Download DNA sequencing: a generation game - Dr John Milton

DNA sequencing: a generation game
Dr John Milton
VP Research,
Oxford Nanopore Technologies
Today
The DNA sequencing explosion
How applications have evolved
How users have evolved
Today’s technologies
Tomorrow’s technologies
© 2009 Oxford Nanopore Technologies Ltd
CONFIDENTIAL
From discovery to technology explosion
1868: Discovery of DNA
1953: Watson and Crick propose double helix structure
1977: Sanger sequencing
1985: PCR
2000: Working draft human genome announced (Sanger
method)
$ human
Genome
2005: 454 sequencer launch
(pyrosequencing)
2006: Genome Analyzer launched (Solexa sequencing)
2007: SOLiD launched
(ligation sequencing)
2009: Whole human genome no longer merits Nature/Science
paper
2010: “third-gen” systems on the horizon
$2-3 million
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$3 billion
$250k
$50k
$20k
?<$5k?
Volume of DNA data: the early years
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Sequence data output
UK’s Sanger Centre, 2007-today
Sept
2007
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Sept
2008
Sept
2009
CONFIDENTIAL
March
2010
© Macmillan: Nature 1st April 2010
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‘next gen’ systems today (UK)
Source: http://pathogenomics.bham.ac.uk/hts/
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‘next gen’ systems today (US)
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Turning DNA data into knowledge
Tomato Wheat
Human Microbiome Project
Neanderthal
Chimpanzee
Chicken
Corn
Bovine
Panda
Malaria parasite
Arabidopsis
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Anthrax
Which applications are labs performing?
Source: GenomeWeb Survey 2010
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The rise of epigenetics
Genome
“what may happen”
Epigenetics
“how ‘what may happen’ may vary”
3rd dimension of the genome
Gene expression / protein analysis
“what actually happened”
In this cell, at this time
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Technologies
CONFIDENTIAL
Implications of advancing technology
Expansion in computing required to capture all
variation and interpret its meaning
 democratisation of DNA information
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CONFIDENTIAL
DNA sequencing generations
Then + Now
1st Gen
Sanger
•Low
throughput
•High cost
•Accurate
•Broad user
base
Sanger
Now
2nd Gen
-parallised
•Optical
•Amplification needed
•Highly parallel
•Improved cost and
Throughput
•More centralised
users
GAII (Solexa/Illumina)
SOLiD (Agencourt/LIFE)
FLX (454/Roche)
Now + anticipated
2nd Gen
-single mol or electronic
•Optical
•Single-molecule
•Highly parallel
•Cost similar
•New applications
•Or electronic,
clonal
Helicos
Pacific Biosciences
Ion Torrent
(LIFE Starlight)
Anticipated
Next
-single mol AND electronic
•Direct electrical (no optics)
•Single-molecule, highly parallel
•Transformation of workflow
•Designed to broaden user base,
deliver step change in cost, power
•New applications
Nanopores
Estimated cost of a human genome using these technologies
$70M
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$200k --- $50k ---- $20k --- 15k---
14
?$5k - $?
Sanger Sequencing (CE)
3730: “workhorse of the HGP”
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CONFIDENTIAL
Illumina GA (‘Solexa sequencing’)
sequencing by synthesis
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SOLiD: sequencing by ligation
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454: pyrosequencing
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Helicos: Heliscope
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Coming soon
Ion Torrent
$50k
Clonal
Short run time
Errors? Yield?
Pacific Biosciences
$750k
Single molecule
Long read lengths
Errors? Yield?
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CONFIDENTIAL
What is a nanopore?
Nanopore = ‘very small hole’
Electrical current flows through the hole
Introduce analyte of interest into the hole  identify “analyte” by
the disruption or block to the electrical current
Current
flow
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21
Engineering nature’s nanopores
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Nucleotide Recognition
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23
Movie can be found at: http://www.nanoporetech.com/sequences
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24
Application
Specific
Platform Technology
Adaptable protein nanopore:
DNA Sequencing
Proteins
Polymers
Small Molecules
Generic Platform
Sensor array chip: many nanopores in parallel
Electronic read-out system
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Ultimately: will we sequence every person?
Every cancer:
Accurate diagnosis and
targeted treatment?
Every baby:
Lifetime ‘baseline’ resource,
disease prevention?
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Every infectious agent:
Control of disease
spread and resistance
Ultimately: will we sequence every species?
http://seedmagazine.com/interactive/genome/
1995
2005
2002
2000
2002
© 2009 Oxford Nanopore Technologies Ltd
2009
Thank you
questions?