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A DNA Sequencer Cheap Enough For (Some) Doctors' Offices

timothy posted more than 2 years ago | from the soon-next-to-blood-pressure-booth-at-the-store dept.

Biotech 136

cylonlover writes "Until recently, DNA decoding machines — fitting in the US$500,000 to $750,000 price range — would take weeks or even months to sequence a human genome, and the whole procedure would cost $5,000 to $10,000. That could be about to change, however, as Life Technologies introduces the Benchtop Ion Proton Sequencer — a machine that may finally deliver the power of genetics into the hands of ordinary doctors thanks to its $149,000 price tag and ability to decode a human genome in one day at a cost of $1,000."

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Unforeseen consequences (5, Funny)

bonch (38532) | more than 2 years ago | (#38695404)

Warning--side effects may occur [imgur.com] .

Re:Unforeseen consequences (3, Funny)

grantek (979387) | more than 2 years ago | (#38695432)

This is a completely different machine, it's not the one that TSA agents will use to remotely scan your DNA...

Re:Unforeseen consequences (1)

AHuxley (892839) | more than 2 years ago | (#38695494)

Give blood for a US visa? They can look for the strength of your VMAT2 (God Gene, spiritual experiences) gene.
If you light up, your fanatic potential is noted.

Re:Unforeseen consequences (0)

Anonymous Coward | more than 2 years ago | (#38695990)

"If you light up, your fanatic potential is noted & an invitation to join the Republican party is dispatched."

FTFY

Re:Unforeseen consequences (1)

GameboyRMH (1153867) | more than 2 years ago | (#38697762)

In Dead Space 2 the Unitologists would do various physical and psychological tests on prospective members to weed out the skeptics.

Re:Unforeseen consequences (4, Funny)

justforgetme (1814588) | more than 2 years ago | (#38695642)

omg, the days of GATTACA are finally here! Now I'll never fly to mars ${sadface}

Re:Unforeseen consequences (1)

Samantha Wright (1324923) | more than 2 years ago | (#38695738)

You may still fly to Mars! But best give up on Jupiter; your heart is crap.

Re:Unforeseen consequences (0)

Anonymous Coward | more than 2 years ago | (#38696166)

Awesome movie. Sad reality though.

Re:Unforeseen consequences (1)

smi.james.th (1706780) | more than 2 years ago | (#38696474)

Weren't they going to Titan in Gattaca?

FWIW, $1000 is still somewhat expensive and it's just scanning genes at the moment. It's not actively messing with the genes of a zygote as was happening in Gattaca.

For the moment, anyway.

Re:Unforeseen consequences (5, Insightful)

zippthorne (748122) | more than 2 years ago | (#38697330)

Half of what was happening in Gattaca. Not even the interesting half.

Messing with genes was the logical response to the first half, though, which was gene discrimination. Or did you not notice that the main character was smart enough and driven enough to become a rocket engineer, but because of a chance of a flaw in other areas was relegated to menial labor.

It's not just that they wouldn't let him be an astronaut, either. They wouldn't even hire him as an engineer at all, as a "bad risk." And his love-life was implied to have suffered as well, with the matchmaking sequencers on every street corner....

The movie was about the horrors of discrimination, and the virtue of overcoming them, not gene manipulation, which is not a necessary precondition to gene discrimination. Regardless, I think it was probably supposed to be an allegory to present-day race discrimination, but with a narrative trick to make the character white, so white people wouldn't have any preconceived notions getting in the way of the message, rather than a direct prediction of the future, however prescient it may appear to have been.

Re:Unforeseen consequences (1)

smi.james.th (1706780) | more than 2 years ago | (#38697378)

That's a very good post. Someone mod parent up, please!

Re:Unforeseen consequences (2)

mrops (927562) | more than 2 years ago | (#38699002)

Gene discrimination has been happening for ever, some call it Evolution.

Re:Unforeseen consequences (1)

Paul Fernhout (109597) | more than 2 years ago | (#38699564)

Whie I like your general points on the movie, if Gattaca's biotech was so advanced, why could the protagonist not just alter his own DNA etc.? Or maybe Gattaca's biotech was not really as advanced as one might think?

Re:Unforeseen consequences (1)

serialband (447336) | more than 2 years ago | (#38699940)

The biotech was the plot vehicle for the real story of the discrimination and it wasn't really about the tech. The movie was more about the human drive and imagination.

There are always plot holes in movies. If you're going to pick at everyone of them, you couldn't enjoy very many movies.

Re:Unforeseen consequences (1)

Anonymous Coward | more than 2 years ago | (#38696214)

Doctors over diagnosis there patients anyway---- You go in for an exam come out with high blood pressure ( the "old standard" was normal pressure for years) cancer, some 10 acute "diseases" that seem to be false. Now you want to give them this to aid in them sucking your health and wallet dry. I would be useful but it should be kept to someone medically trained to use/understand DNA and what the problem maybe.

Before you go on over what doctors I go to, it was meant to poke fun at the medical industry. Several people go in for one thing and end up continue to come out with something else. Everything is a disease solely for the prescription drug industry to make money. Very sad, you want to eat healthy foods but they have pesticides through out (even organic has some downside to it), the meat is littered with antibiotics or hormones.Now the medical industry is destroying human health with a vast rainbow of drugs that cause more problems then what you were diagnosed with

Re:Unforeseen consequences (1)

MacGyver2210 (1053110) | more than 2 years ago | (#38696252)

It turns you into Jeff Goldblum?

Re:Unforeseen consequences (2)

cbiltcliffe (186293) | more than 2 years ago | (#38698584)

They also conveniently forget to mention the "side effect" that you need a $75,000 computer setup to analyze the data the $149,000 machine spits out. So in reality, this is actually a $225,000 machine, plus an IT person to manage the hardware.

Re:Unforeseen consequences (1)

climb_no_fear (572210) | more than 2 years ago | (#38699898)

Not to mention that it wouldn't hurt if you doctor was a trained geneticist...

Hospitals (2, Insightful)

Anonymous Coward | more than 2 years ago | (#38695488)

I predict that the first buyers will be University research hospitals, and the Mayo Clinic.

It needs to drop a bit more before seeing it at your local pediatrician's.

Re:Hospitals (1)

jamstar7 (694492) | more than 2 years ago | (#38695606)

Love to scam one of these puppies up when the price drops to a couple K. Especially if it has a 'write mode' as well.

