Enabling Genomics Research:
How do Platform Technologies Fit with
Next Generation Applications?
Jonathan Witonsky, Industry Manager
Drug Discovery Technologies
and Clinical Diagnostics
October 29, 2008

Focus Points
Background: Genomics Technologies and Applications
e.g. Gene Expression Analysis Applications
Markets: Growth Driven by Established and Emerging Trends
e.g. Nucleic Acid Purification and Isolation Markets
Supply-side Analysis: Product Positioning and Marketing
e.g. Next Generation Sequencing Technology
Demand-side Analysis: Usage of Genomics Technologies
e.g. Correspondence between Technologies and Applications
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Background
Genomics Technologies and Applications
3

Background
DNA Sequencing
Nucleic Acid Isolation qRT-PCR
Technology
PCR DNA Microarray
Technologies
Reagents Consumables
Instrumentation Software
Applications
Gene Expression Epigenetics
Sequencing Genotyping Cytogenetics
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Background (contd…)
Timeline of High-growth Periods for Genomics Applications
epigenetics / molecular cytogenetics (microarray)
genotyping
gene expression analysis
de novo DNA sequencing /
resequencing for SNP discovery
1998 2000 2002 2004 2006 2008 2010 2012 2014
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Background (contd…)
e.g. Gene Expression Analysis
Typical platform technology: Typical platform technology:
Real-time PCR Standard DNA Microarray
Gene Expression Analysis
Low density (moderate market growth) Sweet Spot for
Novel Platform
Medium density (high market growth)
Technologies
High density (moderate market growth)
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Markets
Growth Driven by Established and Emerging Trends
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Markets
2012
Customer Priorities
1. Regulated in vitro
diagnostics
2007
2. Multiple
commercialized
Customer Priorities applications
1. Validation 3. Research
research workflows involve
2002
2. Clinical approval multiple genomics
technologies
3. Forensics and
Customer Priorities 4. Ultra-high
infectious disease
1. Proof-of-principle testing throughput
technologies
2. Basic research and
discovery
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Markets (contd…)
e.g. Nucleic Acid Purification and Isolation
Percent of Revenues by Nucleic Acid Type (U.S.), 2007
Plasmid DNA Fragment DNA
27.1% 15.4%
0% 5 – 7%
Growth Growth
12 – 14% 16 – 18%
Growth Growth
RNA
29.7%
Genomic DNA
27.8% Note: All figures are rounded; the base year is 2007. Source: Frost & Sullivan
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Supply-side Analysis
Product Positioning and Marketing
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Supply-side Analysis
Product Positioning #1 Product Positioning #3
Nucleic Acid
Gene SNP
qPCR qPCR Expression Genotyping
Detection/
Quantitation
Epigenetics
Gene SNP (DNA Cytogenetics
DNA Microarray Expression Genotyping Methylation, (CNP/CGH) DNA Microarray
ChIP-chip)
SNP Discovery Nucleic Acid
de novo SNP
CE Sequencing CE Sequencing Sequencing
and
Genotyping
Detection/
Resequencing Quantitation
Epigenetics Epigenetics
Next Generation de novo
SNP Discovery
(DNA Cytogenetics Next Generation de novo
SNP Discovery
(DNA Cytogenetics
and and
Sequencing Sequencing
Resequencing
Methylation, (CNP/CGH) Sequencing Sequencing
Resequencing
Methylation, (CNP/CGH)
ChIP-chip) ChIP-chip)
Product Positioning #2 Product Positioning #4
Nucleic Acid Nucleic Acid
Gene SNP Gene SNP
qPCR Detection/ qPCR Detection/
Expression Genotyping Expression Genotyping
Quantitation Quantitation
Epigenetics Epigenetics
SNP Discovery SNP Discovery
Gene SNP (DNA Cytogenetics Gene SNP (DNA Cytogenetics
DNA Microarray Expression Genotyping Methylation, (CNP/CGH)
and DNA Microarray Expression Genotyping Methylation, (CNP/CGH)
and
Resequencing Resequencing
ChIP-chip) ChIP-chip)
