Score: 3, Interesting

Well, it's $1000 for the consumables for the device, and the operator's time. Then there's the cost of the machine, building, admin, etc.
In reality though, this is extraordinarily cheaper than what is done at present. Currently, if a physician suspects a genetic disorder, then they the typical process used in a medical genomics laboratory is to use a "matching" technique where the patient's DNA is matched to known mutations. Typically, this costs around $500-700 per mutation tested against. For a number of diseases, this only gives a 75-80% accuracy, because certain genes are prone to new spontaneous random mutations, and have a lot of "normal" functioning variants - so simply checking for a known good gene isn't an option. As a result, these patients end up only with a presumptive diagnosis, leading to difficulties in family and reproductive counselling (i.e. do siblings need to be aware of the risk of passing on a genetic disorder to their offspring?)
Sequencing is occasionally performed in patients with unknown presumed genetic diseases, where a suspected gene is known - but the cost is very high, and it is infrequently done, unless a whole family are affected, and it is possible to identify which the culprit gene is likely to be.
Total genome sequencing, while not a panacea, would greatly help the diagnosis and research into newly recognised, presumed genetic diseases. If the total cost of the testing can be brought down to $2000 per analysis, then that would be cheap compared to the current techniques for genetic diagnosis.
Finally, as to the MRI - the actual cost of an MRI scan including scanner, building, maintenance, staff, admin is about $300-600 depending on scan complexity (or at least, that's the "bulk" price charged by private MRI facilities to insurers or hospitals who have exceeded the capacity of their own MRI scanners).
Re:Pretty little by mspohr · 2013-03-01 08:01 · Score: 1

The cost may be $1000 but the US health industry will charge you $10,000.
Of course, then, since nobody knows what most of this means, it will lead to lots more overpriced testing and consultations.
This is a good way to get lots of money out of patients with no benefit to the patient.

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I don't read your sig. Why are you reading mine?

Re:Public health by hoboroadie · 2013-03-01 05:11 · Score: 1

I'm pretty sure you'll still want a raw sample, perhaps in ten years?

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They feared that it could be used to suppress protest or support unpopular rule.

Torrents? by Anonymous Coward · 2013-03-01 05:12 · Score: 0

Ion Torrent? Quick illegalize it! They are trying to pirate our genomes!

The Next Revolution in Airport Security by Anonymous Coward · 2013-03-01 05:17 · Score: 0

MANDATORY Genome Scans for Everyone

Re:thank by Anonymous Coward · 2013-03-01 05:19 · Score: 0

Uh, guys... the parent's offtopic, too, yet was modded up. Suggestion: Don't give mod points to anyone with less than a six digit UID.

Guess I have to metamoderate when I can log in...

Insurers busy writing new legislation. by hoboroadie · 2013-03-01 05:23 · Score: 1

One more reason to ban/regulate insurance, and make health insurers compete free-market against the free national public health service. As that would require the consent of our Fearless Leaders,

we're boned.

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They feared that it could be used to suppress protest or support unpopular rule.

You think so? by Anonymous Coward · 2013-03-01 05:29 · Score: 0

oh you naive child. There's a lot of money in medicine.

Oh yeah, doing that is already barred in the US

Social Security # by Anonymous Coward · 2013-03-01 05:29 · Score: 0

Just make it the new social security number.

Re:Social Security # by Anonymous Coward · 2013-03-01 07:38 · Score: 0

it's an MD5 of your genome?

Re:Public health by Anonymous Coward · 2013-03-01 05:31 · Score: 0

As long as you don't sequence known pathogens, who care what kind of meat it is?

That's kinda funny. by Anonymous Coward · 2013-03-01 05:34 · Score: 0

I consider electing Mike Huckabee to be like electing a thief and an arsonist.

echart? by Anonymous Coward · 2013-03-01 05:42 · Score: 0

What is that?

Re:echart? by Anonymous Coward · 2013-03-01 06:36 · Score: 0

XML is a bloated data structure used to store data in "human readable" format. Whether a human can understand what it means is beside the point. A much better format for data is to use protocol buffers. That brought the size of OpenStreetMap down to 19GB from what would have been a 370GB XML file.

The Cloud? by Anonymous Coward · 2013-03-01 05:43 · Score: 0

Wouldn't the machine be about one quarter the size if it just took input, sent data off to the cloud for crunching, received the output, then output it's report? Then there would be no need to house 400 million transistors.

Sure, it's nice to do everything in one enclosed unit, and there's hipaa, but it doctors could but something for 1/4 the price and hook it up to AWS/Azure/etc then you'd really have something. They would collectively take up a lot less space and use up a lot less earthly resources...but of course that makes too much sense and would never work.

