May 01, 2006
Berkeley Group Puts DNA Sequencer On Chip

UC Berkeley chemistry professor Richard A. Mathies along with his Ph.D. candidates Robert G. Blazej and Palani Kumaresan have taken the standard Sanger process for DNA sequencing and shrunk a DNA sequencer down to a chip.

The upshot, Mathies says, is that the chips' small size and integration should reduce reagent and personnel costs to the point where it should be possible to sequence a complete genome for as little as $50,000. Mathies, whose team publishes its work online this week in Proceedings of the National Academy of Sciences, says UC Berkeley has licensed patents on the technology to Microchip Biotechnologies of Dublin, California.

They've combined all the steps on a chip.

The hand-held device is able to combine these three main sequencing steps – thermal cycling (to generate the different length DNA strands); sample purification; and capillary electrophoresis – into a single automated process. The size of the device means it requires a fraction of the expensive chemical reagents normally needed for DNA sequencing, greatly reducing the running costs.

Small means cheap. The smaller the cheaper.

Here's the abstract of the PNAS paper:

An efficient, nanoliter-scale microfabricated bioprocessor integrating all three Sanger sequencing steps, thermal cycling, sample purification, and capillary electrophoresis, has been developed and evaluated. Hybrid glass-polydimethylsiloxane (PDMS) wafer-scale construction is used to combine 250-nl reactors, affinity-capture purification chambers, high-performance capillary electrophoresis channels, and pneumatic valves and pumps onto a single microfabricated device. Lab-on-a-chip-level integration enables complete Sanger sequencing from only 1 fmol of DNA template. Up to 556 continuous bases were sequenced with 99% accuracy, demonstrating read lengths required for de novo sequencing of human and other complex genomes. The performance of this miniaturized DNA sequencer provides a benchmark for predicting the ultimate cost and efficiency limits of Sanger sequencing.

Here's the company which is commercializing the UC Berkeley work:

Microchip Biotechnologies Inc. (MBI) has been formed to commercialize leading-edge microfluidic and nanofluidic sample preparation technologies for the DNA sequencing, biodefense, and other life sciences applications. Founded in July 2003 by leaders in the field of life science instrumentation who helped create the genomics revolution and by leaders in microfluidics, MBI is developing breakthrough patent-pending nanofluidic technologies into products that meet the needs for high-quality nanoscale sample preparation.

Based in part on technologies exclusively optioned from the University of California at Berkeley, MBI is creating a product platform to produce a family of scaleable NanoBioProcessor™ products that perform sample preparation as a front-end for existing and future analytical instruments. The NanoBioProcessor™ will introduce mini-robotics with on-chip nanofluidic processing controlled by on-chip MOV™ valves and pumps. This novel technology to create arrays of valves and pumps has the potential to revolutionize fluidics and make complex devices manufacturable and affordable. MBI is also developing bead-based technologies to capture and purify biological materials before on-chip bioprocessing.

With so many academic and commercial research groups trying to drive down the cost of DNA sequencing by orders of magnitude and with so many demonstrating promising technologies the days of high priced DNA sequencing look to be short-lived.I'll be surprised of DNA squencing for a person costs more than $10,000 10 years from now.

Really cheap DNA sequencing will lead to massive comparisons of DNA sequence differences between people in combination with large numbers of details collected about each person. Medical histories, life histories, IQs, personality tests, and other measures of each person will get compared in combination with their DNA sequences in order to identify all the genetic variations that cause differences in who we are.

Share |      Randall Parker, 2006 May 01 10:06 PM  Biotech Advance Rates

Bob Badour said at May 3, 2006 6:37 PM:

What I found amusing was the fmol unit of measure. While anything starting with femto is really tiny, that's still 600 million strands of DNA.

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