Think 'gene hacking' as the next 'nerd' occupation...

Re:Hospitals (0)

Anonymous Coward | more than 2 years ago | (#38695622)

DNA is a read-only media. They'd also need to invent DNA-RW.

Re:Hospitals (1)

lightknight (213164) | more than 2 years ago | (#38696274)

More interested in the capacity to read / write DNA in vivo, but I'll take what I can get.

Re:Hospitals (5, Informative)

Samantha Wright (1324923) | more than 2 years ago | (#38695634)

Gene hacking already is the next nerd occupation (I should know; I'm in the middle of it. Mozilla even funds projects for it.) Here's one starting place if you're really interested. [wikipedia.org]

About the read/write thing: synthesizing large amounts of DNA from scratch still costs ungodly amounts of money. Further, the ABI IonTorrent system being advertised here is a destructive read; you have to treat a blood sample with a large number of chemicals and then stuff it in a big machine. It's no Star Trek scanner.

Re:Hospitals (1)

justforgetme (1814588) | more than 2 years ago | (#38695672)

synthesizing large amounts of DNA from scratch costs ungodly amounts of money

can't you just write one DNA sequence, put it in a cell and grow it?

Re:Hospitals (4, Informative)

Samantha Wright (1324923) | more than 2 years ago | (#38695718)

Yes, but it's fraught with errors, and making a single molecule longer than a few thousand bases costs a great deal. A bacterial genome is 0.4-3 million bases; humans are 3.1 billion in total. That's why only the Venter Institute has done it [wikipedia.org] .

Re:Hospitals (1)

justforgetme (1814588) | more than 2 years ago | (#38695766)

You really shine in biology, don't you?
BTW, homepage down?

Re:Hospitals (0)

Anonymous Coward | more than 2 years ago | (#38698118)

Yeah, but 99.5% of the 3.1B base pairs in humans are the same. I could see some kind of production line for that as a starting material that you can buy over the internet. Then you need to "tweak" the last .5% and voila, you have your own custom made human, a clone army, whatever.

Re:Hospitals (1)

Samantha Wright (1324923) | more than 2 years ago | (#38699910)

5% of the whole human genome is under evolutionary pressure (i.e., we know it does something.) 1% of it contains protein-coding genes, most of which are non-negotiable and critical to living. It's actually only about 0.1% of the total DNA that changes from person to person.

Re: Your sig (4, Funny)

srussia (884021) | more than 2 years ago | (#38695860)

I am a biologist. Ask me questions in my journal. I'll give car/computer analogies if possible!

No need for the invite. This is Slashdot. You had us at "Samantha".

Re:Hospitals (1)

Forty Two Tenfold (1134125) | more than 2 years ago | (#38696438)

Gene hacking already is

Yes. [stopklatka.pl]

Re:Hospitals (1)

pjt33 (739471) | more than 2 years ago | (#38696612)

Since you didn't link them, I assume you missed the previous [slashdot.org] Slashdot discussions [slashdot.org] on gene hacking as a nerd occupation.

Re:Hospitals (4, Interesting)

bill_mcgonigle (4333) | more than 2 years ago | (#38695756)

It needs to drop a bit more before seeing it at your local pediatrician's.

And I'm not sure that it ever will. How long has generating a CBC been a solved science? But the pediatrician will still send you over to the hospital's phlebotomy lab to get one.

I guess they do do instant strep tests in the office. When a DNA sequence costs $15 including equipment perhaps they'll do it.

Re:Hospitals (2)

cperciva (102828) | more than 2 years ago | (#38696520)

The only reason they do instant strep tests at MD offices is that they want to know the results before you walk out the door. The same goes for rapid STD tests: If you walk out the door and have to come back to get the results later, there's a chance you won't return.

A DNA test is the ultimate in non-urgent tests, and is going to remain something you head off to the phlebotomist to get done... right up until the day where they are done routinely at birth and you leave the hospital jugging a baby, birth certificate, and a flash drive containing its DNA sequence.

Re:Hospitals (0)

Anonymous Coward | more than 2 years ago | (#38697070)

you leave the hospital jugging a baby, birth certificate, and a flash drive containing its DNA sequence.

Actually, you don't leave the hospital with a birth certificate. They are issues a few weeks later and mailed to you. At least that's how it is here in Michigan.

Re:Hospitals (2)

RDW (41497) | more than 2 years ago | (#38697146)

... right up until the day where they are done routinely at birth and you leave the hospital jugging a baby, birth certificate, and a flash drive containing its DNA sequence.

Which might happen sooner rather than later:

http://www.forbes.com/sites/matthewherper/2012/01/10/not-quite-the-1000-genome-but-maybe-close-enough/ [forbes.com]

"Yale geneticist Richard Lifton, who was the first to document the use a DNA sequence to diagnose a disease, is looking at utilising the Proton for clinical work. In the state of Connecticut, where Yale is based, infants are tested for 43 different genetic mutations that need to be detected early in infancy. The Proton could be a better way to do that that traditional methods, especially given its ability to deliver results quickly."

There's going to come a point when even whole genomes are cheaper to do than a few dozen separate conventional tests.

Re:Hospitals (1)

timeOday (582209) | more than 2 years ago | (#38698272)

Why wait until birth? If your DNA doesn't pass muster, you'll probably be rejected as a zygote and head off to the incinerator with 99% of your siblings.

Re:Hospitals (0)

Anonymous Coward | more than 2 years ago | (#38696566)

It needs to drop a bit more before seeing it at your local pediatrician's.

And I'm not sure that it ever will. How long has generating a CBC been a solved science? But the pediatrician will still send you over to the hospital's phlebotomy lab to get one.

I guess they do do instant strep tests in the office. When a DNA sequence costs $15 including equipment perhaps they'll do it.

