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Graphs Show Costs of DNA Sequencing Falling Fast
kkleiner writes "You may know that the cost to sequence a human genome is dropping, but you probably have no idea how fast that price is coming down. The National Human Genome Research Institute, part of the US National Institute of Health, has compiled extensive data on the costs of sequencing DNA over the past decade and used that information to create two truly jaw-dropping graphs. NHGRI's research shows that not only are sequencing costs plummeting, they are outstripping the exponential curves of Moore's Law. By a big margin."
my nuts. make it happen.
How about the cost of analysis of said genomes?
Comment removed based on user account deletion
What is DNA sequencing, exactly?
Are different methods required depending on what part is being sequenced? IOW, why was it so hard to finish what was started?
What's it useful for (apart from the obvious "note some symptoms and see if they correlate to some particular sequence")?
The graphs seem to indicate that the cost is still north of $12,000 which isn't exactly cheap.
Question for the bio-folks: is there a way for someone (okay, me) to DIY this? I'm curious to know my own genome, but I'm *very* leery of having that data living in some company's database. What I'd like to be able to do is have the data, and be able to look up how any discoveries later on map to what I've got. Is that possible? What I don't want is what seems to be the prevalent pattern right now of companies telling customers: "You have indicators for x & y. Re-do this & pay us again in a few years when we discover more."
Now if only the doctors get on the bandwagon and start diagnosing people based on an individuals genome.
Huh?
If someone has a genetic disease, it's pretty apparent that they have it without sequencing anything.
Familial history gives an excellent idea of any propensity for genetic disorders.
The only thing the DNA sequencing will do is add another test, give MDs another revenue stream and a method for CYA, and at the end, our health care costs go up even more.
1 cent apiece to find out why CowboyNeal is the way CowboyNeal is?
I'm not a lawyer, but I play one on the Internet. Blog
We've been observing this decrease over the last few years at our sequencing lab too. Some people might find it fascinating, but I, as a bioinformatician, find it frightening.
We're still keeping up at maintaining and analysing our sequenced reads and genomes at work, but the amount of incoming sequencing data (currently a few terabytes of data per month) is increasing four-to-five-fold per year (compared to doubling each 18-24 months in Moore's law). Our lab had the first human genomes at the end of 2009 after waiting for almost 9 years since the world's first human genome, now we're getting a few genomes per month. We're not too far away of running out of installing sufficient processing power (following Moore's law) and no longer being able to process all of this data.
So yes, the more-than-exponential decrease in sequencing costs is cool and offers a lot of possibilities in getting to know your own genome, advances in personalized medicine, and possibilities for population-wide genome sequencing research, but there's no way we'll be able to process all of this interesting data because Moore's law is simply way too slow as compared to advances in biochemical technologies.
--- Sigmentation Fault - Comments Dumped
How 'bout that burger?
...Oct 2007?
I saw the same thing back in the mid-1990s.
Sequencing technology was ramping up hyper-exponentially.
That means that it curves up on semi-log paper.
It was outstripping Moore's Law, and crushing our data systems.
Finished DNA sequence only needs 2 bits/base pair,
but the raw data behind those 2 bits can be much bigger;
in our case, the raw data was scanned images of radiograms.
In the early '90s, a typical sequencing project was a few hundred DNA fragments.
Each fragment is a few hundred base pairs.
You put each fragment in a file, and put all the files in a subdirectory on disk.
The file system becomes your de facto database, and it works OK,
because there are only ~10K base pairs in the whole project.
When I got there, a typical sequencing project had grown to a few thousand fragments.
They were still keeping everything in the file system,
and it took a dozen networked DECstations with big (1GB!) drives to manage all the projects.
Then the biologists went 40x in one generation.
(Remember, RAM only goes 4x per generation.)
That meant that a sequencing project now had 40K fragments.
They bought HUGE (9GB!) drives, and had a TB of storage online,
which was unprecedented at the time.
They were still keeping all the fragments in files in subdirectories,
because who has time to rewrite your data systems when you have all that DNA to sequence.
The system was slowly grinding to a halt;
the weekly (tape) backups were taking longer than a week to complete;
they fell behind on their OS updates.
Eventually there was file system corruption,
and then the whole thing came crashing down around our ears.
It was an exciting time.
FWIW, the graphs in the article show don't show continuous hyper-exponential growth.
They show two discrete jumps (doubtless due to introduction of new sequencing technologies),
one in 2003 and one in 2008.
After each jump, the growth rate returns to exponential (straight line).
And the last three data points show the cost bottoming out at $0.30/MBase.
Of course, that may just be the plateau before it falls off the next cliff.