It that made it cost $250 per person, then you'd really have something though.

I worked at a DNA sequencing company for 5 years by volvox_voxel · 2013-03-01 05:51 · Score: 5, Interesting

Sequencing has enabled all sorts of medical diagnostics and research that were previously unavailable. It was quite exhilarating to to read in Journals like Nature about people that had late stage cancer being sequenced to find out that they were misdiagnosed with the wrong cancer. Just a few years ago, it was impossible to determine what type of cancer a cancer was before it spread. Once it has metastasized, it was all a guessing game. With sequencing you can know for sure, and give you the right medicine to address that cancer.

I've always considered biology to be hundreds of years behind physics and the other "hard sciences", because they never had the tools to deal with it.The CPU power, the RAM, the hard-disk space, even the cloud infrastructure are all needed to make DNA sequencer efficient. The last instrument I worked on was a low cost DNA sequencer that could yield a sequence in one day. At the end of a run, to do the basecalling and base alignment of the data, you would need significantly more horsepower than what was on the meager instrument. The cloud allows you access to a supercomputer the the short time that you need it, so the customer is not burdened by the huge computational complexity involved.

As the cost sequence drops (and continues to drop), whole new fields of research have opened up. Bioinformatics where biology and computer science meet is a pretty hot topic. We have a deluge of data, but we don't yet have all the good algorithms necessary to unlock all the secrets we wish to solve. The Rosetta stone of the 21st century. This is the biggest complaint I hear about from biochemists.. Making sense of the data. Data leads to knowledge leads to wisdom, but data is not knowledge.

I consider DNA sequencing to be an enabler, just like the steam-engine, or the electric light. It is now possible to look deeply at things we never could, like meta-genomics. Did you know that you have more bacteria in your body then all other cells in your body put together? ..And did you know that you can't grow most of them on a petri dish? We have been to mars, but we don't even know the bacteria in our own gut. Meta-genomics is a form of "shot-gun sequencing" .. In the lab you understand the biology by making millions of replicas of it in the petri dish.Not all bacteria grow on a petri-dsh . With shot-gun sequencing, you sequence enough sample so you can digitally reconstruct what organisms were there to begin with. This has enabled us to [begin to] understand the biochemical messaging between soil bacteria and the roots of plants, understand the biochemistry of food digestion to generate bio-fuels more efficiently, etc .. Interesting times...

GATTACA by Anonymous Coward · 2013-03-01 05:53 · Score: 1

'nuff said.

Sequence once, analyze later by Kjella · 2013-03-01 05:54 · Score: 2

Since your genetic markup doesn't change (except for stray mutations but AFAIK not that spread to every cell in your body - single sperm cells are different) the question is can you pay off $1000 over your whole life and medical history? With every advance likely to come 10-50 years down the road? A quick search came up with this from Employer Health Benefits 2012 Annual Survey: The average premium for single coverage in 2012 is $468 per month or $5,615 per year. So over 70 years (probably some of them on a family plan, offset by paying for a family plan) you're likely to spend $400k on health plans.

That means you have to improve efficiency by 0.25%, either by simple prevention, earlier detection, finding the right diagnosis earlier, better treatment before we get to all the possibilities of genetic medicine and it will pay off. Not in the US of course, where they'll drop you like a hot potato and/or pocket the savings themselves, but in other countries with universal healthcare lifetime costs are on the same order. I just did the math here in Norway and to DNA sequence everyone would be 25-30% of one year's healthcare budget. If I divide by an average lifespan of about 80 then about 0.33% of the healthcare of a lifespan. That doesn't sound like an unreachable goal to me.

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Live today, because you never know what tomorrow brings

missing the point by Anonymous Coward · 2013-03-01 05:56 · Score: 0

It's a one time procedure, so it is not going to be as profitable as other procedures. It might not even be worth investing in the machine, depending on the up front cost.

Thank God for Obamacare by bigsexyjoe · 2013-03-01 06:05 · Score: 1

Insurance companies can't look at pre-existing conditions in the US anymore. Remember?

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Democracy Now! - your daily, uncensored, corporate-free

Good that we have PPACA / obamacare or this would by Joe_Dragon · 2013-03-01 06:11 · Score: 1

Good that we have PPACA / obamacare or this would or been used to build a nice Pre-existing condition black list.