And insurance companies still fight if a CBC includes platelets (adds maybe $1 to the bill)....
good luck getting any useful medical utility, other than the cheap ability for health and life insurance companies to GATTACA us
(I'm and MD and PhD and I don't like this idea)

my penis (-1)

Anonymous Coward | more than 2 years ago | (#38695490)

your anus

Don't believe the hype (5, Informative)

Anonymous Coward | more than 2 years ago | (#38695504)

There are two unfortunate challenges that the Ion Proton approach hasn't yet solved. The first is that the steps required to get the DNA out of human cells and into the sequencer (DNA extraction and especially library preparation) are still frustratingly complex. Their OneTouch device simplifies parts of the library prep but there are still many steps that require highly skilled people doing hours to days of work.
The second major issue is that the genome is being read out in fragments of 200-400 nucleotides, then needs to be assembled. The human genome is full of repetitive regions that are much longer than 200-400nt and when one gets a sequence read from one of these regions, it's can be very difficult to determine which of the copies of the repeat region that sequence came from. Better statistical models and algorithms for genome assembly may solve this to some extent, but there are fundamental limits to what can be done with short sequence reads. Other sequencing technologies don't suffer the short read problem, Pacific Biosciences' hardware for example can read several thousand nucleotide fragments. Mate pairing strategies might be used on the Ion instrument but the library prep for these involves considerably more challenging and manual lab work.

Re:Don't believe the hype (3, Insightful)

ColdWetDog (752185) | more than 2 years ago | (#38695560)

The third problem (once you solve the first two) is what the hell you do with all that information. At present, having a complete readout of your genome doesn't get you very far. Even after you've figured out what diseases that you are more at risk for, what do you do? Well, you keep an active, healthy lifestyle, drink in moderation, don't smoke etc. You didn't need all of that info for me to tell you that.

I don't see this in doctor's offices (except for the boutique practices that do everything to / for you for the specific purposes of lightening your wallet). Maybe it will allow smaller research groups to tackle projects that they couldn't afford to do. But it's a long way to clinical utility.

Re:Don't believe the hype (4, Informative)

Samantha Wright (1324923) | more than 2 years ago | (#38695670)

You archive it until you need it. A situation-specific microarray might cost a hundred dollars; those tend to stack up with every hospital visit. With whole exome sequencing like this, you pay the fee once, and have all* the data medical science will ever need about you.

* Not counting repetitive elements, promoter regions, UTRs, spacer DNA, or the epigenome, all of which are known to describe at least a few diseases.

Re:Don't believe the hype (2)

RDW (41497) | more than 2 years ago | (#38696432)

With whole exome sequencing like this, you pay the fee once, and have all* the data medical science will ever need about you...* Not counting repetitive elements, promoter regions, UTRs, spacer DNA, or the epigenome

Not just exome, but whole genome in about a year (they claim), so everything except the epigenome. Some interesting discussion here:

http://pathogenomics.bham.ac.uk/blog/2012/01/ion-torrent-proton-the-chip-is-not-the-machine/ [bham.ac.uk]

http://seqanswers.com/forums/showthread.php?t=16709 [seqanswers.com]

Re:Don't believe the hype (2, Informative)

Anonymous Coward | more than 2 years ago | (#38695818)

The third problem (once you solve the first two) is what the hell you do with all that information. But it's a long way to clinical utility.

Well, if by "long way" you mean five years, then yes, it's a long way.

On the other hand, in five year when this technology gets of the ground, it will transform diagnostic medicine in the same way that the automobile transformed personal transportation.

One huge application is diagnosis of infectious disease. Not only will you know whether what you have is viral or bacterial, if it's bacterial you'll know exactly which antibiotics will work. And you'll probably even be able to correlate you infection with known outbreaks: "There's been 50 other infections with this pathogens in the northeast corner of this city over the last two weeks."

The other huge application is birth defects. Many birth defects are recessive and this technology will tell couple which birth defects they are both carriers for - and could pass on to their children. Also, in the case of most mental retardation, the actual causative mutation isn't known (it doesn't have distinct symptoms) but when the comprehensive databases of human mutations start coming online, it will be possible to know exactly which mutation is causing the problems. And, in rare cases, that will even lead to successful therapy (the other cases will have to wait for general gene therapy).

Bottom line: high throughput sequencing for medical diagnosis is going to be one of major advances of this century.

Re:Don't believe the hype (2)

Rutulian (171771) | more than 2 years ago | (#38698514)

One huge application is diagnosis of infectious disease. Not only will you know whether what you have is viral or bacterial, if it's bacterial you'll know exactly which antibiotics will work. And you'll probably even be able to correlate you infection with known outbreaks: "There's been 50 other infections with this pathogens in the northeast corner of this city over the last two weeks."

I think you're overselling this a bit. Sequencing a human genome is not going to tell you whether you are infected with a pathogen, and it won't identify the pathogen. To do that, you will need to isolate the organism and sequence it that way. Also, having the genome of an organism does not automatically make it easier to determine things like antibiotic resistance. In some ways it makes it more difficult, because you have too much information. High throughput sequencing is definitely a great advance for the scientific community but, like all great advances, it's a tool that is useful for some things, not a magic answer machine.

Oh and by the way, everything you mention for diagnosis above can already be done with current methods faster and cheaper than with whole genome sequencing.

Re:Don't believe the hype (4, Informative)

Samantha Wright (1324923) | more than 2 years ago | (#38695658)

Pacbio promises a trillion unicorn farts per second. It's hard to take them seriously. As far as medical applications are concerned, the read length in the Ion Torrent system is ten times the size it needs to be, since most (known) diseases occur due to mutations in the very specific and non-repetitive exome, or in its close vicinity. No one (that I know of) has ever seriously proposed using this hardware for de novo sequencing of large eukaryotes, especially since the machine currently on offer doesn't have the well capacity to sequence the whole human genome!

That being said, there's always paired-end reads. I'm guessing the protocol for doing so with this system doesn't exist yet, but they tend to solve most of the repetitiveness problems for shorter read lengths.

Re:Don't believe the hype (3, Interesting)

backslashdot (95548) | more than 2 years ago | (#38695794)

"the read length in the Ion Torrent system is ten times the size it needs to be"

Uh no. Not at all.

"most (known) diseases occur due to mutations in the very specific and non-repetitive exome"

The problem is that if it does occur outside of this, there's be no way to tell where exactly it is. Second, even if it is within the non-repetitive region .. a mutation could make matching the sequences difficult since it wouldn't be certain if you're dealing with an overlap or a mutation. The reason most known diseases occur due to mutations in non repetitive areas is because those are the easiest areas to detect. The unknown diseases probably occupy the other spots.

For disease specific mutations such as cancer the only way to detect the mutations is with long reads. If you want to cure cancer there needs to be a way to do long reads with single cell sequencing.

Re:Don't believe the hype (2)

RDW (41497) | more than 2 years ago | (#38696572)

For disease specific mutations such as cancer the only way to detect the mutations is with long reads.

