Cancer Genomics

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Cancer Genomics
Chin-Yo Lin MMBIO Cancer Research Workshop June
13, 2007
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genomics
molecular biology
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PhD Thesis Research Functional analysis of the
conserved carboxyl-terminal domain of the mitotic
polo-like kinase Plk
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High-throughput
Robotics and Automation
Comprehensive
Informatics
Highly Parallel
Miniaturization
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Robotics and Computational Power, circa 1970
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Robotics and Computational Power, 2002
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Genome
Transcriptome
Proteome
The Central Dogma of Biology
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I. Technological advances and new experimental
paradigms
96 Capillary Sequencer
Sequencing Gel
1,000-1,500 bases/day
1,000,000 bases/day
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454 Sequencer
Solexa Sequencer
20-40,000,000 bases/day
1G bases/run
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Western Blot (1 protein)
11.5-Tesla Fourier transform ion cyclotron
resonance mass spectrometer (thousands of
proteins).
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• The genomic era of biomedical research

The Pre-genomic Era
Disease Locus Disease Genes
Cause
Genotype
Environmental Factors
Clinical Presentation Imaging Histological
Analysis Biochemical Assays Microbial Assays
Phenotype
Disease
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• The genomic era of biomedical research

The Genomic Era
Genome-wide Variatons
Cause
Genotype
Environmental Factors
Microbial genomes Pathogen-host interactions
-Omic Descriptions (Mechanistic)
Phenotype
Disease
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Genome
Transcriptome
Proteome
SNPs CGH Methylation Regulatory Elements
Expression Profiles RNAi
Marker Discovery Interactions Post-translational
Modifications
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8000 gene cDNA arrays
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25,000 gene cDNA arrays
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ERb-regulated Genes are Enriched for Those which
Function in DNA Replication and Cell Cycle
Regulation
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Expression Profiles of the ERb-regulated
Expression Cassette
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Expression of ERb and Regulated Genes in Patient
Samples
Expression profiles determined on Affymetrix
U133A/B Arrays
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Association of the ERb-regulated Expression
Cassette with ERb Expression in 69 ER Breast
Tumors
in vivo
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Validation of the ERb-regulated Expression
Cassette Genes in T-47D cells by real-time qPCR
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Expression Profiles of ERb and the Expression
Cassette Cluster Tumor Samples into Good and
Poor Disease Outcome Groups
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Expression Cassette Predicts Disease Outcome in
an Independent Cohort of 45 Patients Described
by Sotiriou et al.
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The rest of the iceberg
Classification Marker and Target Discovery
Integration of Approaches and Information
Genomics Transcriptomic Proteomics Population
Studies Phenogenomics Comparative
Genomics Pharmacogenomics Chemical
Genomics Structural Genomics
Personalized Medicine
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If we knew everything about you and your
disease
Personalized Medicine Risk/Susceptibility Prognosi
s Tailored Treatment
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PacBio Plans to Sell First DNA Sequencers in
2010 Aims for 100 Gigabases Per Hour By Julia
Karow Editor, In Sequence MARCO ISLAND, FL
(GenomeWeb News) Pacific Biosciences said at a
meeting last week that it is working on a
next-generation DNA sequencing instrument that it
believes will eventually be able to produce 100
gigabases of sequence data per hour, or a diploid
human genome at 1-fold coverage in about 4
minutes. Sometime in 2010, the Menlo Park,
Calif.-based company plans to sell its first DNA
sequencing systems, performance specifics of
which have yet to be determined, to early
adoptors, PacBio Chairman and CEO Hugh Martin
told GenomeWeb Daily News sister publication In
Sequence last week. The price of the instrument
will likely be in the range of that of next-gen
sequencers sold by 454/Roche, Illumina, and
Applied Biosystems, he said, which sell for
approximately 400,000 to 600,000. Speaking in
a packed auditorium at the end of the Advances in
Genome Biology and Technology meeting in Marco
Island, Fla., on Saturday, PacBio's Co-founder
and Chief Technology Officer Stephen Turner said
that after achieving a set of milestones in
November, the company decided to start developing
the system commercially, and talking about its
progress. Since it was founded in 2004 as
Nanofluidics, the company has not talked about
its plans or technology in public. The company's
single-molecule, real-time, or SMRT, technology
is based on zero mode waveguides that were
