October 06, 2008
$5000 Complete Gene Sequencing In 2Q 2009

Our biotechnological future is coming even faster than I expected. A Mountain View California biotech start-up, Complete Genomics, operating in stealth mode since a 2006 founding, has announced availability of personal complete DNA sequencing for $5000 in 2Q 2009. If they pull this off it is an amazing achievement.

The cost of determining a person’s complete genetic blueprint is about to plummet again — to $5,000.

That is the price that a start-up company called Complete Genomics says it will start charging next year for determining the sequence of the genetic code that makes up the DNA in one set of human chromosomes. The company is set to announce its plans on Monday.

Cheap! Starting to feel tempted yet?

Some scientists associated with this start-up are heavy hitters.

"I have great confidence that it's right," said Lawrence Berkeley National Lab geneticist Michael Eisen. "I don't know exactly what the underlying method is, but George Church isn't a kidder."

George Church is a Harvard University geneticist who helped found the Human Genome Project and was responsible for the first commercial genome sequence. He's also an adviser to the Mountain View, California-based Complete Genomics, provider of the $5,000 genome — and joining Church is Illumina co-founder Mark Chee, Institute for Systems Biology president Leroy Hood and Massachusetts Institute of Technology bioengineer Douglas Lauffenburger

But Complete Genomics is going to start out aiming at institutional customers. You might have to wait for individual customer access.

Based in Mountain View, Calif., Complete Genomics has raised $46 million in three rounds of financing since its incorporation in 2006. Unlike its commercial next-gen sequencing rivals – Roche/454, Illumina, Applied Biosystems (ABI) and Helicos – Complete Genomics will not be selling individual instruments, but rather offer a service aimed initially at big pharma and major genome institutes.

Complete Genomics is building what Reid calls “the world’s largest complete human genome sequencing center so we can sequence thousands of complete human genomes, so that researchers can conduct clinical trial-sized studies.” If all goes according to plan, that 32,000-square-feet facility will deliver 1,000 human genomes in 2009 and an eye-popping 20,000 genomes in 2010.

At $5000 per genome I think they'll easily sell out their capacity for the first 1000 genomes in 2009.

With materials costs of only $1000 per genome they think they'll sequence 1 million genomes in the next 5 years.

The company also said it intends to open additional genome sequencing centers across the U.S. and abroad. Over the next five years, the company projects that 10 such centers will be able to sequence 1 million complete human genomes.

Our problem becomes how to make sense of all this DNA sequencing data? That data needs to be matched with lots of physical measurements, medical histories, psychometric tests, exercise tests, and other data gathering to allow correlation of all the DNA sequencing differences with various human characteristics.

The approach uses DNA nanoballs. These things are called concatamers which probably refers to concatenation.

The first step is to prepare a gridded array of up to a billion DNA nanoballs, or DNBs. These DNBs are concatamers of 80-basepair (bp) mate-paired fragments of genomic DNA, punctuated with synthetic DNA adapters. The 80-bp fragments are derived from a pair of roughly 40-bp fragments that reside a known distance apart (say 500 bases or 10,000 bases). “We insert an adapter to break the 40 bases into 20 bases or 25 bases,” which acts like “a zip code or address into the DNA,” says Drmanac.

The sample preparation amplifies the DNA templates in solution rather than an emulsion or on a platform. It produces about 10 billion DNBs – each about 290 nm in diameter – in just 1 ml solution. “We spent lots of energy to make them small and sticky to the surface,” says Drmanac. The DNBs are spread onto a surface gridded with 300-nm diameter wells (prepared using photolithography) spaced just 1 micron apart. The DNBs settle into the wells like so many balls dropping into the pockets of a roulette wheel.

One promising use of cheap DNA sequencing data is in the study of cancer cells. Sequencing of tens of thousands or even hundreds of thousands of cancers will lead to much better identification of how DNA mutations contribute to cancer development.