IonTorrent? LOL. by Cyberax · 2013-03-01 06:14 · Score: 2

IonTorrent has been promising wonderful new machines _just_ next quarter for almost two years now. So far, they have delivered only a few machines to select customers under NDAs. And they still haven't solved a couple of crippling problems: homopolymer resolution and fairly short read length.

Also, they haven't showed anything on this year's AGBT (it's like CES, only for biotech) last week. So I won't be holding my breath waiting for $1k genome sequencing machines.

Re:IonTorrent? LOL. by rodarson2k · 2013-03-01 11:18 · Score: 1

TFA was written based on an interview that took place in April of LAST YEAR.
It shows a graph indicating that cost is decreasing too fast that is also based on data ending at the beginning of last year. Conveniently before 2012 actually happened, where the cost sat completely flat for 12 months and even increased in Q4 as Illumina released new (more expensive) reagents.
(updated image:) http://www.genome.gov/images/content/cost_per_genome.jpg
Re:IonTorrent? LOL. by volvox_voxel · 2013-03-01 14:25 · Score: 2

It's interesting that Ion Torrent has been getting so much more media exposure than Illumina, the market leader. By all accounts, from actual users, the data quality is better. Getting low error rates may involve much more sampling. This is very much akin to the bit error-rate probability in digital communication, and the number of packets you need to transmit to reduce the error to acceptable levels (but in this case, there is no forward error correction).
Illumina uses fluorescent labeling which has a much better inherent signal-to-noise ratio than sensing-pH where you have to deal with surface effects from the wells, not to mention the homopolymer issues inherent to their chemistry..
The one allure that ion-torrent has, is that it doesn't involve any optics, and thus can potentially be made much cheaper (how cheap it is depends on their error rates though). I know that there are several companies that are trying to make sequencing cheaper. There is a lot of interesting work being done in the sequencing world. The top of the line DNA sequencer from 2010 was equivalent to 60,000 top-of the line instruments from 2006. The progress is currently beating moore's law.
Re:IonTorrent? LOL. by Cyberax · 2013-03-02 19:46 · Score: 1

Well, our startup has been recently acquired by Illumina so I might be a little biased. But from our previous experience, IonTorrent produces much worse data and it's not that cheap. Illumina also owns a company producing very nice enzyme (Nextera) that makes life much easier for molecular biologists. Staying quiet is actually a nice feature of Illumina - it just delivers results without much fanfare. IonTorrent in comparison overpromises and underdelivers.

There are other companies to watch - nanopore-based sequencing is interesting and in theory it can revolutionize everything, but it's also incredibly complicated.

Where do they sample DNA from, is it all the same? by Anonymous Coward · 2013-03-01 06:23 · Score: 0

How different is DNA from an immature red blood cell compared to say a tissue sample?

Re:I worked at a DNA sequencing company for 5 year by CptNerd · 2013-03-01 06:25 · Score: 3, Insightful

Data -> information -> knowledge -> wisdom

There are also non-gene mechanisms that need to be understood as well, since the genome is a blueprint, but what happens when the cell actually starts using that blueprint? Anyone who's had a house built knows that it's the contractors that actually make the house, not the architect, and there are an unknown number of contractors inside individual cells that control what gets built. What makes a particular cell use the "retina" part of the blueprint, and another cell use the "heart muscle" part? I don't believe we know all the answers outside the genome, yet. All those cellular contractors and we don't understand their language (yet).

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By the taping of my glasses, something geeky this way passes

Evolution by kanweg · 2013-03-01 06:36 · Score: 1

So, we could have the full sequences of many many people of different origin, not to mention of many different animals. While it would require quite a bit of data-crunching, I hope that it allows us to look back into our distant past, learning more about evolution.

Bert
And if it brings some intolerant religious folks to take their favorite myth book a little less serious, that is a very very nice bonus.

Gattaca by Anonymous Coward · 2013-03-01 06:48 · Score: 0

It was illegal to misuse an individual's genetic code data in the movie though it was defacto standard practice anyway... even the police enforced the DNA privacy invasions despite doing such was the opposite of the law.

What make you think it's not going to happen for real here?

Re:thank by RMingin · 2013-03-01 06:49 · Score: 1

You would mean greater than six digit, not less than.

I'm in favor.

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The preceding comment is my own, and in no way construes an opinon of the Emperor of Mankind.

Just so you know by Anonymous Coward · 2013-03-01 06:51 · Score: 0

It's pretty stupid to compare this to the sequencing of the human genome which was done de novo.

What about gene patents? by Anonymous Coward · 2013-03-01 07:13 · Score: 0

What happens if you get your genome sequenced and find out you have one of the genes that have been patented? Do you own someone money then? Can you not submit your DNA for any further study because some other company has the rights to version of the gene you have?