Looks even better in terms of raw data in spreadsheet format DNA sequencing analysis data. The fact that per Mb drops from thousands of dollars to under a dollar is astounding.
When the foot seeks the place of the head, the line is crossed. Know your place. Keep your place. Be a shoe.
What happens is that in July 07 a new way to do it was introduced. As it was a new technique, it started of 'expensive' and became cheaper. The last three months it is again in the standard just as it was before.
As if you compare the drop in household costs of one family, where the family moved house to a cheaper estate.
So yes, in numbers ist has become cheaper, but also it must be clear you are comparing two ways of doing things and obviously people will select the cheaper one.
Don't fight for your country, if your country does not fight for you.
by any mechanism available to us. we're just responding to the need, they repeat. they really know stuff that we do not. they reek of good (as in pure) intentions. trouble believing? look at what we're 'believing in' now? better yet, come to one of the many scheduled million baby+ play-dates, consciousness arisings, photon sharing sessions, georgia stone editing(s),,, & a host of other life promoting events.
a few of them (pure intentions), already occurring, by the way;
1. DEWEAPONIZATION (not a real word, but they like it) almost nothing else good happens until some progress here.
2. ALL BABYS CREATED/TO BE TREATED, EQUALLY. (a rough interpretation (probably cost us. seems like a no-brainer but they expressed that we fail on that one too(:)->) 'we do not need any 300$ 'strollers', or even to ride in your smelly cars/planes etc..., until such time as ALL of the creators' innocents have at least food, shelter, & some loving folks nearby.' again, this is a deal breaker, so pay attention, that's cheap enough, & could lead to our survival?
3. THOU SHALT NOT VACCINATE IRRESPONSIBLY. this appears to be a stop-gap intention.
the genuine feelings expressed included; in addition to the lack of acknowledgment of the advances/evolution of our tiny bodies/dna (including consciousness & intellect), almost nobody knows anymore what's in those things (vaccines) (or they'd tell us), & there's rumor much of it is less than good (possibly fatal) for ANY of us. if it were good for us we'd be gravitating towards it, instead of it being shoved in our little veins, wrecking them, & adversely affecting our improving immune systems/dna/development? at rite-aid, they give the mommies 100$ if they let them stick their babys with whoknowswhat? i can see why they're (the little ones) extremely suspicious? they're also asking that absolutely nobody be allowed to insert those corepirate nazi 'identity' 'chips' in their tiny frames. they know who they, and we, are, much better than we ever will? many, oddly? have fading inclinations to want to be reporters of nefarious life threatening processes, ie. 'conspiracies', as they sincerely believe that's 'stuff that REALLY matters', but they KNOW that things are going to be out in the open soon, so they intend to put their ever increasing consciousness, intellect, acute/astute senses & information gathering abilities, to the care & feeding of their fellow humans. no secrets to cover up with that goal.
4. AN END TO MANUFACTURED 'WEATHER'.
sortie like a no-(aerosol tankers)-fly zone being imposed over the whole planet. the thinking is, the planet will continue to repair itself, even if we stop pretending that it's ok/nothing's happening. after the weather manipulation is stopped (& it will be) it could get extremely warm/cold/blustery some days. many of us will be moving inland..., but we'll (most of us anyway) be ok, so long as we keep our heads up. conversely, the manufactured 'weather' puts us in a state of 'theater' that allows US to think that we needn't modify our megaslothian heritage of excessiveness/disregard for ourselves, others, what's left of our environment etc...? all research indicates that spraying chemicals in the sky is 100% detrimental to our/planet's well being (or they'd talk to US about it?). as for weather 'extremes', we certainly appear to be in a bleeding rash of same, as well as all that bogus seismic activity, which throws our advanced tiny baby magnets & chromosomes into crisis/escape mode, so that's working? we're a group whose senses are more available to us (like monkeys?) partly because we're not yet totally distracted by the foibles of man'kind'. the other 'part' is truly amazing. we saw nuclear war being touted on PBS as an environmental repair tool (?depopulation? (makes the babys' 'accountants' see dark red:-(-? yikes. so what gives? thanks for your patience & understanding while we learn to express our intentions. everybody has some. let us know. come to some of our million baby play-dates. no big hurry? catch your breath. we'll wait a bit more. thanks.
do the math. check out YOUR dna/intentional healing potential. thanks again.
as long as government stays out with its regulations and subsidies that promote monopolies, the costs will continue dropping.
This just shows how invalid all of the ideology is behind this notion that inflation is the right thing, that government needs to be in health insurance and health care and that private sector cannot do efficient job in health care and insurance.