This really isn't true. Though it would be nicer to have longer reads, short read sequencing (exomes or whole genomes) is actually proving to be very successful at picking up many novel mutations in cancer. Discovering tumour-specific somatic mutations is a particularly nice application for this technology, as you can often do a direct pairwise comparison with the patient's normal germline DNA (e.g. blood DNA if you're working with solid tumours). Typically results will be validated by another technique (e.g. conventional Sanger sequencing), but with a decent analysis pipeline you shouldn't get too many false positives from the NGS.

Re:Don't believe the hype (2)

lbbros (900904) | more than 2 years ago | (#38696056)

There's another problem to bear in mind: coverage. What is coverage exactly? In terms of "next generation sequencing" (to which this machine belongs to) is how well a part of the genome is covered (sequenced), and that in turns means that the number of fragments (100-150 in the case of Ion Torrent) read for a specific region must be high as possible (those are called "reads").

A good coverage allows you ensure that what you're seeing is real and not some sequencing errors (all technologies suffer from certain types of errors). In the case of Ion Torrent, you usually sequence fragments up to 1 Gbp of sequenced material (G base pairs of DNA), which isn't enough to cover the inter-genic regions or other structural DNA. So usually you do a "reduction step" by either only selecting a handful of genes to be sequenced (mutation screening for example) or by sequencing only the "exome" (exons are the parts of DNA that are actually transcribed to mRNA, the exome is a collective term for all the exons in the genome). That may be useful per se but it's nowhere near a complete genetic map for one individual.

Equipment to do that is much more expensive (500K USD, not counting reagents and other machines).

Re:Don't believe the hype (1)

RDW (41497) | more than 2 years ago | (#38696464)

If the 'Proton 2' chip (which we probably won't see this year) lives up to the hype, then with reasonable assumptions about read length and numbers of active sites, it may manage whole genome at 30x:

http://seqanswers.com/forums/showthread.php?t=16709 [seqanswers.com]

Re:Don't believe the hype (1)

mapkinase (958129) | more than 2 years ago | (#38696284)

PacBio produces a lot of errors.

What does it all mean? (0)

Anonymous Coward | more than 2 years ago | (#38695518)

Not to demean this excellent advance in the technology but it should be called out that the pace of understanding what all these raw sequences mean is not on a growth path too. Anyone have some ideas for accelerating our understanding of semantics?

It really is a daunting task. The protein codings are just the beginning. We are making some progress on the various (more to come?) regulatory mechanisms and from there we need to know how all of that interacts over the lifetime and various differentiate cell states. Throw in environmental factors and wow, that's a big space to map out. It needs automation but how?

Re:What does it all mean? (1)

guttentag (313541) | more than 2 years ago | (#38695626)

It means that Facebook is going to buy Walgreens or CVS, install these machines in every location and offer sequencing for free (as in you'll have to watch ads during the procedure and they will copyright your DNA). While you are strapped into a chair, a button you cannot reach will light up and you will be invited to opt out of their plan to sell your DNA, simply by pushing the lighted button. This might not seem like a big deal until Zynga targets you with some pointless free game that you are genetically predisposed to become addicted to (free as in you can do absolutely nothing even faster if you give them money).

Re:What does it all mean? (2)

Samantha Wright (1324923) | more than 2 years ago | (#38695698)

There are a few key puzzles we need to crack—protein dynamics, mostly—and then we'll have the ultimate acceleration method: we'll be able to simulate it all. Right now we're content with trying to sort out those challenges, and fixing the disorders we already know how to recognize. It'll keep us busy for a long time. In the interim we'll just play with increasingly clever tricks to sort out the patterns in the sequences, and catalogue lots of people so we have things to work with when the time comes.

Re:What does it all mean? (1)

Rutulian (171771) | more than 2 years ago | (#38698606)

No, I don't think so. Simulation of complex biological systems, especially when you include molecular details like protein folds and conformation changes, takes a tremendous amount of computer time. If you can approximate some things using empirical measurements, you can speed things up a bit, but even so we are pretty far from knowing all of the rules we need to know to simulate even relatively straightforward things like the progression of an infection in a host.

People were saying similar things decades ago when mechanistic enzymology was a hot field. "All we need to know is get binding and catalytic parameters for every enzyme in primary metabolism, and then we will be able to model it." Now, decades later, we still can't even simulate a simple pathway like glycolysis much less all of the interacting pathways.

Re:What does it all mean? (1)

Samantha Wright (1324923) | more than 2 years ago | (#38699896)

The reason I say exhaustive physical simulation is the silver bullet to biological problems is that, while it may be fantastically slow and inefficient, it will finally get us an honest and reliable model of what's really happening. We can then study that model, and determine what optimisations and simplifications we can reliably make.

Traditionally, when biologists try to simplify a system (such as just looking at enzyme binding graphs, an act that makes me nauseous because it's so abstract and useless) we do so with radical reductionist objectives (i.e., only looking at the interactions of couple of genes and their products) and a grossly incomplete picture (of the physics involved in those phenomena.) Further, most such studies are done with empirical measurements, which are really a game of broken telephone and fraught with error margins. It's taking the problem of determining which straw was responsible for breaking the camel's back—and putting it in a wind tunnel.

The modern bioinformatics perspective, of holistic collection followed by logically-backed reduction, avoids all these problems. I'm not saying we'll be simulating biological organisms with absolute fidelity forever, merely that we can't really appreciate the biology until we've seen it in its native environment.

A single server (1)

jamesh (87723) | more than 2 years ago | (#38695528)

The Ion Proton Sequencer uses analysis software called Ion Reporter to analyze the data of a single genome on a single server. This speeds up the process considerably and removes the IT-related bottlenecks

Genius! A cluster of computers is an obvious bottleneck and they have made the step of getting a single server to do all the work. I hope they have a patent on that idea.

However, the most important factor in reducing the sequencing speed so dramatically is the introduction of the next generation of Ion Torrent semiconductor chip technology.

Oh. Right. So this is really just using _better_ hardware to do the job.

Re:A single server (1)

lbbros (900904) | more than 2 years ago | (#38696072)

In fact, I think it's just hype. To do proper analysis runs you *need* parallel computing, as these tasks are primarily CPU bound. But a whole load of RAM doesn't hurt, either, especially if you analyze more than one genome at once.

