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The Boys of Summer


By Kevin Davies

September 15, 2009 | First Base | CHI’s semi-annual Exploring Next-Generation Sequencing conference has been one of the highlights of a busy conference calendar, and the meeting in September in Providence—combined with a track on next-gen data analysis—won’t be any exception. With that in mind, this issue of Bio•IT World contains a 16-page special report on next-generation sequencing informatics.

It’s been an eventful summer of news in next-gen sequencing, highlighted by a steady stream of published human genome sequences. Over the past few months, we’ve seen not one but two Korean genomes published. The Genome Center at Washington University, St Louis, published the second leukemia genome in the New England Journal of Medicine, a feat unto itself but revealing some useful biological insights into the mutational basis of the disease.

In May 2007, Life Technologies’ Kevin McKernan graced the cover of Bio•IT World beside one of the SOLiD prototype instruments. Two years later, his team published its first human genome analysis, that of a Yoruban HapMap sample. While it would be nice to see a detailed comparison between this analysis and Illumina’s data on the same genome (published at the end of 2008), McKernan’s group is pushing on with SOLiD 4.0 and a bake-off isn’t on the cards.

Also this summer, Stephen Quake and two of his Stanford colleagues published details of his genome sequence—the first using single-molecule sequencing. Quake is the co-founder of Helicos Biosciences, and achieving its first human genome is a huge shot in the arm for the company, even if some commentators have grizzled at the misleading cost and number-of-author comparisons presented in the paper.

The financial markets perked up as well. Pacific Biosciences pulled in $68 million, while Complete Genomics found $45 million, which it says will help it sequence 10,000 human genomes next year. Those are still huge promises to keep, especially when the first goals fell short. 10,000 genomes is about 20 times more capacity than a leading genome center.

The increasing pace of published human genomes is a useful indicator of the progress in next-generation sequencing, but it is by no means the only one. I’m grateful to Oxford Nanopore’s chief informatician, Clive Brown, for drawing my attention to the stats maintained by the Wellcome Trust Sanger Institute (WTSI). This summer, WTSI surpassed 10 Terabases (Tb) of cumulative genome sequence data, and is generating an astonishing 400 Gigabases of sequence per week—that’s the equivalent of about seven human genomes, and double what it was last winter. The NCBI’s Sequence Read Archive is growing at 1 Tb a month.

Fall Forward
This Fall also promises to be a busy one for Bio•IT World.

In October, we host our first conference in Europe, in conjunction with BioTechnica 2009 in Hannover, Germany. (See pages 26-27 and at
 www.bio-itworldexpoeurope.com.) We’ll have highlights in the next issue of Bio•IT World.

We’re launching a series of live web symposia on a variety of topics ranging from data management for next-generation sequencing to cloud computing; remote data capture to trends in translational medicine. These will run from September through December every 1-2 weeks.

We’re introducing an exciting new e-newsletter that complements the stories you typically find here in Bio•IT World. Debuting in September, Pharma Services News, written and edited by John Russell, will examine the bio-IT and drug development world from the view of the services provider. From ‘omics and software-as-a-service to medicinal chemistry and clinical trials, there is virtually no part of the drug discovery pipeline that cannot be outsourced to a group that can do the work faster, cheaper, and better than pharma. We look forward to highlighting many of these organizations and their interactions with the pharma industry.

October also marks the launch of our Best Practices Awards for 2010. Following the success of this year’s competition, which attracted a record 72 entries, we have high hopes for next year. Beginning in October, academic and industry organizations can submit accounts of outstanding case studies and best practices in any facet of life sciences/drug discovery. We particularly encourage nominations from the vendor community, who can encourage their clients to take the time to submit. As always, winners will be judged by an expert panel, feted at a gala dinner at next year’s Bio-IT World Expo in Boston, and honored with detailed coverage in a subsequent issue of Bio•IT World.


This article also appeared in the September-October 2009 issue of Bio-IT World Magazine.
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