35 replies to this topic

[manofsan]

And here's a nice feature on the really ambitious efforts, which conceive of genome sequencing for $100, never mind $1000

http://www.technolog.../Biotech/20640/

[niner]

Wow, that's really cool. It's not just cheaper, but potentially better as well. They can push a 2Mb oligo through a microchannel, which causes it to uncoil and straighten out. They have a library of 1024 different 5-base oligos (all possible) each tagged with an identifiable fluor. They do single molecule detection of the fluors bound to the DNA strand, and get both sequence and spacial information. This lets them easily resolve duplications and inversions which would be harder using current methods. It's pretty amazing technology.

[Mind]

Another write-up about the $100 genome

Nearly a year later, but not much new information. The inventor says it is about 5 years away from commercial development. Still, good to see progress and new ideas making it into genomics.

[Mark Wittekind]

This is fantastic news. I heard about this just recently from a friend of mine. Of course, it may not be beneficial to have your genome sequenced as of yet. However, it's obvious that this will help stimulate research and funding from those who were weary about the possibilities and cost effectiveness of these technologies. It will also make comparative research much more effective.

Great link!

[manofsan]

The price of whole-genome sequencing is dropping yet again, to $48000 as Illumina launches its new service:

http://www.technolog...medicine/22793/


Not bad, but I'm still hoping for that $1000 genome, or even less. I wonder how long I'll have to wait?

[Mind]

How long?

Just a gut feeling here - 4 years. I was thinking 2, but there is a chance the economy could keep tanking, setting things back a bit.

It took 2 years for the first 2 orders of magnitude drop in price. We need nearly 2 more orders of magnitude drop to get to $1,000.

While $48,000 is still out of reach for most consumers, the price reflects an exponential drop in the cost of sequencing technologies in recent years. James Watson's genome, sequenced in 2007, cost about $2 million, and Knome initially offered its service at $350,000. A third company, Complete Genomics, announced plans for a $5,000 sequencing service, although this will initially be available only to academic institutions and industry for research and clinical trials rather than for personal use. "It's like watching the price of gas fall," says George Church, a genomics technologist at Harvard University who has developed his own sequencing technology.

[Boondock]

It's dropping at a remarkable rate. If it's $1,000 in 3 or 4 years, I'm getting this done.

[athrahasis]

There really is no reason they wont build a complete chip solution. When that happens we should see sub $200 testing. I say about 4 years.We should start making bets now!

Edited by athrahasis, 14 June 2009 - 11:02 PM.

[openeyes]

It's dropping at a remarkable rate. If it's $1,000 in 3 or 4 years, I'm getting this done.

Same here, provided the $1000 includes in depth analysis/consultation on what it all means, like part of a thorough physical. For now analysis would be in addition to the $48,000 sticker price.

[forever freedom]

This is great. I hope to see really low prices soon, it will be interesting what changes in society it will bring once everyone can have their genomes sequenced.

Edited by forever freedom, 26 June 2009 - 11:49 PM.

[apoptosos]

george church said it would be free in the near future, like cellular phones are today (based on a plan)

[niner]

What would you get from a full genome that you wouldn't get from a catalog of all known SNPs? I guess there would be a few things that might show up, like gene duplications and other large-order weirdness, but would we know what any of that meant? It seems like with a cheap SNP scan, at worst you would need to re-scan after a few years if/when critical new SNPs were discovered.

[forever freedom]

What would you get from a full genome that you wouldn't get from a catalog of all known SNPs? I guess there would be a few things that might show up, like gene duplications and other large-order weirdness, but would we know what any of that meant? It seems like with a cheap SNP scan, at worst you would need to re-scan after a few years if/when critical new SNPs were discovered.

Maybe not now but we're constantly (and exponentially, may i say? not sure on this one) discovering more about what the genes mean and do.

[air90]

Pacific Biosciences is hoping to set a new benchmark with technology that watches DNA being copied in real time. The device is being developed to sequence DNA at speeds 20,000 times faster than second-generation sequencers currently on the market and will ultimately have a price tag of $100 per genome.

Lets hope they hit their target.

[manofsan]

Pacific Biosciences is on target to give us the $100 genome really soon:

http://futurememes.b...tion-point.html

Leading third-generation sequencing company Pacific Biosciences affirmed at the Cold Springs Harbor Laboratory Personal Genomes meeting September 14-17, 2009 that the company has 12 prototype instruments in operation and continues to be on track for ~$100 (“the cost of a nice dinner”) whole human genome sequencing to be commercially available in the second half of 2010. NimbleGen indicated that they may have a $2,000 exome sequencer available in 2010.

Oh yeah! So once the price of sequencing is no longer an obstacle, then what is the next big bottleneck to target?
Data management and analysis/interpretation?

[Mind]

A related thread about the efforts of 23andMe and decreasing SNP testing costs.

[Mind]

Here is one prediction that will be tested soon - $1,000 genome by the end of 2009.

[Mind]

Complete Genomics says they are now doing complete sequencing for $4,400, however this is apparently only the cost of the chemical reagents used in the process, not the full "business cost".

