By Janet Fang
Posting in Food
As next-generation sequencers enter the clinic and into public health, researchers are asking for independent analyses to help sort through the marketing claims in this competitive industry.
Desktop sequencers promise to democratize genomics, but it’s difficult for researchers who aren’t experts in sequencing technology to sort through the overheated marketing claims made in this fiercely competitive industry. Nature News reports.
Three benchtop sequencing instruments are currently available. The 454 GS Junior (Roche), MiSeq (Illumina), and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Pictured here, in that order.
As next-generation genome sequencing heads into the clinic and public health, it’ll be targeted at people who don’t necessarily fully understand these issues.
Up until now, people looking for comparisons have had to depend on blog posts, which can be useful but hard to find, and on marketing information, which can be quite aggressive. (The Personal Genome Machine vs MiSeq videos played off the Mac vs PC ads.)
“People are crying out for independent analysis,” says study researcher Nicholas Loman at the University of Birmingham, UK.
A team including Loman, Mark Pallen from University of Birmingham, and John Wain from University of East Anglia decided to compare the 3 by using them to sequence the bacterium E. coli, which caused an outbreak of food poisoning in Germany last year.
And the winner? Well, each platform has strengths and weaknesses… and when it comes to genome sequencing, there’s no one-size-fits-all solution, the study finds.
- The MiSeq had the highest throughput per run and lowest error rates.
- The Ion Torrent PGM had the most throughput per hour.
- The 454 GS Junior generated the longest reads and most contiguous assemblies – but had the lowest throughput.
- And unlike the MiSeq, both the PGM and 454 have problems with accuracy concerning homopolymers, or stretches of repeating bases. Basically, that inhibits the ability to do good public health analyses of bacterial genomes.
The work was published in Nature Biotechnology this week.
And just last week, Technology Review reported that Roche backed off its hostile takeover bid for Illumina, after shareholders rebuffed Roche’s all-cash offers (which have grown to $6.8 billion). In 2007, Roche purchased next-generation sequencing company 454 Life Sciences. The big question is whether it and other large pharmaceutical companies will do better purchasing or partnering with instrument makers, as well as clinical sequencing service companies.
[Via Nature News]
Images: genome by DaveFayram via Flickr, sequencers from Nature News
Apr 24, 2012