Re:A single server (1)

RDW (41497) | more than 2 years ago | (#38697090)

Reports elsewhere suggest they'll be selling a "$75,000 server" with this machine, which will apparently be able to spit out a fully processed whole genome in a day, and lets them market the whole thing as an 'appliance'. This will be enough for many labs. But if the Proton is anything like their previous sequencer, the unaligned sequence data will just be in a standard text file format that can be uploaded to the local cluster (if you have one) and processed any way you like. Large genome centres may go this route if the basic technology lives up to the hype.

Re:A single server (1)

cbiltcliffe (186293) | more than 2 years ago | (#38699072)

Yes, and I'm betting that $75k server has just a few processor cores in it, which really takes care of the parallel computing problem nicely.
I'm guessing for that kind of money, it's probably a quad core, 4 CPU machine, at least. I can't imagine it needing enough storage to burn through $60,000+ worth of hard drives, so it's got to be a monster processing machine.
My wife (yes, there are married slashdotters!!!) currently works with the previous instrument that Ion Torrent released, about a year ago. It uses a server that's not as expensive as this, and has a few (I think 6) TB of storage. Even if this machine needed exponentially more storage, 60 TB RAID is about than $10,000, even at current flood sale hard drive prices.
Throw in the markup that Life Tech puts on everything they outsource, and you're looking at probably $40k worth of actual computing power.
Heck, for that price, maybe their "server" is actually a small cluster and SAS, conveniently fitted into a single 24Uish rack.

How does that compare to X-ray machines? (2)

jcr (53032) | more than 2 years ago | (#38695534)

A hundred and fifty grand doesn't sound like a whole lot of money for medical equipment.

-jcr

Re:How does that compare to X-ray machines? (4, Funny)

ColdWetDog (752185) | more than 2 years ago | (#38695576)

"Ah, I see you have the machine that goes ping. This is my favorite. You see we lease it back from the company we sold it to and that way it comes under the monthly current budget and not the capital account. "

Yay, progress! (2, Insightful)

martin-boundary (547041) | more than 2 years ago | (#38695546)

Patient: "So, snif, bhat dh'you bheckon I habh, snif, bhoctor?"

Doctor: "Well, it looks like you have a common cold. But let's be sure, shall we? I just got this new DNA sequencing machine. Come back tomorrow."

The next day...

Patient: "Hebho bhoctor, bhat dho I habh?"

Doctor: "Well, it looks like you have a common cold. That will be $1000."

Re:Yay, progress! (1)

guttentag (313541) | more than 2 years ago | (#38695702)

Patient: "Hebho bhoctor, bhat dho I habh?"

Doctor: "Well, it looks like you have a genetic predisposition to paying exorbitant sums of money for things you don't need. It's called Gullibility. Don't be so sad, it's very common in this country, like a cancer! Just remember that even though it eats some people alive, some people survive! You just need to have balls like Lance Armstrong, avoid drugs and wear yellow shirts in the summertime. That will be $1000. Now that I know what to look for, I can zero in on this and accurately determine the likelihood of recurrence if we sequence your DNA just one more time and you give me your debit card pin number."

The next day...

Re:Yay, progress! (0)

Anonymous Coward | more than 2 years ago | (#38695772)

Currently it's like this:
  Patient with walking pneumonia: I'm really sick - I think I may have walking pneumonia - can I have some antibiotics?
  Doctor: I have no way of knowing what you have - but there are some vague claims that over use of antibiotics leads to resistance - so just go home and see what happens.
  Patient: "goes home" for a couple weeks. That is, patient spends next couple weeks out in community infecting other people - including an old person who ends up in the hospital costing everyone's insurances tens of thousands of dollars.

Then original patient gets worse and goes back to doctor.
  Patient with walking pneumonia: It's been two weeks and I'm getting worse. It's really hard to breathe.
  Doctor:OK, I still have no way of knowing what you have - but I've got a vacation coming up and don't feel like dealing with this with this so just go to the hospital.
  Patient: goes to hospital
  Hospital Doctor: What you have is probably bacterial but I have no way of know which strain of bacteria is infecting you so I'll just give you this broad spectrum antibiotic.

Overuse of broad spectrum antibiotic at hospital leads to development of resistance - and then there's a nasty outbreak of bacterial pneumonia in the hospital that can't be cured with even their broad spectrum antibiotic.

Or, in a few with years when high throughput sequencing is available:

Patient with walking pneumonia: I feel really sick - I think I may have walking pneumonia.
  Doctor: Hmm, you're still early in the infection so it could just be a virus but let's use our high throughput sequencer to check. Just cough into this tube.
  Doctor (a couple hour later): Yes, you do actually have walking pneumonia - and it's a strain that's resistant to penicillin so we'll give you a different antibiotic that's work on this particular strain.
  Patient - gets better in a few days and doesn't infect anyone else

Re:Yay, progress! (2)

cbiltcliffe (186293) | more than 2 years ago | (#38699796)

Doctor: Hmm, you're still early in the infection so it could just be a virus but let's use our high throughput sequencer to check. Just cough into this tube.

  Doctor (a couple hour later): Yes, you do actually have walking pneumonia

You know those crime shows on TV that where the cop and a computer guy have a crap video from a 320x240 surveillance camera, and the cop asks the computer guy "Can you enhance that?" and the video zooms right in on the suspects face, which then turns from about a 9 pixel smudge into a 10 Megapixel image that's clear enough to see the pimple on the perp's nose?

Yeah....

Just so you know, high throughput sequencing is currently available, and has been for a year or two. The problem is all the lab work that needs to be done to isolate the DNA, purify it, and put it into a solution that this instrument can analyze. (Not to mention in a case like this, the viral DNA would also have to be separated from the patient's DNA, which would probably at least double the processing time.)

All that stuff is manual lab work that can not currently, or for the foreseeable future, be automated, and it takes much longer than a couple of hours.

Re:Yay, progress! (0)

Anonymous Coward | more than 2 years ago | (#38696278)

Implying the primary result of this kind of technology being more accessible is your (apparently terrible) doctor milking you for money is ridiculous. I guess you would prefer that MRI machines were still only for the super rich.

Re:Yay, progress! (2)

LordKronos (470910) | more than 2 years ago | (#38697232)

Huh? In what way does the cold virus alter your DNA, such that a DNA sequencing machine could be used to diagnose it? And you know, doctors currently have all sorts of diagnostic tests at hand that could be used unnecessarily, yet I've never heard of doctors using an x-ray, EKG, MRI, or anything of the sort to diagnose a cold.