[forever freedom]

Apparently we'll not get complete genome sequencing for 1,000 by the end of this year but it was close. Anyways, price keeps falling dramatically so we'll get there very soon.

Edited by forever freedom, 08 November 2009 - 04:45 PM.

[kismet]

Close as in "order of magnitude" close? Yep. Bait and switch prizes do not count. Companies could give away whole genome sequencing for free if they wanted, but what counts is whether someone can sell it and make money (otherwise it's not becoming mainstream).

[Ghostrider]

Close as in "order of magnitude" close? Yep. Bait and switch prizes do not count. Companies could give away whole genome sequencing for free if they wanted, but what counts is whether someone can sell it and make money (otherwise it's not becoming mainstream).

I thought it was at $48k a few months ago. I'd be impressed if it fell so far so fast...hope it's true though.

[manofsan]

The cost of full genome sequencing has dropped yet again, according to the latest announcements by Complete Genomics:

http://www.technolog...ne/23891/page1/


Hey, so we're finally there - the day of affordable sequencing has arrived.

So when will these services really become widely available to the masses?
How long until they tangibly impact our day-to-day healthcare, and our visits to the doctor's office?

Who here is planning to get their genome fully sequenced? Anyone against doing it?

[niner]

I dunno. What can it show you that a SNP scan doesn't? Long repeats? Are there any diseases or conditions that can only be found be a complete sequencing? Barring that, I think the best use of such cheap sequencing is to sequence really large numbers of people in order to get an accurate look at the range and diversity of the human genome, with an eye toward developing an even quicker, cheaper way to do the analysis without having to look at every single base.

[manofsan]

There are all kinds of subtleties that are coming out by examining the over-arching sequence structure, etc.

Even once full-genome sequencing is economical and widespread, we'll still want to take the tech to the next level by looking at epigenetics, etc.

So there will always be more detail required.

[Ghostrider]

The cost of full genome sequencing has dropped yet again, according to the latest announcements by Complete Genomics:

http://www.technolog...ne/23891/page1/


Hey, so we're finally there - the day of affordable sequencing has arrived.

So when will these services really become widely available to the masses?
How long until they tangibly impact our day-to-day healthcare, and our visits to the doctor's office?

Who here is planning to get their genome fully sequenced? Anyone against doing it?

Complete Genomics, a start-up based in Mountain View, CA, has again lowered the stick in the financial limbo dance of human genome sequencing, announcing in the journal Science that it has sequenced three human genomes for an average cost of $4,400.

Wow, that was a big drop.

[Elus]

http://www.completeg...blicationPR.pdf

I believe it's $1700 now.

[31stCentury]

I can't imagine what new questions and answers will be discovered by this rapid advancement!

I'm especially looking forward to population studies involving very old people. With what we find out about the genetic and epigenetic mutations of aging genomes, maybe gene therapies can finally begin treating aging this comming decade. Can't wait!

[Elus]

It would be especially interesting to sequence the genomes of centenarians. This would allow us to compare the genomes of short and long lived individuals, and hence allow us to evaluate the key proteins that promote longevity.

Here's an interesting article about one such study. Is there a 'Centenarian Gene'? http://www.thecenten...arian-gene.html

[babcock]

A new proposed method for sequencing DNA will significantly lower cost and time involved in sequencing.

http://www.scienceda...91220143923.htm

Boston University biomedical engineers have devised a method for making future genome sequencing faster and cheaper by dramatically reducing the amount of DNA required, thus eliminating the expensive, time-consuming and error-prone step of DNA amplification.

[Mind]

These last 2 posts have less to do with the actual current price, but speak of the potential for dramatically lower prices for sequencing in the near future. Interesting to see how nanotech (as predicted) is finding its way into different engineering fields and could produce dramatic gains in efficiency and value.

Carbon nanotubes show promise for high-speed genetic sequencing (with video).

Traditional methods for reading the genetic script, made up of four nucleotide bases, adenine, thymine, cytosine and guanine (labeled A,T,C,&G), typically rely on shredding the DNA molecule into hundreds of thousands of pieces, reading these abbreviated sections and finally, reconstructing the full genetic sequence with the aid of massive computing power. A decade ago, the first human genome—a sequence of over 3 billion chemical base pairs—was successfully decoded, in a biological tour de force. The undertaking required around 11 years of painstaking effort at a cost of $1 billion dollars. In addition to the laboriousness of existing techniques, accuracy is compromised, with errors accumulating in proportion to the number of fragments to be read.

A new strategy involves the use of nanopores—orifices of molecular diameter that connect two fluid reservoirs. A constant voltage can be applied between two electrodes located at either end of the nanopore , inducing an ionic current to flow through the length of the nanopore's enclosed channel. At this scale, the passage of even a single molecule generates a detectable change in the flow of ionic current through the pore. This current is then electronically amplified and measured. Only fairly recently have state of the art micro-manufacturing techniques enabled researchers to construct nanopores at the scale of individual molecules, opening up many new possibilities for single-molecule manipulation and research.