Genetic Future

I’ve just discovered a very promising new blog in the genomics sphere (well, technically it’s a newly relaunched blog) run by a group at the University of Birmingham.

Two posts by Nick Loman are of immediate interest to readers here. Firstly, I highly recommend Nick’s thorough dissection of accusations made by Applied Biosystems’ Kevin McKernan in a recent submission to a UK House of Lords enquiry, which include the claim that the Sanger Institute‘s adoption of technology from AB competitor Illumina were driven by bias. Here’s a key paragraph, but if you’re interested in the competition in the next-gen sequencing space you should read it all:
Our reading of the situation was that Illumina have been successful because they were early to market, offered the best throughput and had a relatively simple sample preparation and data analysis pipeline. Solexa has a reputation for its decent sample preparation workflow due to its “walk away” Cluster Station machine. Solexa also produces easy to manipulate FASTQ read files which are read by all the short read mappers without the additional informatics distraction of SoLiD’s “colourspace”. Solexa has also found a way to scale rapidly from 1 gigbase per run and 36-base reads with its Genetic Analyzer 1. Now they are now routinely able to produce over 10 gigabases (and climbing) with 75-base reads and paired-ends to make analysis easier. 454 has also found a highly successful niche, particularly in bacterial applications and metagenomics, due to its longer reads, short run time and user-friendly software. SoLiD’s advantages were harder to define, sometimes characterised as “the worst of both worlds”, with a laborious sample preparation workflow, long running time, short reads and an unfamiliar output format.

Secondly, Nick has tabulated the data from James Hadfield’s handy Google map of next-generation sequencing facilities, to provide a list of the institutes in the UK working with new sequencing technologies and the number of machines owned by each facility. It’s clear from the list that Illumina’s dominance over AB’s SOLiD technology is not restricted to the Sanger Institute: even outside the Sanger, there are 12 Illumina machines compared to 3 SOLiD instruments.

Comments

  1. #1 Nick Loman
    August 12, 2009

    Hi Daniel, thanks for the link and for the warm welcome to the blogosphere! I guess the pressure is on now to keep the blog regularly updated with interesting tidbits!

  2. #2 Daniel MacArthur
    August 12, 2009

    Hey Nick,

    No problems! Yes, be warned – the warm welcome only extends for as long as your posts remain consistently interesting, after which the blogosphere will turn on you like a pack of rabid animals. So keep up the good work, or else!

  3. #3 JohnV
    August 12, 2009

    Don’t mind the rest of us sharpening our pitch forks and passing out the torches.

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