Yeah, I know, it was probably a joke and not meant to be taken seriously, but your score was +3 Insightful, not +3 Funny.

Re:Yay, progress! (0)

Anonymous Coward | more than 2 years ago | (#38697558)

More likely scenario, given the current state of the American healthcare system:

Doctor: Well it looks like you have a common cold. Best thing to do would be to get some bed rest.
Patient: But I don't think that's it. Where's that new DNA sequencing machine I've heard about in the news?
Doctor: I can assure you that there is absolutely no indication for such a test with the symptoms you're having.
Patient: How can you be sure? Why not just give me the test?
Doctor: It is an expensive test, and the likelihood that it would tell us something that would drastically change --
Patient: Don't you greedy doctors care anymore these days? I'm the patient. I demand to have the test!

The next day...

Doctor: The test results are back. You have a common cold.

Five years later...

Public: Gee, why is our healthcare system so bankrupt?

Re:Yay, progress! (1)

timeOday (582209) | more than 2 years ago | (#38698402)

Alternately, "I'm afraid you have Bird Flu, please come with me!"

The reason "the common cold" hasn't been cured is because "it" is actually hundreds of different virii. If only there were a way to tell which is which...

In the future the doctor will swab your throat, upload some markers, and the next day the correct prescription (from hundreds) will be FedEx'd to your door.

Another medical money-grubbing bullshit (-1)

Anonymous Coward | more than 2 years ago | (#38695612)

We still don't know how DNA/RNA/epigenetics work. So-called "junk DNA" are simply ones we don't know what they do.

Our "modern" medicine is still not that far off from the old-school quackery. Ask a practicing physician friend.

Re:Another medical money-grubbing bullshit (3, Informative)

Samantha Wright (1324923) | more than 2 years ago | (#38695734)

The term "junk DNA" is now only used by shoddy science journalism. We're quite comfortable with how DNA and RNA do what they do. There's a mystery about what happens on the protein side, and the question about what functional bits of RNA (called microRNA) interact with what genes is sheerly a matter of ridiculously obtuse combinatorics. Say whatever else you will about them, fat cancer research budgets have taught us a lot about the essentials.

Re:Another medical money-grubbing bullshit (1)

jo_ham (604554) | more than 2 years ago | (#38696528)

Can they help us crack Photosystem II? That bastard is frustrating chemists the world over (as far as knowing sort of how it works but not enough of the really key details).

Re:Another medical money-grubbing bullshit (0)

Anonymous Coward | more than 2 years ago | (#38697774)

I'll add a clarification about Junk DNA for non-biologist slashdotters:

Although some may use the term 'Junk DNA' erroneously, as analagous to 'DNA with unknown function', this does not mean that the term is not valid. In fact, most of the human genome is certainly junk, in the sense that it demonstrably has no function whatsoever. For example, approximately one-third of the genome is made up of many thousands of copies of long-dead transposable elements (known as LINES and SINES; look them up). A further 10% of the genome is made up of other nonfunctional transposable elements, and about 8% is made up of dead viruses. Much intronic sequence is also junk.

While it has long been understood that some of the 98.5% of the genome that is non-coding DNA is functional, this only represents a small fraction of total non-coding DNA, and in invariably located within the ~10% of the genome that is evolutionarily conserved. This 10% figure also constitutes the most plausible upper limit for functional DNA.

In summary, the current figures we have are that two-thirds of the genome is known to be junk, less than 9% is known to be functional, and almost all the remaining fraction, being non-conserved, is very likely to also be junk.

Re:Another medical money-grubbing bullshit (1)

Rutulian (171771) | more than 2 years ago | (#38698712)

Well, yeah, and the appendix was also a junk organ until quite recently. Just because we don't know what it does doesn't mean it is non-functional.

Hands of ordinary doctors (4, Interesting)

nbauman (624611) | more than 2 years ago | (#38695640)

Yes, you bring your doctor a thumb drive with 3 billion base pairs of your genome, coding for 23,000 genes. Do you know what he says?

"What am I supposed to do with that?"

Years ago, people thought that we could find Mendelian genes for all the important things in health and disease. Now it turns out that most of the important things we want to know are controlled by hundreds or thousands of genes, each of which increases the risk by 1%, sometimes less. That's for things like cholesterol, autoimmune diseases, cancer susceptibility, etc.

For the most part, your family history is a better predictor than any genome screening. Gene tests usually aren't useful unless you have a particular gene in your family and you want to find out whether you have it, like the BRCA genes for breast cancer. If your mother died of breast cancer at age 40 because of the BRCA1 gene, and you don't have the BRCA1 gene, you don't have to worry.

Re:Hands of ordinary doctors (1)

EnsilZah (575600) | more than 2 years ago | (#38695742)

Well, obviously you don't bring the raw data to your doctor.
How about you run it through some statistics software and it gives you a list, 5% increased chance for breast cancer, 7% chance of heart attack by age 50, then your doctor can suggest more frequent checkups, changes in diet.

How about this, your government subsidizes a sequencing for every individual (I know getting into Gattaca territory here, also Americans would scream 'socialism!'), say in reverse order, oldest to youngest until you can do one at birth, then you gain a wealth of statistical data with each subsequent year.

Re:Hands of ordinary doctors (1)

nbauman (624611) | more than 2 years ago | (#38699490)

OK, you run it through this wonderful statistics software and it gives you a list.

Your doctor says, "Normally you would have a 10% chance of getting breast cancer (when you're still young enough that treating it would make a difference), so you should get a mammogram every 2 years. But you have a 5% increased chance for breast cancer, so you have a 10.5% chance of getting breast cancer. You *really* should get a mammogram every 2 years."

There is an increasing list of mutations that really do make a significant difference in risk, like 50% or 85% risk, such as BRCA1 and BRCA2 for breast cancer. I think it's up to a couple of hundred by now. Most of them are fairly rare, with the disease occurring in maybe 1/100,000 births. Most of the people who have these genes know that they have it in their family. (Another difficulty is that unlike breast cancer many of these diseases have no cure or treatment.)

You could make a single gene chip to test for all of these genes, although it's a waste to test me for sickle cell anemia since I don't have any Mediterranean or African ancestry, and it's a waste to test me for Huntington's disease since I've never had it in my family. But if it's cheap enough, and the patents expire, you might as well make a singe test for all the *known* mutations to test at birth. But there's no benefit in sequencing the *entire* 3 billion bp human genome, given our current state of understanding and our understanding any time in the near (5-10 years) future.