CE Sequencing CE Sequencing
Epigenetics
Next Generation Next Generation de novo
SNP Discovery
(DNA Cytogenetics
and
Sequencing Sequencing Sequencing
Resequencing
Methylation, (CNP/CGH)
ChIP-chip)
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Supply-side Analysis (contd…)
e.g. Next Generation Sequencing Technology
Genome Sequencer Genome Analyzer SOLiD™
FLX System System Analyzer
(Roche Applied Science) (Illumina, Inc.) (Applied Biosystems)
• Ancient DNA • De novo Sequencing • Targeted Resequencing
• ChIP-seq/Methylation/ • Whole-Genome Resequencing • Gene Expression
Epigenetics • Discovery of Somatic Genomic • MicroRNA Discovery
• Eukaryote Whole Genome Variation • Whole Genome Sequencing
• Expression Tags • Metagenomics
• HIV Sequencing • Epigenomics
• Metagenomics & Microbial • Targeted Sequencing
Diversity • Whole-Transcriptome Profiling
• Mitochondria/ Viruses/ Plastids/ • Protein-DNA or Protein-RNA
Plasmids Interactions
• Prokaryote Whole Genome
• Sequence Capture Targeted
Region
• Small RNA
• Somatic Variation Detection
• Transcriptome Sequencing
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Demand-side Analysis
Usage of Genomics Technologies
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Demand-side Analysis
Research Focus Area
Research Group 5
tends to be a Research
category in itself that Group 1 focus
Group 4 can
can, however, be can be pursued
be pursued
pursued in parallel in parallel with
Research Group 3 tends to be separately or
with other research all the other
pursued with Group 2. together with
areas of focus. areas.
Group 2.
Research Group 3 Research Group 2 Research Group 4 Research Group 5 Research Group 1
• Developmental • Cardiovascular • Infectious Disease/ • Cancer Research / • Gene Expression /
Biology • Metabolic Microbial detection Oncology Regulation
• Stem cells/ develop- • Pre-clinical studies & ID • Drug Discovery / • Gene Function
mental biology • Immunology Target Identification • Protein Expression
• Service provider /
-central core facility Research groups 4 and 6 tend
Research Group 6 to not go together.
• Evolutionary Biology (negatively correlated)
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Demand-side Analysis (contd…)
Applications
Research Group 3
tends to be a
category in itself that
Group 4 can be can, however, be
pursued pursued in parallel
Application
separately or in with other
Group 6 focus
parallel with the applications.
Group 2 can be can be pursued
Research Group 5 tends to pursued separately other groups in
in parallel with
be pursued with Group 1. or together with the other sub-
all the other
Group 1. branch.
applications.
Application Application Application Application Application Application
Group 5 Group 1 Group 2 Group 4 Group 3 Group 6
• Whole genome • SNP Discovery / • Histone • Clone • Ribosomal • Focused gene
gene expression Resequencing modification identification sequencing expression
profiling • Other mutation profiling / ChIP- and verification • Drug metabolism profiling
• Whole genome screening chip • CDNA pharmacogenic • Novel or rare
genotyping • Copy number • Regulatory sequencing profiling transcript
studies variation / loss of protein factor • De novo • SAGE profiling / expression
heterozygosity binding studies sequencing digital gene profiling
studies • DNA Methylation expression
• Microsatellite State Profiling profiling
(STR) analysis • Small RNA/micro • Splice variant
• Candidate gene RNA expression expression
genotyping profiling profiling
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Demand-side Analysis (contd…)
Technologies
Technology Group 2
tends to be a Technology
Group 1 can category in itself that Groups 5 and 6
be adopted can, however, be can be pursued
separately or adopted in parallel in parallel with
Technology Group 4 tends
together with with other all the other
to be adopted with Group 3.
