This document summarizes a presentation about announcements from Oxford Nanopore Technologies at the Advances in Genome Biology & Technology meeting. Oxford Nanopore unveiled two new sequencing devices - the desktop-sized GridION and the palm-sized MinION sequencer, which resembles a USB stick. Both devices use nanopore sequencing to directly sequence DNA or RNA in real-time without the need for sample preparation. This technology could potentially sequence an entire human genome in 15 minutes. Oxford Nanopore is aiming for increased sequencing accuracy and lower costs with these portable, easy-to-use sequencers.

1. Discussing the announcements from
Oxford Nanopore Technologies
Keith Bradnam, Feb 23rd, 2012
Some 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 from
GenomeWeb (http://genomeweb.com), from Nick Loman’s blog (http://
pathogenomics.bham.ac.uk/blog/), and from Oxford Nanopore’s website (http://
nanoporetech.com/).

2. AGBT meeting
Marco Island, Florida
Feb 15–18
Advances in Genome Biology & Technology meeting. Very popular for vendors of next-gen
sequencing equipment. Sold out very quickly this year.

3. ‘Wordle’ based on 3,386 tweets
Taken 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 after
the meeting.

4. The announcement by Oxford Nanopore made a lot of headlines (and not just in the scientific
media).

5. Why so much buzz?

6. That’s a genome sequencer that literally fits in the palm of your hand.

7. What is nanopore
sequencing?

8. 1998
The concept is not new. Patents go back at least as far as 1998.

9. 2001
Agilent made some news about nanopore technology in 2001.

10. Spun out from University of Oxford, 2005
The company itself has been around for almost 7 years.

11. Video
At this point we watched a video about nanopore sequencing from the Oxford Nanopore
website

12. Who are Oxford
Nanopore?

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. 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. 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. 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. GridION
GridION is the main technology announced by Oxford Nanopore. Each ‘node’ is about the
size of a DVD player and can be scaled up in rack-mounted storage.

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. 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. 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
cartridges
The $30,000 price was something I saw on a couple of websites, but I’m not sure how
accurate or reliable this is.

21. MinION
Dispatch your minions to do your MinION sequencing

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. 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 Low
Couldn’t find any specific information as to how long the GridION cartridges would last if run
24 hours a day. I only saw mention of ‘several days’

24. Applications

25. • Genome assembly (no more mate pairs!)
• Easy ‘exploratory’ sequencing
• Field-testing of samples (e.g. malaria)
• Classroom teaching tool

26. Caveats

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 — for
whatever reason — are less likely to ‘bump’ their way into a nanopore?

28. Final thoughts

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 removed
The USB stick aspect of this is why I think it has attracted so much media attention. But of
course, the underlying technology behind GridION and MinION has attracted a very
enthusiastic response by many scientists too.

30. This? or this?

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 envy
I have a 256 MB USB drive...which is incapable of sequencing — or storing — vertebrate
genomes.

32. Things to tell your grandchildren:
"and we used to work in large buildings
called sequencing centers"