August 10, 2009
Stephen Quake Sequences His Genome For $50k

Stanford microfluidics researcher Stephen Quake used a new DNA sequencing machine from Helicos Biosciences (a company he co-founded) to sequence his own genome in a week to 95% completeness for only $50,000.

The first few times that scientists mapped out all the DNA in a human being in 2001, each effort cost hundreds of millions of dollars and involved more than 250 people. Even last year, when the lowest reported cost was $250,000, genome sequencing still required almost 200 people. In a paper published online Aug. 9 by Nature Biotechnology, a Stanford University professor reports sequencing his entire genome for less than $50,000 and with a team of just two other people.

In other words, a task that used to cost as much as a Boeing 747 airplane and required a team of people that would fill half the plane, now costs as much as a mid-priced luxury sedan and the personnel would fill only half of that car.

“This is the first demonstration that you don’t need a genome center to sequence a human genome,” said Stephen Quake, PhD, professor of bioengineering. “It’s really democratizing the fruits of the genome revolution and saying that anybody can play in this game.”

What we see here is a rate of cost decline that is much faster than the rate at which computing power drops in cost. The cause is very similar: use smaller and smaller devices to manipulate matter on a smaller scale. Small is cheap. This trend makes me optimistic that the rate of advance of development of rejuvenation therapies is accelerating. More powerful and cheaper tools should give us better treatments faster.

Quake discovered he has a rare gene that causes heart problems. But he also has genes that make him respond well to statins. Not clear if those genes predict how much his cholesterol will drop on statins or whether he'll have side effects from taking statins. Given that statins sometimes cause damaging side effects on muscle and also on memory the ability to get yourself genetically checked to predict drug side effects will be one of the earliest uses of widespread gene sequencing.

Quake also has a gene associated with disagreeableness. I wonder whether this gene makes smart driven people more creative and productive by making them less accepting of the status quo.

The sequencing machine detected both single letter differences (single nucleotide polymorphisms) and larger copy number variations where sections of the genome are repeated.

The study, conducted by Dmitry Pushkarev, Norma Neff and Stephen Quake was carried out using less than four runs of a single HeliScope™ Single Molecule Sequencer, and achieved 28X average coverage of the human genome. The sequencing allowed the detection of over 2.8 million single nucleotide polymorphisms (SNPs), of which over 370,000 were novel. Validation with a genotyping array demonstrated 99.8% concordance. The unbiased nature of the single-molecule sequencing approach also allowed the detection of 752 copy number variations (CNVs) in this genome.

Note the point about how many were novel. We have lots of SNPs still to discover.

Once this technology enters into wide use a flood of genetic data will be produced. We then need to do a massive compare of people for their genetic differences, health differences, personalities, intelligence, preferences, appearances, and other qualities to try to pin down which genetic variations matter and how.

Share |      Randall Parker, 2009 August 10 08:40 PM  Biotech Advance Rates


Comments
Lono said at August 11, 2009 8:46 AM:

Excellent! - This is great great news!

Getting closer...

(Now we just need to perfect human cloning and artificial wombs and I can create my army of hyper-intelligent super-loyalists!)

:-)


bbartlog said at August 11, 2009 9:10 AM:

*less* than $50K, even. But after seeing the general description of the process I'd love to see the cost breakdown. It sounded like some of the major components were
- days of labwork by highly trained academics
- time on an expensive machine
- a boatload of computing power to reassemble the sequence(s)
- (possibly) supplies of expensive reagents

All of these except maybe the last should be reducible. Train lab techs to do some of the steps instead of professors. Make more machines so the unit cost comes down. Let computers keep getting cheaper :-).

Engineer-Poet said at August 13, 2009 12:24 PM:
Quake also has a gene associated with disagreeableness. I wonder whether this gene makes smart driven people more creative and productive by making them less accepting of the status quo.
"The reasonable man adapts himself to the world; the unreasonable man persists in trying to adapt the world to himself. Therefore all progress depends on the unreasonable man." -- George Bernard Shaw

The lack of an innate trend towards progress in the most conformist societies may show the value of disagreeableness.

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