originally developed by Turner and others at
Cornell University's Nanobiotechnology Center.
Essentially, ZMVs are nanometer-scale holes in a
100-nanometer metal film deposited on a clear
substrate. Due to the behavior of light aimed at
such a small chamber, the observation volume is
only 20 zeptoliters, enabling researchers to
measure the fluorescence of nucleotides
incorporated by a single DNA polymerase enzyme
into a growing DNA strand in real time. On a
prototype system, PacBio researchers have so far
observed read lengths of a little over 1,500
bases and a rate of 10 bases per second, and have
been able to analyze up to 3,000 zero mode
waveguides in parallel. Since its founding, the
company has raised approximately 71.5 million in
venture capital from Kleiner Perkins Caufield
Byers, Mohr Davidow Ventures, Alloy Ventures,
Maverick Capital, and others, and has received
6.6 million in funding from the National Human
Genome Research Institute. Over the next year,
PacBio plans to raise an additional 80 million
and is in the midst of growing its headcount from
just over 100 to 200 employees "as fast as we can
do it," according to Martin.
100 gigabases per hour
single-molecule approach
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SALT LAKE CITY (GenomeWeb News) Next-generation
sequencing firm VisiGen Biotechnologies plans to
offer a service based on its real-time
single-molecule sequencing technology by the end
of next year, CEO Susan Hardin said
today. Speaking at the Association for
Biomolecular Research Facilities conference here,
Hardin said that the company plans to launch a
service based around its "nano-sequencing
machine" technology by the end of 2009, and to
follow that with the launch of equipment and
reagents in another 18 months to two
years. Hardin said that the technology, which
uses engineered DNA polymerase that acts as a
"real-time sensor" for modified nucleotides,
could enable researchers to sequence an entire
human genome in less than a day for under
1,000. The company is currently working on its
first version of the instrument, which can
generate around 4 gigabases of data per day. At
that throughput, she said the technology could
sequence 44 human genomes per year at 10-fold
coverage for around 1,000 per genome. The
single-molecule approach requires no
amplification, which eliminates a great deal of
the cost relative to current sequencing
technologies, she said. In addition, read
lengths for the instrument are expected to be
around one kilobase, which is longer than any
current next-gen sequencing platform. For
example, the GS FLX system from Roche's 454 Life
Sciences subsidiary generates reads of around 250
base pairs, and the company expects to extend
that to 400 bases in the next version of its
platform. Illumina's Genome Analyzer and Applied
Biosystems' SOLiD sequencers both have reads of
around 30 base pairs. ABI's 3730 capillary
electrophoresis system, by comparison, produces
reads on the order of 700 to 800 base
pairs. VisiGen is not the only next-generation
sequencing firm looking to market a system with
long read lengths, however. Last week, Pacific
Biosciences said that it is currently seeing read
lengths of around 1,500 bases for its system,
which it plans to launch in 2010. The company
claims that its technology will be able to
generate 100 gigagbases of sequence per
hour. Hardin said that with improvements in the
hardware, reagents, and software for the VisiGen
system, its current throughput of one megabase
per second could increase to 50 megabases per
second. VisiGen's technology exploits
polymerase's natural biological role in
synthesizing DNA. The company labels the enzyme
with a donor fluorophore and attaches acceptor
fluorophores to nucleotides so that whenever one
of these nucleotides enters the active site of
the polymerase, energy is transferred from donor
to acceptor. In this process, called fluorescence
resonance energy transfer, the acceptor gives off
light of a particular wavelength that the
instrument uses to identify the base. Hardin
said that the acceptor fluorophore is removed
during nucleotide incorporation, which ensures
that the DNA that results has no modifications
that might slow down the polymerase. Currently,
she said, the company is working on refining its
chemistry and detection technologies. In
particular, she said, the team is working on
slowing down the nucleotide incorporation step in
order to detect a stronger fluorescence
signal. Hardin noted that the company also was
awarded its first US Patent today, No. 7,329,492,
"Methods for real-time single molecule sequence
determination." Hardin founded VisiGen in 2000.
The company has received undisclosed investments
from Applied Biosystems and SeqWright, and also
is supported by grants from the Defense Advanced
Research Projects Agency, the National Human
Genome Research Institute, and the National
Institute of General Medical Sciences. In 2006,
VisiGen entered the Archon X Prize for Genomics
competition, which is promising 10 million to
the first team to sequence 100 human genomes in
10 days for no more than 10,000 per genome.
sequence an entire human genome in less than a
day for under 1,000
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Where is the wisdom we have lost in
knowledge? Where is the knowledge we have lost in
information? T.S. Elliot