There are some useful genetic tests to diagnose cancers for example. You're 60 years old, you get a routine blood test, and you have chronic lymphocytic leukemia. Now there's a DNA test. For patients with a marker called ZAP-70, median survival is 5 years. For patients without the ZAP-70 marker, median survival is 25-30 years (without treatment). Big difference.

Sequencing your entire genome is a cool thing to do. I'd like to have a copy of my entire genome sequence, so every time I read about the discovery of a new function for a gene, I could look up my allele. It's about as cool as a backyard telescope and about as useful.

Re:Hands of ordinary doctors (1)

FairAndHateful (2522378) | more than 2 years ago | (#38695760)

For the most part, your family history is a better predictor than any genome screening. Gene tests usually aren't useful unless you have a particular gene in your family and you want to find out whether you have it, like the BRCA genes for breast cancer. If your mother died of breast cancer at age 40 because of the BRCA1 gene, and you don't have the BRCA1 gene, you don't have to worry.

While I fully agree with this, I can see the potential value of screening for all genetic markers for disease at once, including the ones we are not aware of yet. "We think you're clear now, but there's a slight possibility of a future problem with bone-us eruptus. To make sure you're in the clear, we just need to test for this newly discovered genetic marker for... Oh... I see... You have... Well, 18th chromosome, 1017th pair... Okay, you're clear... Haha, yeah, I guess that would have been a stressful couple of days waiting for the test results! Well, enjoy the rest of your day." Also, it'd be nice to have the complete sequence to yourself and off of your medical records, in case the insurance companies start looking for that stuff. Worried about a marker? Look it up yourself! You've already had the test!

Re:Hands of ordinary doctors (1)

nbauman (624611) | more than 2 years ago | (#38699526)

"There's a 0.001% possibility of a future problem. Oh, I see, 18th chromosome, 1017th pair... 0.0009% possibility."

Re:Hands of ordinary doctors (3, Insightful)

pesho (843750) | more than 2 years ago | (#38695802)

Yes, you bring your doctor a thumb drive with 3 billion base pairs of your genome, coding for 23,000 genes. Do you know what he says?

"What am I supposed to do with that?"

You hit the nail on the head. There is very little if any useful information for a doctor in full genome sequence, and most of it can be obtained with much cheaper genetic tests. ABI is ramping up the hype because they really need this instrument to be a good seller. Their first bet in the field was on a sequencing by ligation machine (SOLID) which did not sell very well.

Re:Hands of ordinary doctors (0)

Anonymous Coward | more than 2 years ago | (#38695850)

Yes, you bring your doctor a thumb drive with 3 billion base pairs of your genome, coding for 23,000 genes. Do you know what he says?

"What am I supposed to do with that?"

You hit the nail on the head. There is very little if any useful information for a doctor in full genome sequence, and most of it can be obtained with much cheaper genetic tests.

I feel like I'm watching a bunch of guys on horses making fun of the first automobiles. We're seeing the beginnings of the biggest revolution in medicine since antibiotics. This is going to be huge.

Sure, if you already know what you're sick with then a specific test for that condition will, in certain cases, be cheaper. But the point is you don't know.

You walk into the doctor's office with symptoms that could be cold, flu, the onset of bacterial pneumonia, etc. - and, in a few years, high throughput sequencing will tell you exactly which antibiotics/anitvirals (if any) to take.

You have a kid and when he's a few years old it becomes clear that he's got mild mental retardation. You want to know whether the obstetrician messed up during the birth, or your spouse dropped him on his head when you weren't around, or whether he got into the cleaning chemicals under the sink, or whether he got meningitis - or what. Well, if it's genetic, in a few years high throughput sequencing will be able to give you an answer.

Re:Hands of ordinary doctors (1)

pesho (843750) | more than 2 years ago | (#38699424)

I feel like I'm watching a bunch of guys on horses making fun of the first automobiles. We're seeing the beginnings of the biggest revolution in medicine since antibiotics. This is going to be huge.

Sure, if you already know what you're sick with then a specific test for that condition will, in certain cases, be cheaper. But the point is you don't know.

You walk into the doctor's office with symptoms that could be cold, flu, the onset of bacterial pneumonia, etc. - and, in a few years, high throughput sequencing will tell you exactly which antibiotics/anitvirals (if any) to take.

Your car analogy is not very appropriate. To begin with I have been riding the automobile in question for couple of years, and its predecessors (microarrays) for about 10 years. You are completely missing the point that the problem here is not the amount of information that a doctor can potentially get from the full genome sequencing. The problem is that at the current state of the art we are unable to digest this information to a point where a doctor can act on it. The reason is that once you go beyond the simple Mendelian genetics, the interactions between different factors become exceedingly complex. You need to take into account multistate interactions of the genome sequence with epigenetic and environmental factors. In addition, having the genomic sequence will not solve your problem of not knowing what to look for. It will tell you even less about what kind of infection you have. In this case we don't really need to use the latest gadget to replace cheap, fast and reliable immunology tests? Kind of reminds me about the machine that says 'BING'. [youtube.com]

As it stands now, doctors have more information that they can process. So if your are looking for a revolution that is just starting look at technologies for integrating large amounts of 'fuzzy' information from patient records, medical textbooks and literature, and various medical test to produce accurate diagnosis. Technologies like IBMs Watson and the NIH sponsored i2b2 [i2b2.org] is the next big thing in medical care.

You have a kid and when he's a few years old it becomes clear that he's got mild mental retardation. You want to know whether the obstetrician messed up during the birth, or your spouse dropped him on his head when you weren't around, or whether he got into the cleaning chemicals under the sink, or whether he got meningitis - or what. Well, if it's genetic, in a few years high throughput sequencing will be able to give you an answer.

You can get the answer if it is genetic now. So going back to the original comment: What are you and your doctor are going to do about it??

Re:Hands of ordinary doctors (1)

nbauman (624611) | more than 2 years ago | (#38699666)

What you're watching is a bunch of guys who have been burning through billions of dollars on the War On Cancer, and still haven't been about to cure (most) cancers. They've hit a few home runs, like chronic myelocytic leukemia and acute lymphocytic leukemia in children, and some of the major cancers have longer life expectancies and less brutal treatments, but it never delivered the promise Mary Lasker and Richard Nixon made of curing cancer (thought it's better than pissing it away on the military). We've learned. Curing cancer is difficult.