Just a very little while ago in this thread I compiled some data from various sources (including gov't statistics and some research papers) that shows that private health care and insurance were affordable and in fact preferred by population before the gov't and insurance and health provider companies have colluded and before gov't provided the moral hazard in form of Medicare and Medicaid (and CHIP), the prices for health care and for health insurance were low and most people preferred having private insurance plans even to things like Blue Shield/Cross.
Health insurance and medical treatment are just normal goods, there is nothing magical about them, the normal rules of market apply. Prices fall with increase in production and competition. That's before gov't gets involved, collusion and price fixing happens as well as gov't money influx and prices rise sky high, completely out of whack (same with education prices, and all other things government money is spent on.)
Markets that are less influenced by government regulations and subsidies than others, such as computers and various medical procedures that are not covered by government money (lasic eye surgery), have more competition, innovation and prices go down in those markets, not up. This is true even as new advances are made, new technologies are introduced. Those technologies are not cheap, but they are used massively in competitive manner and prices fall.
You are not paying millions of dollars for your computers, and you are able to buy many computers for a reason. That reason being that government is mostly uninvolved.
This is why I am and will always be against such things as government regulating anything, including 'net neutrality' laws, etc. AFAIC any government initiative and a law and a subsidy and a tax can be explained by reversing the official intent for it.
So if government is supposedly involved into making medical insurance less expensive and more affordable, expect the insurance to become less affordable and more expensive.
If government is saying it will protect you from terrorists, expect completely nonsensical policies that will at the end create more terrorists (all this while your real rights will be stripped off you and you'll be left sitting there, holding your dicks in your hands, with no right to anything at all.)
If government is saying it will fix the economy by printing money and spending, then you know what's coming - complete destruction of economy, collapse of the monetary system.
If government is saying it's going to bring you clean energy by various mandates, expect huge energy shortages, eventual failure of those clean energy policies to deliver enough energy, loss of real industries and real innovation and eventual situation, where most of the country is forced backwards, to use the most dirty but cheapest way to get energy.
If anything good comes out of the incoming economic disaster, hopefully it will be that the Keynesian policies, the policy of having a federal bank, the fiat currency, regulation of economy and money by government might be discredited completely (of-course nothing happens completely), but hopefully mostly, as the government shows itself not just totally impotent in these issues, but actually is shown to be the driving force behind the economic disasters of 20-21 centuries.
You can't handle the truth.
"they are outstripping the exponential curves of Moore's Law. By a big margin"
Moore's law simply states that the quantity of transistors that can be inexpensively placed on a circuit doubles every two years.
This is a relatively new area of science. New techniques can be expected to evolve, as would refinements of existing techniques. As it moves from the domain of a very few skilled individuals at universities to more of a commodity where $100 buys you your family tree, economies of scale kick in. And then there's the technical refinement of a new process where successive revisions, even if transistor counts/quality/sizes remained the same, would ensure its own rate of change.
So, off the top of my head, there are at least four different factors in addition to Moore's law. It's hardly surprising it's outstripping one of the five. Any new area of technology that also leverages transistor advances should do so.
Personally, I blame Jerry Springer.
Have gnu, will travel.
The Economist had an excellent article about this a while back. Using the number of blades in a razor as the example. The made a graph of time, on the bottom, and the number of blades on the left. Then they drew a curve that fit. For a long time, there was only one blade. Then there were two, and that held a while. Then came three, then four, and now we have five. Now, using sound mathematical methods to extrapolate this curve, The Economist projected that by 2020, a razor will have something like 40 or 50 blades.
The lesson? Just because this worked for Moore's Law, doesn't guarantee that this will hold true for other industries.
Schroedinger's Brexit: The UK is both in and out of the EU at the same time!
Moore's Law is about the number of transistors on a wafer and other directly-related hardware density issues, not about cost - and certainly not the cost of gene sequencing.
It must have been something you assimilated. . . .
The only question that remains is, "How long does it take?"
Don't stop where the ink does.
Reading is great, but there's like 30 bajillion (okay, maybe only 30) next-generation DNA sequencing companies out there grabbing money and kicking butts. What strikes me as odd is that there hasn't been comparable advancement in DNA synthesis (it's still at $0.30/bp using phosphoramidite synthesis), save for ligation and oligo libraries. Meanwhile my cells are busy synthesizing my own genome for less than $0 per chromosome.
The graphs seem to indicate that the cost is still north of $12,000 which isn't exactly cheap.
Dude, you are reading the graph incorrectly. Look carefully at the (logarithmic) scale: the cost is actually around $30,000 !! (No, those are not factorial signs, I am just expressing my shock by the 30 thousand figure.)
