Helicos High Speed Gene Sequencing

[19Tranc3r92]

Good music.

[theSweetmonster457]

how do they put the data together at the end?

[MegaVldmr]

@theSweetmonster457 Using computer trying to find overlaps between sequenced fragments.

[jonahfox]

Cool, I wonder how much it costs lol

[ntp1789]

@jonahfox 100k at least

[vldmr0tube]

even if error rate is 1% after first run, after 3 runs it's already 0.0001%!!!

So it really worth it considering speed of the method.

[pedrolikes2008]

They can find the sequence of each small DNA fragment attached to the PoliA strand but how do they join all those fragment readings in the correct order to build the correct entire original genetic sequence?

[umartdagnir]

@pedrolikes2008 They are aligned by computer to a reference genome. So you cannot sequence something new, you rather look for differences in genome of something that was sequenced before.

[northerntropics]

@pedrolikes2008 After you do the chopping some fragments contain some part of the sequence of other fragments. A computer program puts the pieces together.

[Adz795]

Wasn't this a commercial???

[nyinvestor]

It's great tech, but the market's not large enough, that's why the stock's been hurting. I'm much more excited about Wafergen (WGBS) and their Smartchip Platform. They just released Aug 2010, and their trade volume bounced 4x's with a 14% gain. If they get a single Pharma by December, we could see a lift up to $4-5, with a possible acquisition next summer. Take a look at the tech and the stock- I think they're going places.

[ShortyTigers]

@nyinvestor WGBS? what a shit stock! You must be one of those people on message boards trying to shove that shit in peoples faces. haha you poor bastard get a life dude...

[GARRYKINGLIVE]

the image data is gonna be a bitch to store and analyse!

[plasticbarf]

cool dude

[montelka]

not to sound pesimistic....but the degree of error might be higher i dont trust the "washing of unincoperated nucleotides"

that is where errors start

[Casshyr]

@montelka also, without amplification step, this means the instrument gotta be really sensitive. But such high sensitivity means instrument needs to be highly maintained, and also can potential pick up a lot of random noise signal

[northerntropics]

@Casshyr My photo camera has similar 'sensitive' technology. Once in a while a pixel malfunctions. Nothing that can not be fixed in software.

[Casshyr]

@northerntropics Agree, but there is a review published in Nature about 1 year ago comparing accuracy between different sequencing methods, and Helicos has one of the lowest accuracy call. Of course it has its own advantages, but just saying that compare to other methods out there, it's one of the worst in terms of accuracy.

[vldmr0tube]

@Casshyr

You can just have additional runs to increase SNR if you are unsatisfied with the one you have...

[Casshyr]

@vldmr0tube I guess the error rate is just too high such that you will need so perform so many additional runs in the end, it's just not worth it. And the technology is not exactly cheap either. That doesn't mean this won't happen tho, i'm sure single molecule sequencing will be the future someday, once they perfect the method further.

[northerntropics]

@montelka unincorporated nucleotides with the fluorescent marker in spots not tagged as targets would not be such a problem right? Software simply ignores them. Heck with a billion per run you can ignore some suspect signals too. Right?

[montelka]

brilliant...i hope they make it someday soon, because i'll definately buy one.

[demansou]

Expensive but incredibly brilliant!

[GARRYKINGLIVE]

these third gen sequencing platforms are just revoluntionary but imagine the terabytes of data produced! thats where computation comes in. This is great

[Psycatalyst]

This is just as costly as most other sequencing machines because you got to pay for the fluorescent dNTPs and the Data processing must be a bitch if it does not come with a program. I think the nanopore sequencing may cost lesser

[belate2]

This is a good stock to buy. It's available at a reasonable price as of 10-19-09. It will go bezerk if someone like General Electric buys it up or buys into it. Or it may stand well on its own, leastwise that's what my money says.

[drmorrisj]

I disagree with Richard Pickman in terms of the ease of use. This is the problem with the SOLiD. The solid has very short reads (actually 250bp). This makes assembly very difficult. This is why my lab is going with the GS FLX instead of the SOLiD or this cute machine for that matter. They are going to have to do better than this.

[yanij]

which version of SOLiD are u using? the average bp of SOLiD should be around 50bp rather than 250.

[DisturbedRocks111]

i dont understand...what will this accomplish? (go easy on me lol i have no knowledge of genes etc)

[redbaronnl1]

It accomplishes much faster DNA sequencing. With the old method it took months to do what this technique does within hours

[7677890]

Basically, you can search someone's DNA for genes which cause disease, just using a few cells.

[XooxerX]

That's friggen clever as hell! Kudos Helicos!