You're also watching a bunch of guys who have followed so many wild goose chases that they don't want to follow another one.

Back in the 1990s, I wrote an article predicting the wonderful world of computerized courts in the 21st Century. You'd go into the court records office, press a few buttons, and your documents would appear on the screen like magic. (According to IBM.) Then around 2005 I had to go down to the Federal courthouse in Manhattan to look up the documents in a patent trial that was going on there. I will leave it to your imagination. It was easier to get court documents in Herman Melville's time.

Re:Hands of ordinary doctors (1)

Demonoid-Penguin (1669014) | more than 2 years ago | (#38695810)

Yes, you bring your doctor a thumb drive with 3 billion base pairs of your genome, coding for 23,000 genes. Do you know what he says?

"What am I supposed to do with that?"

Maybe you should get a doctor that knows what an USB thumb drive is?

Then you can move onto the next problem.... (who's your daddy?)

Attracting Fast Food Fans (-1)

Anonymous Coward | more than 2 years ago | (#38695712)

What to Expect: An extra large, cheesy pizza delivered right to your doorstep. Perfect for those wishing to try a new type of pizza in Nürnberg. http://pizzaliefer.de/baguette-heimservice/90469-kettelersiedlung-n [pizzaliefer.de] ürnberg kettelersiedlung nürnberg

ion proton. really? (1)

schmeathouse (2552756) | more than 2 years ago | (#38695740)

just wtf is an "ion proton"? a proton is an ion. so what then is an ion proton? a $150,000 benchtop 1 day human genome sequencer and marketing couldn't come up with a better name? or at least a more correct one like "proton ion".

Re:ion proton. really? (1)

lbbros (900904) | more than 2 years ago | (#38696026)

The name for the technology is "Ion Torrent", and albeit the wording there is terrible, it detects, using a semiconductor, the flows of protons in solution to determine which DNA base is being read.

Boon for salesmen (1)

JimboFBX (1097277) | more than 2 years ago | (#38695940)

I know someone who (was) married to a guy who's only 26 and he makes six figures selling some sort of medical machine. Apparently he plays video games all the time and is lazy and just works sparingly and travels a few times a month. You have to wonder about how much mark up is on these medical machines if a guy who works only only a few days a week or month with little schooling can earn 6 figures in commissions

Any Nefarious Uses for This_ (1)

Froggels (1724218) | more than 2 years ago | (#38696068)

What kinds of nefarious outcomes can this technology lead to? Insurance companies and DHS using it in ways that help no one but themselves (and the children) immediately come to mind.

Doesn't reducing speed mean slowing down? (1)

DigitalReverend (901909) | more than 2 years ago | (#38696418)

FTFA: "However, the most important factor in reducing the sequencing speed so dramatically is the introduction of the next generation of Ion Torrent semiconductor chip technology."

Shouldn't it be increasing sequencing speed, or reducing sequencing time?

This FP f0r GNAA (-1)

Anonymous Coward | more than 2 years ago | (#38696488)

a fact: FreeBSD long time FrreBSD came as a complete save Linux from a words, don't get for the record, I you join today!

cool (1)

JustNiz (692889) | more than 2 years ago | (#38696874)

Now my doctor can make some interesting mutant fish for the aquarium in his waiting room..

You have a cold? hum, let's look at your DNA (1)

youn (1516637) | more than 2 years ago | (#38696918)

we are about to be served with a "let's look at your DNA" at every visit for completely unrelated diseases in every possible scenario possible. This is going to get annoying very fast

And does it really cost $1000 to do a sequencing? (1)

NotSoHeavyD3 (1400425) | more than 2 years ago | (#38697118)

Just curious since I remember reading, admittedly on a blog, somebody take that "It takes X dollars to do 1 MRI" statement on. Basically the idea was that MRI's have a huge fixed cost. (IE you have to pay for the machine and tech before you do even the first MRI) However the additional cost from each MRI was basically nothing.(Since the machine has to be already there, it's going to use the same amount of power no matter what and the tech has to be there.) So from an economic point of view it didn't make sense to put a huge cost on each individual MRI since that would encourage docs to not use the machine. (When they really should try to schedule as many as possible since each one was additonal money and didn't really cost anything.) Is the deal the same with this sequencer? (IE once you have the machine and the guy to run it a single sequence basically costs nothing.)

Re:And does it really cost $1000 to do a sequencin (1)

RDW (41497) | more than 2 years ago | (#38697372)

'Is the deal the same with this sequencer? (IE once you have the machine and the guy to run it a single sequence basically costs nothing.)

No, the $1000 (or whatever the figure turns out to be) is just for consumables. You need to spend this on every run.

Re:And does it really cost $1000 to do a sequencin (1)

NotSoHeavyD3 (1400425) | more than 2 years ago | (#38697720)

Thanks for the info, ignorance fought

Re:And does it really cost $1000 to do a sequencin (1)

alphatel (1450715) | more than 2 years ago | (#38697542)

Just curious since I remember reading, admittedly on a blog, somebody take that "It takes X dollars to do 1 MRI" statement

The DNA sequencing table [dnasequencing.org] shows a precipitous drop in costs down below $10,000 and under .10 per genome or check the latest genome chart [genome.gov] . However this cost only calculates raw full human sequence not just a particular strand or some desktop device that does limited work.

What for? (-1)

Anonymous Coward | more than 2 years ago | (#38697332)

Why on Earth would anyone want such a thing? By "anyone" I mean, other than insurance companies, employers, and crooks.

Free for every clinic (1)

sgt scrub (869860) | more than 2 years ago | (#38698518)

A DNA scan of all bacteria/virus from patients with infections would be boon to public health. I can think of two good reasons it should be free to do DNA scans on every patient with an infection. Tabulating the data to watch for the spread of a desease. Studying the changes in bacteria/virus DNA as they develop resistances to treatments. I can also think of three good ways to pay for it. The government wanting to control desease outbreaks. Researchers wanting data for research. Pharmaceutical companies wanting data to make drugs to sell.

Nice, but what's the point? (1)

msobkow (48369) | more than 2 years ago | (#38699482)

It's nice that the price of using DNA sequencing technology is coming down, but I have a question:

So what?

Doctors aren't trained to use DNA sequencing equipment. And even if they were, how many disorders can be diagnosed by gene sequencing? Other than confirmation of genetically carried disorders, gene sequencing would never even be able to help diagnose anything.

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