Group 3. technologies. areas.
Technology Technology Technology Technology Technology Technology
Group 4 Group 3 Group 1 Group 2 Group 6 Group 5
• Multiplex Assay • Next generation • PCR/ Thermal • RNA • Gel Based • Microarray
sequencing Cycling interference (Northern/ • Robotics /
• Capillary • DNA/RNA (RNAi/siRNA) Southern / Automated
electrophoresis isolation & • Transfection Western) liquid handling
sequencing purification
• Single molecule technologies
detection • qPCR/RT-PCR
platforms
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Demand-side Analysis (contd…)
e.g. Drivers of Adoption: Next generation sequencing
Application Group 1
• SNP Discovery / Resequencing
• Other mutation screening
• Copy number variation / loss of
heterozygosity studies 1.27
• Microsatellite (STR) analysis
• Candidate gene genotyping studies Adoption of
Next generation
sequencing
.76
Application Group 5
• Whole genome gene expression
profiling
• Whole genome genotyping studies
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Demand-side Analysis (contd…)
e.g. Drivers of Adoption: Microarray
Research Group 1
• Gene Expression / Regulation
• Gene Function
• Protein Expression
.41
Research Group 5
• Cancer Research / Oncology .32
• Drug Discovery / Target
Identification Adoption of
Microarray
.71
Application Group 5
• Whole genome gene expression
profiling
• Whole genome genotyping studies
.52
Application Group 6
• Focused gene expression profiling
• Novel or rare transcript expression
profiling
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Demand-side Analysis (contd…)
e.g. Correspondence between Technologies and Applications
qPCR/
Focused gene
This chart shows the perceived correspondence between the Candidate gene RT-PCR
expression profiling
various technologies (red boxes) and applications (blue circles). genotyping studies
The selection applications closest to each technology are those
that are most closely associated with it and those that most
distinguish it from other technologies. Novel or rare transcript
expression profiling
PCR/ Splice variant Copy number variation/ loss
thermal expression of heterozygosity studies
CDNA profiling
Clone identification cycling
Sequencing
and verification
De novo
sequencing Next Other
generation Microsatellite Whole genome
mutation
sequencing (STR) analysis genotyping studies
Capillary rescreening
electrophoresis DNA methylation
sequencing SNP discovery /
DNA/RNA state profiling
resequencing
isolation & Multiplex
Ribosomal purification SAGE Histone
assay
sequencing technology profiling modification Microarray
profiling/
Robotics/ automated ChIP-chip
liquid handling Small RNA/ micro RNA
Gel Based expression profiling
Single molecule Drug metabolism Whole genome gene
detection platforms pharmacogenic expression profiling
DNA
footprinting profiling genotyping
RNA interference
(RNAi/ siRNA )
Regulatory protein
Transfection
factor binding studies
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Demand-side Analysis (contd…)
Conclusions
• Majority of respondents are aware of most of the genomic technologies. Awareness is higher for PCR,
DNA/RNA isolation, qPCR and Gel-based. It is lowest for Single molecule detection platforms and Next
Gen sequencing.
• Most of the genomic technologies have been already adopted by majority of the respondents. Almost
universally adopted technologies include PCR, DNA/RNA isolation, qPCR, and Transfection.
• Technologies with the potential for a higher rate of adoption in the next 12 months include: Microarray,
RNA interference (RNAi/siRNA), Multiplex assay, Single molecule detection platforms, and Next generation
sequencing.
• A majority of the respondents are very satisfied with PCR and capillary electrophoresis sequencing.
• In hospitals/clinical labs more than 80% are very satisfied with robotics and 70% with gel-based
technologies.
• Satisfaction is lowest for microarray and RNA interference.
• The key reasons for satisfaction are: usefulness to research and ease of use.
• The key reasons for dissatisfaction with various technologies are: difficulty of use, high operating cost,
expensive or difficult sample preparation, and low accuracy.
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