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The MinION - Genome Sequencing in a Handheld Device

posted by janrinok on Thursday May 21 2015, @11:26PM   

[Editor's Comment: This article might sound a bit like a soyvertisement but it has been submitted by one of our community and someone who is well qualified in his field - David Eccles from the Malaghan Institute of Medical Research in New Zealand. It is interesting to read about what is considered currently to be state of the art in field genome sequencing.]

David Eccles (gringer) writes:

On the 14th and 15th of May, 2015, Oxford Nanopore Technologies held their inaugural nanopore sequencing conference, London Calling. The conference was set up to inform people about the current progress of Oxford Nanopore's first sequencing device, the muesli bar-sized, USB-powered MinION. Over 250 people were in attendance at the conference, representing 35 countries, including two from New Zealand: Nicole Moore from Environmental Science and Research, and David Eccles from the Malaghan Insititute of Medical Research. Over the course of two days, these attendees discovered how the MinION is quietly turning the world of sequencing inside out.

Everything needed for sample preparation and sequencing can fit into a single piece of checked luggage on an airplane. The MinION is robust enough to make it across unsealed roads to remote parts of Africa, where it has been used for sequencing on-location during the Ebola outbreak. The MinION has also been put through its paces for tracking the traffic of organisms. Detection at the species level can be achieved in under 20 minutes of sequencing, and very subtle changes for the same species from different origins can be identified in less than an hour.

Clive Brown, Chief Technical Officer for Oxford Nanopore Technologies, gave a brief summary of what is to come in the near future of nanopore sequencing:

• A fast mode for sequencing, allowing a human genome to be sequenced with high reliability in a 2-day run.
• An improved Mk II sequencer, with six time the throughput and six times the run time of the first sequencer.
• A clip-on sample preparation laboratory (Voltrax), allowing preparation and sequencing directly from blood in 20 minutes.
• Time-based pricing, reducing the minimum cost of a single-molecule sequencing run to $50.
• A 48-cell desktop sequencing device (PromethION) that can produce over 6 terabases of sequence per day, making sample preparation time the slowest part of the sequencing process.

• TGAC and Optalysys (Score: 3, Interesting) by takyon on Thursday May 21 2015, @11:56PM

  by takyon (881) <takyonNO@SPAMsoylentnews.org> on Thursday May 21 2015, @11:56PM (#186258) Journal

  http://www.theplatform.net/2015/03/25/a-light-approach-to-genomics-with-optical-processors/ [theplatform.net]

  These are all issues that TGAC considered during its massive sequencing effort to unravel the “simple” bread wheat genome. To do this and more human-focused genomic analyses, the center became home to one of the top systems in the world, utilizing a massive shared memory machine. TGAC has an SGI UV 2000 system with 2,500 “Sandy Bridge” Xeon cores and 20TB of shared memory—the latter a necessary feature to keep as much of the genome data in place for analysis versus moving to and from disk during sequence alignment. In essence, during this critical element of bioinformatics, the system seeks strings of DNA characters within a larger string (typically a genome) to find similar genes and thus determine common ancestry, for example. It’s like a complex, memory-intensive “spot the difference” puzzle, which means it can be useful to keep one entire genome (if possible) entirely in memory.

  But even with the performance and efficiency savings of a large shared memory machine, it’s still racking up major power and cooling costs. But what if it was possible for this type of processing to happen within a small desktop-sized machine that could plug into a standard main for power and process, on the spot, a human genome? If proven functional at scale, optical processors could displace standard clusters for gene sequencing in a far more power efficient way—there is little heat generated, especially compared to silicon technologies. And even more interesting, what if memory and the scalability limits therein were no longer a concern?

  These “what ifs” seem to present a rather tall order, but TGAC is working with Optalysys on a prototype processor that uses low-power lasers instead of standard electronics for processing. The goal is to do this genomics work using 95 percent less power than standard processing technologies.

  ∑☣ ≤ 🏃🏃🏃 👽

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