Sunday, August 16, 2009

Gene machines

Ever wonder how automated genetic sequencing works?

The blog post linked to below gives a detailed description of the Illumina platform, complete with illustrations.

Genetic-Inference: ... Second gen sequencing has allowed us to re-sequence many human individuals; the 1000 Genomes Project is using 454, SOLiD and Illumina machines to sequence hundreds of individuals. This sort of thing has allowed us to get an idea, not just of what a single genome looks like, but how the genome changes from person to person; we can look at how much variation there is in the genome, how different populations differ in their genome structure, and even what makes a cancer genome different from a healthy genome.

However, second gen sequencing is not without its flaws. While it has got cheap ($40-50 to sequence a human genome these days) [typo? I think he means $40-50k], it still requires a lot of reagents, a lot of work and a lot of cost (the RT-bases aren’t cheap, and neither are the enzymes used). The low read lengths are still a problem, as they make knowing precisely where you got the bit of DNA from hard to discover (especially if you want to know which of two paired chromosomes it came from), and it takes a very long time to run the machines to completion. In the third part of this series, I will take about the new technologies that are appearing on the horizon; the so-called Third Generation Sequencing machines, which promise to make sequencing an entire human genome cost a couple of hundred pounds and take a few hours.

Last summer at Scifoo I met Jonathan Rothberg, founder of 454 Life Sciences, which makes one of the 2nd generation machines. 454 machines did James Watson's genome and also the neanderthal sequencing for Svante Paabo's group at MPI. We had a pretty interesting conversation, ranging from technology and venture capital to genetics and human biodiversity :-)

Back in 2005 I posted the figure below showing the super-exponential growth rate of sequencing capability. It looks like progress has continued at a similar rate since then.

Geeky scientists and engineers fueled by government grants and venture capital have once again delivered promethean gains to society :-) So much of progress, scientific and otherwise, is driven by the nature of available tools; see related post Prometheus in the basement.

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