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The Next Revolution In Medicine: Genome Scans For Everyone
the_newsbeagle writes "This year, a biotech company called Ion Torrent will introduce a new chip for its genome sequencing machine, which should enable researchers and doctors to scan a complete human genome for $1000 and in just a couple of hours. Compare that to the effort required to complete the first human genome: $3 billion and 13 years. Ion Torrent has nearly reached the $1000-genome milestone by virtue of a process called 'semiconductor sequencing,' and the company's founder says his chip-based sequencing machine benefits from all the efficiencies of the computer industry. At a price point of $1000, genome scans could become a routine part of medicine. And the price could keep dropping. To test out the technology, and to investigate just how useful genome scans are these days for your typical, reasonably healthy person, the IEEE Spectrum reporter got her own genome scanned and analyzed."
Price isn't the only determinant of whether something is a 'routine part of medicine'. For the foreseeable future, there is remarkably little utility that an individual's genome brings to the table. It will become a very important part of medical research, but in terms of an individual's health, not so much.
It will be hyped. It will likely end up like 'full body CT scans" - a bragging tool for the seriously hypochondriac but of no help to the routine patient.
Even the Single Nucleotide Polymorphism (SNP) data which is pretty cheap now (basically what the police use for forensics) helps most people very little. In the context of answering a specific genetic question, perhaps - but not as a routine. When you send someone to a medical geneticist, most of the time and effort revolves around getting the person to understand what you are trying to accomplish and the pros and cons of doing so. Having whole genome sequencing just makes it even harder.
Faster! Faster! Faster would be better!
Either:
1. Using this data for insurance purposes will be banned, which turns "preexisting condition" into a criterion that can only be applied with eyes closed;
or 2. Huge numbers of people will be uninsurable, because the likelihood of their future illnesses will be known before they try to buy insurance.
10 PRINT CHR$(205.5+RND(1)); : GOTO 10
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.
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.
Lost at C:>. Found at C.
And by that he means HR and the insurance industry.
It would be neat to have a nice, light and portable genome sequencer for when I next go eating meat in the UK
It's been up 15 minutes, maybe something's down.
They feared that it could be used to suppress protest or support unpopular rule.
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.
Some people die at 25 and aren't buried until 75. -Benjamin Franklin
I'm pretty sure you'll still want a raw sample, perhaps in ten years?
They feared that it could be used to suppress protest or support unpopular rule.
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.
They feared that it could be used to suppress protest or support unpopular rule.
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...
'nuff said.
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.
Live today, because you never know what tomorrow brings
Insurance companies can't look at pre-existing conditions in the US anymore. Remember?
Democracy Now! - your daily, uncensored, corporate-free
Good that we have PPACA / obamacare or this would or been used to build a nice Pre-existing condition black list.
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.
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).
By the taping of my glasses, something geeky this way passes
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.
You would mean greater than six digit, not less than.
I'm in favor.
The preceding comment is my own, and in no way construes an opinon of the Emperor of Mankind.
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.
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.
Democracy Now! - your daily, uncensored, corporate-free
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.
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).
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.
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?
A 21st century issue: the irony of technologies of abundance in the hands of those still thinking in terms of scarcity.
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.
The preceding comment is my own, and in no way construes an opinon of the Emperor of Mankind.