Please stop saying "decipher" by Anonymous Coward · 2013-03-01 07:19 · Score: 0

Working with Rothberg’s newest machine, a technician will soon be able to decipher a human genome in a few hours, and at the bargain-basement price of $1000.

No they won't. They'll just be able to read it. Most of the human genome hasn't been deciphered at all. I can read the Voynich manuscript, make a list of the symbols and their statistical occurrences and copy the text. That doesn't mean I can decipher it.

genetic marker testing used now by peter303 · 2013-03-01 07:21 · Score: 1

Its not a full sequencing, but a search for about a dozen genetic markers unique to the equine species. I was trying to find an exact description of the test in google, but the best I could was company called InstantLabs selling a machine . It takes two hours to analyze a sample. Not quite GATTACA yet.

Unfortunately each test is species specific. So if you want to test for lots of species you have to run lots of tests, assuming they are available.

Not a revolution by Anonymous Coward · 2013-03-01 08:25 · Score: 0

Genome scans are virtually worthless at this time as nobody really knows how to interpret a "variation" in a genomic sequence. Even worse, if such an analysis existed on a large scale then insurance companies would use statistics to "personalize" health and auto insurance premiums. Be careful what you want.

Not a fair comparison by subanark · 2013-03-01 09:56 · Score: 1

The comparison of the cost and time spent to do the first human genome compared to current runs is hiding the very important fact that if you have an existing genome for a species then doing another one is really easy as you can simply map the reads to the genome instead of having to do de novo. Getting a genome as complete as human these days still takes millions of dollars. And you ain't going to just rely on Ion Torrent. Your going to need Illumina for those large number of small reads and PacBio for those few long reads (look at the allpaths assembler for a pipeline to get a good, but not perfect assembly).

Doing a new genome is very hard and still quite expensive, although technology and techniques have improved things. The rice genome (which is much harder to do than human) is still ongoing using human pattern matching skills to help assemble it. The reality is that for most genomes no one wants to pay millions of dollars to get a full complete genome. A draft genome that is in pieces is still 90% as useful as a complete one that you can get done for around 10K.

Re:Not a fair comparison by Rutulian · 2013-03-01 12:29 · Score: 1

Doing a new genome is very hard and still quite expensive, although technology and techniques have improved things.
Yes, that and the quoted cost is, I'm assuming, $1000 for a single chip run, which gives you a maximum of 10 Gb or only ~3X coverage (actual will probably be less). That's usually how marketing blurbs work. Even for SNP analysis, you are going to need around 40X coverage, so the cost per genome is much higher than what they are saying, and is still at least an order of magnitude more expensive than Illumina.

Re:I worked at a DNA sequencing company for 5 year by aaronb1138 · 2013-03-01 10:22 · Score: 4, Interesting

I have generally considered biology so far behind the other hard sciences, especially physics, precisely because for a very long time they failed to consult with the chemists, physicists, and engineers. It has largely been self-induced, and almost entirely a process of falling behind. Heck we have some hacks out there in biology using morphological databases (today - with all the genetic tools they have!) to reverse engineer evolution, when the biologists are well aware that morphology is a good categorizing and search tool (it tells you where to start genetically looking), not an extrapolation tool for real data and conclusions.

Physics in particular finally just started going the route of butting in wherever they figured out they could be useful to biologists and clinicians especially. CT and MRI are great examples.

Rothberg's own 6 years of research to sequence 9000 letters of genetic code is a perfect example. After a year or so, a physicist or engineer would have said f--- this, there must be some way of automating this process. I suspect most of the scientists at Ion Torrent are chemists, EEs, and physicists. Probably not too many pure biologists (though some biophysicists are probably around).

Re: spam by hoboroadie · 2013-03-01 11:48 · Score: 1

Generally it works when folks browse at +1 or so, but that POS was overlooked, or the mod system broke for a bit.

Don't give mod points to anyone with less than a six digit UID.

I lurked for a year then got a six-digit UID, but the conure died... There's folks with fresh UIDs who've a lot more to say than me, so I for one don't want to see bigotry rear its ugly head.
I do miss the minus karma posting option, for when I want to own my inane comment, but spare the moderators the trouble of bringing it down.

--
They feared that it could be used to suppress protest or support unpopular rule.

Your DNA is like the keys to your house... by Paul+Fernhout · 2013-03-01 11:57 · Score: 1

except you can't easily change the locks...

Anyone who has your DNA sequence could in theory make a plague targeted just at you (maybe wth some collateral damage). That may be as trivial to do in thirty years as "script kiddie" computer attacks are these days. Our society has not yet thought through the implications of all this...

