Wednesday, April 29, 2009

Clifford Reid on Personalized Genomics


Clifford Reid, CEO of Complete Genomics

Kevin Davies opened up the second full day at Bio-IT World 2009 with thanks for the audience for solid participation in tough economic times - attendance at the conference is up compared to last year, which will help the group in their efforts to kick off Bio-IT World Europe in October.
Complete Genomics is "the Netflix of Next-Gen."
- Kevin Davies
Kevin then introduced Clifford Reid for the day's keynote, titled Personalized Genomics - The Impact of Large-Scale Human Sequencing Projects, who began his talk with a review of the costs of sequencing, which started out dropping by 2x per year until 2007, when it began dropping by 10x per year. This drop is the result of the confluence of three technologies:
  • Bio - Oligos (synthetic DNA), enzymes, flourescent molecules, DNA amplification
  • Nano - Photolithography, nano-robotics, CCD optical systems, ZMWs, nanopores
  • Info - Moore's Law (HPC), digital image processing, informatic insight: short paired ends (need to be able to make long reads)
Complete Genomics' approach includes manipulating the DNA to make it easily readable - they start with 500 bases, circularize it, then insert adaptors. These are combined into DNA nano-balls in a test tube, which are then dumped out onto a slide where they self-assemble into a square grid. The grid can be aligned with the imaging CCD pixels, so no pixels are wasted. The slide can hold an entire human genome, and will in the near future be read in a half day.

Sequencing a slide currently costs $5000, with the reagent costs at $1000. The chemical component of sequencing used to be the major cost; now that cost is down to hundreds of dollars per slide, and the costs of imaging and compute are the major factors. As this progresses, the data sets will get huge - 60 TB of images and 1 TB of processed data, requiring thousands of CPUs to process.

Complete Genomics is working in a new vendor model, as an information service provider, not an instrument vendor. They are focusing on scaling through continuous manufacturing technology, they are half a sequencing company and half a computing company, and they rely on two key distribution technologies: FedEx for atoms, and the Internet for bits. This is driving a new user model, the instrument-less genome research center, which are analogous to the fab-less semiconductor firms.

CG's five year mission is to build ~10 genome centers around the world and sequence 1 million human genomes.

The impact of this revolution will mean that academia can tackle large human populations and orphan diseases that aren't otherwise commercially interesting. BioPharma will see a reduction in costs and will attack cancer head-on. Agriculture and energy fields will see an explosion of new, economically viable genomic studies on plants and microbes. Personalized genomics, already in the early stages of use, will continue to grow rapidly.

The field of genetics research is moving from instrument-centric efforts, to a data-centric focus for the next five years, and eventually to a post-discovery action-centric world.

Cliff then noted that major leaps in science comes with advancement in measuring tools that allow new hypotheses to be tested. He took the room back some 400+ years to the invention of light microscopy, which overhauled our view of the world, but noted that it didn't do much for medical progress until the improvements in the 1870s that enabled a view into the cell. The cause of tuberculosis was subsequently identified, and there was more medical progress in 3 years than there had been in the previous 300 years. High-throughput, low cost sequencing will enable large-scale complete human genome studies - the next five years will see the investigation of the genome with a high-resolution gene microscope, and it will do for cancer what the light microscope did for tuberculosis.

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