Thoughts on the recent announcements by Oxford Nanopore Technologies

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Some notes I made for the weekly UC Davis 'Bits & Bites' sequence analysis discussion club.

This was a few days after the GridION and MinION technologies were announced at AGBT.

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Thoughts on the recent announcements by Oxford Nanopore Technologies

  1. 1. Discussing the announcements from Oxford Nanopore Technologies Keith Bradnam, Feb 23rd, 2012Some slides I presented to the UC Davis Bits & Bites sequence analysis discussion club(http://bitsandbites.posterous.com). Some of the information on these slides was taken fromGenomeWeb (http://genomeweb.com), from Nick Loman’s blog (http://pathogenomics.bham.ac.uk/blog/), and from Oxford Nanopore’s website (http://nanoporetech.com/).
  2. 2. AGBT meeting Marco Island, Florida Feb 15–18Advances in Genome Biology & Technology meeting. Very popular for vendors of next-gensequencing equipment. Sold out very quickly this year.
  3. 3. ‘Wordle’ based on 3,386 tweetsTaken from Nick Loman’s excellent blog: http://pathogenomics.bham.ac.uk/blog/2012/02/which-technology-won-agbt/Oxford Nanopore was getting a lot of attention on Twitter before, during, and especially afterthe meeting.
  4. 4. The announcement by Oxford Nanopore made a lot of headlines (and not just in the scientificmedia).
  5. 5. Why so much buzz?
  6. 6. That’s a genome sequencer that literally fits in the palm of your hand.
  7. 7. What is nanopore sequencing?
  8. 8. 1998The concept is not new. Patents go back at least as far as 1998.
  9. 9. 2001Agilent made some news about nanopore technology in 2001.
  10. 10. Spun out from University of Oxford, 2005The company itself has been around for almost 7 years.
  11. 11. VideoAt this point we watched a video about nanopore sequencing from the Oxford Nanoporewebsite
  12. 12. Who are Oxford Nanopore?
  13. 13. • Over 100 employees • Based in Oxford (UK), Cambridge (UK), New York, and Boston • Has raised $120 million in private & institutional funding • Illumina invested $18 million • No product available as of today!I.e. no product that you can purchase yet.
  14. 14. The technology• DNA read as ‘words’ as they pass through nanopore• No theoretical read length limit!• Can sequence directly from blood - no sample prep!• Real time sequencing results (wait time = milliseconds)• No fixed run time: sequencing can be paused & restarted• ‘Run until...’ mode• Can identify methylated & hydroxymethylated cytosine
  15. 15. The technology• Current accuracy = 96%, errors are mostly deletions• Quality does not change with respect to position in read• Each word gives specific signal, decoded with HMM • expect improvements through better training of HMM • some talk of 99% accuracy by launch • substitution errors are rare
  16. 16. The technology• Only ~0.001% of starting DNA is processed• DNA is not altered, you can recover it• Have produced 48 kbp reads from phage lambda• Can prep samples in different ways, pores just need to see dsDNA• Seems to work fine with RNA• Produces FASTQ format
  17. 17. GridIONGridION is the main technology announced by Oxford Nanopore. Each ‘node’ is about thesize of a DVD player and can be scaled up in rack-mounted storage.
  18. 18. GridION• 2000 nanopores per ‘node’ (8000 in 2013)• One or more nodes can be combined• Each node takes one single use disposable cartridge• Cartridge loaded with DNA or protein• Circuits in cartridge last a few days• Available 2nd half 2012
  19. 19. GridION• A 20 node (8,000 nanopores per node) GridION could deliver: • a human genome sequence in 15 minutes • at 50 fold coverage • or 3 Tbp per day (at 300 bp per second)
  20. 20. GridION • Cost: • $30,000 but... • Can pay full price for GridION and consumables, or... • Can get discounted GridION and sign a contract for consumables, or... • Pay full price GridION and get discount on cartridgesThe $30,000 price was something I saw on a couple of websites, but I’m not sure howaccurate or reliable this is.
  21. 21. MinIONDispatch your minions to do your MinION sequencing
  22. 22. MinION• 500 nanopores• Circuits burn out after ~6 hours• ~9 kbp per hour• But can go up to 150 Mbp per hour• Available 2nd half 2012, less than $900
  23. 23. MinION vs GridION GridION MinION 2012 2013 Nanopores 500 2000 8000 Max run time ~6 hours ‘several days’ Cost per Gbp $1000 $25-40 $20-30 Geek factor High LowCouldn’t find any specific information as to how long the GridION cartridges would last if run24 hours a day. I only saw mention of ‘several days’
  24. 24. Applications
  25. 25. • Genome assembly (no more mate pairs!)• Easy ‘exploratory’ sequencing• Field-testing of samples (e.g. malaria)• Classroom teaching tool
  26. 26. Caveats
  27. 27. • Show us the data! • How biased is the sequencing? • Will they achieved increased accuracy?By ‘biased’ I mean...if you were looking to sequence a genome, are there regions which — forwhatever reason — are less likely to ‘bump’ their way into a nanopore?
  28. 28. Final thoughts
  29. 29. Why so much attention? 1. It’s a genome sequencer in a USB stick! 2. In a USB stick!!! 3. Nerds love gadgets 4. The barrier to easy genome sequencing may have just been lowered removedThe USB stick aspect of this is why I think it has attracted so much media attention. But ofcourse, the underlying technology behind GridION and MinION has attracted a veryenthusiastic response by many scientists too.
  30. 30. This? or this?
  31. 31. Other issues • Your PI can now expect you to take your (genome sequencing) work home • Like we needed another way to easily generate terabases of sequence data! • USB stick envyI have a 256 MB USB drive...which is incapable of sequencing — or storing — vertebrategenomes.
  32. 32. Things to tell your grandchildren:"and we used to work in large buildings called sequencing centers"

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