See also my essay:
http://www.pdfernhout.net/recognizing-irony-is-a-key-to-transcending-militarism.html
"... Biological weapons like genetically-engineered plagues are ironic because they are about using advanced life-altering biotechnology to fight over which old-fashioned humans get to occupy the planet. Why not just use advanced biotech to let people pick their skin color, or to create living arkologies and agricultural abundance for everyone everywhere? ..."

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A 21st century issue: the irony of technologies of abundance in the hands of those still thinking in terms of scarcity.

Re: spam by RMingin · 2013-03-01 13:45 · Score: 1

So you claim to have once had a six digit, but the computer died, and you don't know your email address and can't remember your username and pass??

I once had a five digit, but I don't lead posts with it.

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The preceding comment is my own, and in no way construes an opinon of the Emperor of Mankind.

DNA is not a blueprint by Anonymous Coward · 2013-03-01 13:47 · Score: 0

Steve M. Potter
9-19-97
http://www.neurolab.gatech.edu/wp/wp-content/uploads/potter/potteressays/DNAIsNotaBlueprint.html

I hear too often the phrase that DNA is the body's blueprint. It's not.

DNA doesnt say "Here's how to build a person." It is not a blueprint for an organism in the normal sense that we think of blueprints. In them, every detail is specified up front. Not so with DNA. It's as if DNA were more like a blueprint for a machine that seemed to have no purpose. From the looks of it, it certainly isn't for a building, not an architectual drawing at all, but a plan for a complex gadget. But parts of the plan don't make any sense unless you wear various different-colored glasses to read it. And you must lay the plans on a table and look at their reflection in a special, curved, lumpy mirror while standing on marks 1, 2, or 3 that are painted on the floor. Only from those postions do the wiggly lines on the paper appear straight in the reflections. And different sets of lines get straight depending which mark you are standing on. And different straight lines show up, depending on which glasses you are wearing.

So you do all this, and build the mysterious gadget. All it does is spew lots of numbers at you from its LEDs. What are they??? Why, they are Dewey-Decimal Numbers, of course! Call numbers for books! Followed by page numbers and word indexes and word counts. So you go look them all up, and, sure 'nuf, all the disjoint words and phrases and sometimes whole sentences, when appended to each other in order, make a story. What kind of story? It is another plan! It's instructions for how to build another gadget. It is a big drum filled with many little cards with small tasks for construction workers on them. One small task per card, like "Now cut 37 planks 8 feet long, from 1x12 stock," but some common tasks on many cards. The gadget has a voice and a hand for reaching in and pulling out cards. So you plug in the gadget, and turn it on, and the drum turns while it asks you a question, through its voice synthesizer, the cards tumbling over each other.

It asks, "When was the last time you had a banana split?" and gives you 5 choices, since there are 5 buttons to push. "(A) Yesterday, (B) Within the last week, (C) Within the last month, (D) Within the last year, (E) Never." So you are upset that you must choose (E), since you had one 5 years ago, but figure that is the best of the 5 answers. When you push (E), the drum stops, and the mechanical arm moves to the "E" door, opens it, and grabs a card. So you keep repeating the process. It keeps asking you personal questions. You answer them and get a card. The cards, when read in order, are a complete step-by-step instructions for constructing a building. A building that was never drawn on paper. But one that is nevertheless beautiful and aesthetic and functional when completed. It is the perfect house for you!

That is what DNA is like.

The most important misconception about DNA is that all the info is in the double-helix. It is not. Very little of it is. Very little. Just enough to make the first gadget--but not even that, because you have to have lots of info already to even make sense of the plans. You need to have the marks, the mirror, and the glasses.

The DNA is part of a process that includes many interations. Lots of specfic interactions. First, between the fertilized egg's proteins and the DNA. And all the other chemicals in this zygote. After a few cell divisions, the cells start to interact with each other because of their position, stress and strain, the genes that are active in them, etc. The cell-cell interactions allow more changes in subsequent generations of cells.

At all levels, molecules to cell groups, the laws of physics are imposing on the systems, making more specific interactions possible. Like the long-range tug of charged groups on two proteins brings them close enough for Vanderwaals forces to take over and hold them together in a functional pair.

And the developing organism takes

Gattaca by Anonymous Coward · 2013-03-01 16:59 · Score: 0

Someone had to say it.

Yes, but... by Anonymous Coward · 2013-03-01 22:43 · Score: 0

How long until realtime epigenetic scanning? That's when things will get interesting.

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