The informatics of new sequencing technologies

Kevin Davies from Bio-IT World has two interviews up today relevant to new DNA sequencing technologies.

Firstly, there's an excellent interview with Clive Brown, vice president of development and informatics for Oxford Nanopore Technologies - one of the most promising contenders in the rapidly evolving third-generation DNA sequencing market. Brown is renowned for his plain-speaking approach (in the article he's described as "the most honest guy in all of next-gen sequencing", a quote originating from David Dooling), and that shows here in his blunt comments on the recent Helicos genome publication (covered here), the technical and marketing challenges faced by new seq tech companies, and the process of poaching employees from the Sanger Institute.

Secondly, Kevin Davies interviews David Dooling, who heads informatics at The Genome Center at Washington University at St Louis (and also writes an excellent blog, PolITiGenomics). Dooling explains why Wash U. chose to invest in the Illumina platform rather than SOLiD, advocates the use of open source software for large-scale genomics, and discusses the transition to third-generation technologies looming on the horizon.

Meanwhile, for those fortunate enough to have subscriptions, GenomeWeb has a dense crop of interesting articles just out including an intriguing investigation into the real costs of sequencing a human genome. The article notes a surprisingly wide range of cost estimates even for providers employing the same technology (Illumina), especially once frequently under-appreciated costs such as detailed downstream informatic analysis are factored in.

Thus, while Illumina is now offering genome sequences at a retail price of $48,000, Stephen Kingsmore, president and CEO of the National Center for Genome Resources, argues that the true cost of a very high-quality finished sequence is closer to $250,000. Kingsmore argues that a large chunk of this cost comes from the current need for intensive manual analysis of the resulting sequence, a cost that will decline precipitously as sequencing technology and informatics solutions improve. 

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Kevin Davies, you fiend!

Actually, it looks to me like a quote that Kevin meant to attribute to you but forgot; but you'll be pleased to see that I've amended my post above to give you full credit. :-)

Daniel, David,

Thanks for highlighting these interviews. We certainly didn't intend to 'steal' David's excellent characterization of Clive... I'd blame the omission on my copy editor, except I don't have one. Appropriate attribution has now been fixed.

Incidentally, the pieces on Oxford and The Genome Center at Wash U are just two of eight reports on next-gen informatics in our latest issue of Bio-IT World. Others focus on the Short Read Archive, PacBio's Kevin Corcoran and Scott Helgesen, Complete Genomics' Bruce Martin, CLC bio, and GenomeQuest.

http://www.bio-itworld.com/issues/2009/sep-oct/special-report.html

Thanks,
Kevin