So how cheap would DNA sequencing have to get before you'd pony up to get yourself sequenced? Once the price gets down to a few thousand dollars I'll be waiting more for useful information the sequencing data can provide than for a further price reduction. We are going to have to wait a few more years before we know enough about genetic differences for personal sequencing to provide useful information to most of us.

Share |      Randall Parker, 2008 October 06 10:16 PM  Biotech Advance Rates


Comments
Brock said at October 7, 2008 7:59 AM:

Do you think they'll make their money back before someone comes out with a $1000 genome and forces them to retool? :)

So how cheap would DNA sequencing have to get before you'd pony up to get yourself sequenced?

It really depends on the value received, doesn't it? If I got my genome sequenced today it would probably be an interesting conversation piece and not a whole lot more. That's worth about $20. A real medical benefit on the other hand could be worth $5000 easy.

Luckily, I expect the best of both worlds. By the time the medical benefits are worth $5000 it will probably cost $20.

Tj Green said at October 7, 2008 9:02 AM:

I was tempted at $10,000 at $5,000 it is a bargain. This is a powerful diagnostic tool, and the cheaper it gets the more powerful it becomes.

Faruq Arshad said at October 7, 2008 2:23 PM:

Sorry to sound like a cheapskate,but it'll have to be about $500 before I consider it.

Brock said at October 7, 2008 5:19 PM:

Cathy, I don't think John Hawks is on the right track. He's proposing "the DRM strategy" for genotype companies. How's that working for the RIAA and the MPAA?

Sequencing is falling 10x per year. Digital storage costs are falling in price 5x per year. In 2011 when it costs $50 to sequence your genome and $5 to store the 750 GB of data with Google Health or whoever, DNA will go "open" in a big way. 23andMe is just the beginning, but no one will own your data. People won't put up with it. And any company that tries will have 1 year until their customers can go to an open competitor and get their DNA sequenced for $5.

Companies may want to set their offerings apart from the public domain, but it won't happen. The NIH and its European, Japanese, Indiana and Chinese counterparts (plus the world's University labs) will be pouring data into open systems faster than any one company could keep up. Anyone who tries to be closed will be left behind instantly (well, in months).

Randall Parker said at October 7, 2008 5:41 PM:

I agree with Brock. People aren't going to pay for a DNA sequencing without getting the raw data.

Also, I suspect that sequencing and analysis will be done by different companies. Medical labs produce results that you pay doctors to analyze. We'll take our sequences to various online analysis services that will produce different kinds of analyses for different purposes.

Also, John Hawks says all the information about genetic variations is in the public domain. But there's not that much info yet on what it all means. Once we get to knowing how many different genetic variations affect facial shape (for example) then people who just got a few IVF embryos genetically analyzed are going to want to pay experts to tell them what each embryo will look like and act like as an adult. The stakes will be too high to use only free services.

HellKaiserRyo said at October 7, 2008 9:37 PM:

I do not think facial shape selection will yield a higher return on investment than selecting for IQ. IQ can return more on social status (these gains will be negated if everyone does it), unless the child does not have an "appropriate" personality to lead others.

Allan said at October 8, 2008 11:53 AM:

My question is can genes be re-sequenced? (If that is even the right term ...) In other words, suppose I have my genes sequenced and discover that I'm carrier for Down's Syndrome ... Can I have that gene repaired? That's where the value comes in. If I can get mutant genes repaired for either my own health or so that I don't pass it on to my children, then I'd be very interested. Otherwise it's just interesting reading.

Brock said at October 8, 2008 12:10 PM:

Allan,

(1) The thing you're looking for are "Retroviruses" and "Reverse transcriptase." There is already work on this in mice and such.

(2) But even without that, if you find you have gene that will kill you if you take a certain blood pressure medication, that's useful information even if you can't get the gene fixed.

HellKaiserRyo said at October 8, 2008 6:03 PM:

One cannot be a carrier for Down syndrome since it is an aneuploidy.

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