frost & sullivan enabling genomics research analyst briefing
TRANSCRIPT
Enabling Genomics Research:
How do Platform Technologies Fit withNext Generation Applications?
Jonathan Witonsky, Industry Manager
Drug Discovery Technologies
and Clinical DiagnosticsOctober 29, 2008
2
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
3
Background
Genomics Technologies and Applications
4
Background
Reagents
Instrumentation Software
Consumables
Technologies
Nucleic Acid Isolation
PCR
qRT-PCR
DNA Microarray
DNA SequencingTechnology
Applications
Gene Expression Epigenetics
Sequencing Genotyping Cytogenetics
5
Background (contd…)
Timeline of High-growth Periods for Genomics Applications
201420122010200820062004200220001998
de novo DNA sequencing /
resequencing for SNP discovery
gene expression analysis
genotyping
epigenetics / molecular cytogenetics (microarray)
201420122010200820062004200220001998
de novo DNA sequencing /
resequencing for SNP discovery
gene expression analysis
genotyping
epigenetics / molecular cytogenetics (microarray)
6
Background (contd…)
e.g. Gene Expression Analysis
Low density (moderate market growth)
Medium density (high market growth)
High density (moderate market growth)
Typical platform technology:
Real-time PCRTypical platform technology:
Standard DNA Microarray
Gene Expression Analysis
Sweet Spot for Novel Platform Technologies
7
Markets
Growth Driven by Established and Emerging Trends
8
Markets
20122012
20072007
20022002
Customer Priorities
Customer Priorities
Customer Priorities
1. Proof-of-principle
2. Basic research and discovery
1. Regulated in vitro diagnostics
2. Multiple commercialized
applications
3. Research workflows involve
multiple genomics technologies
4. Ultra-high throughput technologies
1. Validation
research
2. Clinical approval
3. Forensics and infectious disease
testing
20122012
20072007
20022002
Customer Priorities
Customer Priorities
Customer Priorities
1. Proof-of-principle
2. Basic research and discovery
1. Regulated in vitro diagnostics
2. Multiple commercialized
applications
3. Research workflows involve
multiple genomics technologies
4. Ultra-high throughput technologies
1. Validation
research
2. Clinical approval
3. Forensics and infectious disease
testing
9
Markets (contd…)
e.g. Nucleic Acid Purification and Isolation
Genomic DNA
27.8%
Plasmid DNA
27.1%
Fragment DNA
15.4%
RNA
29.7%
Percent of Revenues by Nucleic Acid Type (U.S.), 2007
Note: All figures are rounded; the base year is 2007. Source: Frost & Sullivan
12 – 14%Growth
0%Growth
5 – 7%
Growth
16 – 18%
Growth
10
Supply-side Analysis
Product Positioning and Marketing
11
Supply-side Analysis
Product Positioning #1
qPCR
DNA Microarray
CE Sequencing
Next GenerationSequencing
GeneExpression
SNPGenotyping
Epigenetics(DNA
Methylation,ChIP-chip)
Cytogenetics(CNP/CGH)
Epigenetics(DNA
Methylation,ChIP-chip)
Cytogenetics(CNP/CGH)
de novoSequencing
SNP Discoveryand
Resequencing
qPCR
DNA Microarray
CE Sequencing
Next GenerationSequencing
GeneExpression
SNPGenotyping
Epigenetics(DNA
Methylation,ChIP-chip)
Cytogenetics(CNP/CGH)
Epigenetics(DNA
Methylation,ChIP-chip)
Cytogenetics(CNP/CGH)
de novoSequencing
SNP Discoveryand
Resequencing
qPCR
DNA Microarray
CE Sequencing
Next GenerationSequencing
GeneExpression
SNPGenotyping
GeneExpression
SNPGenotyping
Epigenetics(DNA
Methylation,ChIP-chip)
Cytogenetics(CNP/CGH)
SNP Discoveryand
Resequencing
Nucleic AcidDetection/
QuantitationqPCR
DNA Microarray
CE Sequencing
Next GenerationSequencing
GeneExpression
SNPGenotyping
GeneExpression
SNPGenotyping
Epigenetics(DNA
Methylation,ChIP-chip)
Cytogenetics(CNP/CGH)
SNP Discoveryand
Resequencing
Nucleic AcidDetection/
Quantitation
Product Positioning #2
Product Positioning #3
Product Positioning #4
qPCR
DNA Microarray
CE Sequencing
Next GenerationSequencing
de novoSequencing
SNPGenotyping
Epigenetics(DNA
Methylation,ChIP-chip)
Cytogenetics(CNP/CGH)
GeneExpression
SNPGenotyping
SNP Discoveryand
Resequencing
