Keith Bradnam, Feb 23rd, 2012

Discussing the announcements fromOxford Nanopore Technologies

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/).

AGBT meetingMarco 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.

‘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.

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

Why so much buzz?

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

What is nanopore sequencing?

1998

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

2001

Agilent made some news about nanopore technology in 2001.

Spun out from University of Oxford, 2005

The company itself has been around for almost 7 years.

Video

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

Who are Oxford Nanopore?

• 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.

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

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

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

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.

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

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)

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.

MinION

Dispatch your minions to do your MinION sequencing

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

MinION vs GridION

MinIONGridIONGridION

MinION2012 2013

Nanopores 500 2000 8000

Max run time ~6 hours ‘several days’‘several days’

Cost per Gbp $1000 $25-40 $20-30

Geek factor High LowLow

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’

Applications

• Genome assembly (no more mate pairs!)

• Easy ‘exploratory’ sequencing

• Field-testing of samples (e.g. malaria)

• Classroom teaching tool

Caveats

• 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?

Final thoughts

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.

This? or this?

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.

Things to tell your grandchildren:

"and we used to work in large buildings called sequencing centers"