[abbylinda]

Maybe I would understand it better if I turned the sound on...

[vitr1ol]

Ahh, I see, ingenious.

[vitr1ol]

How are the 100bp sequences put back in order again? presumably you end up with the sequence of each section, but not the whole genome, or even genes if they are longer than 100bp...

[RichardPickman]

Computers! You can use scripts to align the short sequences to each other - you have so much coverage of the genome that each location in the genome is present on many different fragments of DNA. "Stack" these to assemble the longer sequence:

________ ____________ ____ _________ ^^^

we can be pretty sure of this area. Imagine other fragments filling the gaps too!

[lockie84]

very interesting technology

[cerman07]

are there limits to reconstructing the genome due the 100bp size limit (due to vntrs, transposons)? also, if the average area per polyT binding site is 1 square micron, how accurate can the imaging be?

[RichardPickman]

See my response to vitr1ol above...

Any inaccuracies will hopefully sufficiently "covered" that we can call it a random error too, but the imaging is rather precise. It knows where the laser is pointing at any moment and the detection limit is quite low.

[magick205]

This is absolutly brilliant. However, what's the base and support cost for this beast? Since you have to flush the test cell after each polymerase run, how much material is lost and is any /can any be recycled? It sounds like a great tool, but I don't think that this is gonna show up in any "mom & pop clone your dead cat" shops any time soon.

[MagsterMagpie]

Fantastic.

[987wolf987]

wow ths like really hardcore stuf

[Westonci]

Hopefully Obama wins the election, because Sarah Palin calls money for scientific research "earmarks"

[leeam2k]

-"WIRD haha! han vuelto a hacerlo.. WIRD!! xD

Un momento! esto no es WIRD verdad? ¿¡porque no hay ninguna revista llamada WIRD!?"

-"No papa esto es WIRED"

jaja aguanten los simpsons

[weylin6]

this seems prone to errors...

[darkein]

"This was a triumph, I'm making a note here.. huge success. It's hard to overstate my satisfaction"

Doesn't the one narrator sound like the person from portal? Robotic at the least.

[boxa888]

large scale cell replication?? with some florecent piece lol.

[LikeAPossum]

Now that is fantastic!

[BeondaPale]

As these technologies get much better, they're also getting much cheaper. Within a decade, genetic hobbyists may well be designing new species from their garage.

"Commerce is our goal here at Tyrell, "More human than human" is our motto"

--Dr. Eldon Tyrel

[Truthiness231]

Beautiful... after every wash of adenine, guanine, cytosine, or thymine they see what stuck, and in the end have each piece of DNA sequenced properly... just, beautiful...

So an entire genome could be done in a day by one person? Biologists could have every animal mapped in no time...

BTW: there is an old article on How Stuff Works about this, but it isn't as good as this vid IMO as far as describing the whole process.

[Truthiness231]

edit: should have said "have every organism* mapped"... not sure why I limited this to one kingdom ^.^

[Seffyzero]

"So an entire genome could be done in a day by one person? Biologists could have every animal mapped in no time..."

No, what they said was: "Sample PREPERATION is simple, and can be performed by a single person in less than a day."

They did not include how long all the other things would take.

[Truthiness231]

Yeah, that's what I thought, I was just making sure I heard things right. It's amazing how genetic engineering is performed these days. ^.^

With the information given by this process, we could eventually compare every known organism with each other and have the best map of evolution ever made (not to mention what this would do for other important fields, particularly medicine, but that's what I'm interested in).

[5998b]

4th

[Eequality72521]

this is awesome, and it like, is legit

[formallyknownasdave]

this seems like one of those mock commercials you see in those apocalyptic movies just before a bunch of monsters appear and kill everyone

Its awesome and scary at the same time.

[Wyhejin]

so true

[noobia]

o shit! i bet it's Umbrella Corporation

[Truthiness231]

LOL yeah this sound like an Umbrella Corp project

[hamzeeco]

lmao!!

[helmus2000]

That is axactly what i was thinking!

It's scary and awesome!!

[mcfilmmakers]

Correction: Those mock commercials you see in those apocalyptic movies look a lot like this video.

Films are reflections on society, not the other way around.

[formallyknownasdave]

@mcfilmmakers

Mock commercials in horror/action movies tend to be more cliche than normal commercials. The synthesized woman's voice, making the commercial creepy and evil, but at the same time believable that it had been created to promote something

Examples:

The umbrella corp. commercial in resident evil, and SkyNet from the terminator (2 I think)

[Peacenik]

hooray for science!

[TornTech]

first comment!