Yes, I know, that actually supports your point even more strongly: while the cost was reduced dramatically from $100 million, it seems to be leveling at a cost that is still way too high for many practical applications in the clinical field outside of research.
https://www.23andme.com/you/faqwin/sequencing/
my emphasis:
What is the difference between genotyping and sequencing?
Though you may hear both terms in reference to obtaining information about DNA, genotyping and sequencing refer to slightly different things.
Genotyping is the process of determining which genetic variants an individual possesses. Genotyping can be performed through a variety of different methods, depending on the variants of interest and resources available. At 23andMe, we look at SNPs, and a good way of looking at many SNPs in a single individual is a recently developed technology called a “DNA chip.”
Sequencing is a method used to determine the exact sequence of a certain length of DNA. Depending on the location, a given stretch may include some DNA that varies between individuals, like SNPs, in addition to regions that are constant. So sequencing is one way to genotype someone, but not the only way.
You might wonder, then, why we don't just sequence everyone's entire genome, and find every single genetic variant they possess. Unfortunately, sequencing technology has not yet progressed to the point where it is feasible to sequence an entire genome quickly and cheaply. It took the Human Genome Project over 10 years' work by multiple labs to sequence the three billion base pair genomes of just a few individuals. For now, genotyping technologies such as those used by 23andMe provide an efficient and cost-effective way of obtaining more than enough genetic information for scientists—and you—to study. Copyright © 2007-2011 23andMe, Inc. All rights reserved.
To be sure you have gained interesting information for your $200, but you have neither your sequence, nor a complete list of differences from a reference human sequence, which of course if you did would give you your sequence.
23andme only gives you a list of many SNPs.
The drop is not necessarily indicative of a long-time trend. The predictions of long-time trends of exponential growth are based on normal rate of network growth. But occasional Bose-Einstein condensation effect can produce very rapid growth spikes. These are due to a new approach that is adapted. The normal growth rates are generally due to efficiency gains due to incremental improvements.
I don't understand why Moore's predictions about integrated circuits would apply to the cost of gene sequencing. Unless there is a relationship that I am missing, let's keep Moore's "law" to the realm of electronics.
As a person in the field, I have to say, that one has to consider a quality of genomes in the field (at least bacterial genomes). So called "complete genomes" submissions of the past, in the form of full continuous sequences of chromosomes and plasmids of the organism, are staying in the past, almost all of the new submissions are WGS (whole genome sequences), which is basically bunch of "contigs", pieces of sequences not connected together, 10s, 100s and sometimes 1000s of them. (This is a result of adopting 454-style sequencing).Those contigs do not cover completely genomes, they leave gaps between them.
But that's a minor problem compared to artificial frameshifts in poly-A areas, one such frameshift in a CDS (coding) area and the gene is gone (they also can occur naturally, which complicates the situation even more).
I do not believe in karma. "Funny"=-6. Do good and forbid evil. Yours, Oft-Offtopic Flamebaiting Troll.
Page advertisement in Nature, a leading science journal. The company was Axeq base in Korea. Here is the ad . The exome is the 2% of the genome that appears to code for proteins.
When the costs become trivial and the speed of analysis becomes quick, we will have a GATTACA world.
Of course it would be great if we could each get out full genomes - full coverage of every chromosome at high confidence - for an affordable price. However, if you did that, you would find that the vast majority of the information would be quite uninteresting or even borderline meaningless. There are large regions of the chromosomes that do not code for anything, and some of those end up being particularly difficult to sequence accurately. While changes in those regions can be important, changes in those regions are likely not anything you could easily search out and compare anyways.
If what you actually want is to know how the expressed parts of your genome compare to known genomic assemblies, that is fairly straightforward now. While not exactly cheap they are not impossible to handle on a reasonable budget. You could look at your favorite genes - particularly if you know of health conditions in your family that may have clear genetic components - and generate some DNA oligos to sequence those. Of course, that sequencing is not really approachable by most people because the sequencers are still quite expensive (unless you want to do sequencing gels which require radioactive and/or carcinogenic dyes and will make you go cross-eyed to boot) so you'll end up having to send out your samples somewhere eventually.
Which is why we have various companies who are doing SNP profiling for a few hundred dollars per person. They can recover the cost of their sequencing and assembly fairly quick at that rate, and provide some of the most useful information to the customers at a manageable price and turnaround rate.
So basically what it boils down to is that if you want to do a full genome, every chromosome, you most likely couldn't afford the equipment and materials to do it yourself. If you want just SNPs or even ESTs, you could possibly do it but it would be vastly impractical to pay for it yourself in comparison to sending it out to an existing company.
I say this as a grad student in a field closely related to genomics, with several genomics papers on my CV from over the years.
Damn_registrars has no butt-hole. Damn_registrars has no use for a butt-hole.
It has to fall even more so that the US government can continue it's eugenics programs in a cost effective manner.
That's monetary cost - not social and personal. ;-)
Soon the $ cost will be free - and mandatory. If you want to fly, or even drive a car.
Hey! And to think, they said it couldn't happen here!
"Flyin' in just a sweet place,
Never been known to fail..."
Moore's Law shouldn't be what the graph is based on. A best fit line would be much more accurate at predicting the price. Technology can have effect on the price. Increase in processor speed and more efficient algorithms can both decrease the time spent processing therefore decreasing the overall cost. But economy of scale will have a much more dramatic effect. When firms increase in size or increase their production, their costs generally go down until they hit a certain point. http://en.wikipedia.org/wiki/Economies_of_scale
Jaw dropping graphs indeed, especially the Cost per Megabase one. Extend the graph further to the right, and it appears that Moore's law will reach $0 some time in 2033.
They mislabeled the graph. That should be $0.1 in the lower left, not $0. Of course, you could say they are rounding, but then they are rounding to a number more granular than what their chosen Y axis range calls for.
Imagine taking 8 Harry potter books ((Goblet of Fire) all from different publishers) and putting them into the shredder. Luckily you placed them in a way such that the lines of the books are intact, and because you have different publishers, the lines don't always match up. And only 60% of the lines from a given book are usable. The rest mangled by the shredder.
/16th's of a page.
You need to find ends from one strip that match the beginning of another strip.
This means that with some patience you could flip through all the scraps and rebuild one copy of Goblet of Fire.
But that 40% of the lines that were mangled by the shredder were at random, some of the passages would not be salvagable, Roughly 1/1600 the of the book would be missing entirely (half a page). Feeding another book into the shredder is kinda expensive to get a quarter page of information, Another 2 to get 3
__ different methods are used to get those last few bits of information -- its technical and boring to grad students.
It's useful for a few things Clinically, you can sequence a carcinoma (cancer) to determine the best course of chemotherapy. If the oxidative damage genes are damaged, you can introduce chemicals that induce oxidative damage. If DNA break repair is damaged, you can go with radiation as a treatment.
For an infection, you can determine if your dealing with a resistant bacteria.. it's a bit expensive right now, but the price will fall.
Tracing back evolution
Bringing back the Mammoth
Building a malaria resistant mosquito.
Building synthetic Spider Silk (with transgenic goat milk (still ironing out kinks))
Finding the Genes that conferred HIV resistance. (some are done)
Complete Genomics claims they will be able to sequence a genome for $5,000. Although, I haven't heard from them in awile..
Now if only the doctors get on the bandwagon and start diagnosing people based on an individuals genome.
Sorry, that'll take 10+ years of basic research, 10+ years of clinical trials to provide practical applications for findings of said research, plus another 10+ years for a new generation of doctors to matriculate with knowledge of said applications. More likely, big pharma will be "farming" human genome data for drugs with rapid development platforms. The scary part here is that, without basic research, more unintended consequences are to be expected...
Because DNA sequencing is so cheap and getting cheaper by the day, every person should be fully sequenced right at birth. Since every human is unique in DNA code and even "identical twins" differ slightly, a unique crypto checksum like SHA-512 should be calculated from the DNA data, for each and every person. The numeric checksum code should then be translated into a sequence of textual phrases, like the S-code vocabulary of SSH host key displays, for easier practical use.
Such a list of words should combine into a globally unique name of each person and the old "family name + given name" method should become only a legacy vanity ID with no legal or bureaucratic significance. It will be impossible to use pseudonyms in this new world, because your DNA is you! No more criminals hiding, no more con artists cashing in, no more unindentifiable corpses after homicides and no more murderers getting away with their crimes unpunished!
I recommend to use chinese and/or redskin vocabulary for the DNS-hash name transliteration, due to their brevity, so you will become "Sitting bull flies over broken arrow yellow tent" or "Pei Xing Li Wang Chua Sechuan Panda" in your official ID card. And there will be no other person in the world with the same name, but you!
This also means the costs to podunk police departments to synthesize and plant DNA evidence where they want drops as well. The proof will be the exponential increase in the number of calls on innocent citizens to 'donate' DNA samples to track down the 'criminal in our midst du jour'. After all: if you've done nothing wrong, you have nothing to hide, right?