de novoSequencing
SNP Discoveryand
Resequencing
Nucleic AcidDetection/
Quantitation
Nucleic AcidDetection/
Quantitation
qPCR
DNA Microarray
CE Sequencing
Next GenerationSequencing
de novoSequencing
SNPGenotyping
Epigenetics(DNA
Methylation,ChIP-chip)
Cytogenetics(CNP/CGH)
GeneExpression
SNPGenotyping
SNP Discoveryand
Resequencing
de novoSequencing
SNP Discoveryand
Resequencing
Nucleic AcidDetection/
Quantitation
Nucleic AcidDetection/
Quantitation
qPCR
DNA Microarray
CE Sequencing
Next GenerationSequencing
Epigenetics(DNA
Methylation,ChIP-chip)
Cytogenetics(CNP/CGH)
GeneExpression
SNPGenotyping
de novoSequencing
SNP Discoveryand
Resequencing
GeneExpression
SNPGenotyping
Epigenetics(DNA
Methylation,ChIP-chip)
Cytogenetics(CNP/CGH)
SNP Discoveryand
Resequencing
Nucleic AcidDetection/
QuantitationqPCR
DNA Microarray
CE Sequencing
Next GenerationSequencing
Epigenetics(DNA
Methylation,ChIP-chip)
Cytogenetics(CNP/CGH)
GeneExpression
SNPGenotyping
de novoSequencing
SNP Discoveryand
Resequencing
GeneExpression
SNPGenotyping
Epigenetics(DNA
Methylation,ChIP-chip)
Cytogenetics(CNP/CGH)
SNP Discoveryand
Resequencing
Nucleic AcidDetection/
Quantitation
12
Supply-side Analysis (contd…)
e.g. Next Generation Sequencing Technology
Genome Sequencer
FLX System(Roche Applied Science)
Genome Analyzer
System(Illumina, Inc.)
SOLiD™
Analyzer(Applied Biosystems)
• Ancient DNA• ChIP-seq/Methylation/
Epigenetics• Eukaryote Whole Genome• Expression Tags• HIV Sequencing• Metagenomics & Microbial
Diversity• Mitochondria/ Viruses/ Plastids/
Plasmids• Prokaryote Whole Genome• Sequence Capture Targeted
Region• Small RNA• Somatic Variation Detection• Transcriptome Sequencing
• De novo Sequencing• Whole-Genome Resequencing• Discovery of Somatic Genomic
Variation• Metagenomics• Epigenomics• Targeted Sequencing• Whole-Transcriptome Profiling• Protein-DNA or Protein-RNA
Interactions
• Targeted Resequencing• Gene Expression• MicroRNA Discovery• Whole Genome Sequencing
13
Demand-side Analysis
Usage of Genomics Technologies
14
Demand-side Analysis
Research Group 1 • Gene Expression /
Regulation• Gene Function
• Protein Expression
Research Group 2 • Cardiovascular
• Metabolic• Pre-clinical studies
Research Group 3• Developmental
Biology• Stem cells/ develop-
mental biology
• Service provider /
-central core facility
Research Group 5• Cancer Research /
Oncology• Drug Discovery /
Target Identification
Research Group 6• Evolutionary Biology
Research groups 4 and 6 tend
to not go together.
(negatively correlated)
Group 4 can
be pursued
separately or
together with
Group 2.
Research
Group 1 focus
can be pursued
in parallel with
all the other
areas.
Research Group 3 tends to be
pursued with Group 2.
Research Focus Area
Research Group 4• Infectious Disease/
Microbial detection & ID
• Immunology
Research Group 5
tends to be a
category in itself that
can, however, be
pursued in parallel
with other research
areas of focus.
15
Demand-side Analysis (contd…)
Application Group 1 • SNP Discovery / Resequencing
• Other mutation
screening
• Copy number
variation / loss of heterozygosity
studies
• Microsatellite
(STR) analysis
• Candidate gene genotyping
Application Group 2 • Histone
modification
profiling / ChIP-
chip
• Regulatory protein factor
binding studies
• DNA Methylation
State Profiling
• Small RNA/micro RNA expression
profiling
Application Group 3• Ribosomal sequencing
• Drug metabolism
pharmacogenic
profiling
• SAGE profiling / digital gene
expression
profiling
• Splice variant
expression profiling
Application Group 4• Clone identification
and verification
• CDNA
sequencing
• De novo sequencing
Application Group 5• Whole genome
gene expression
profiling
• Whole genome genotyping
studies
Application Group 6• Focused gene expression
profiling
• Novel or rare
transcript
expression profiling
Applications
Application
Group 6 focus
can be pursued
in parallel with
all the other
applications.
Research Group 3
tends to be a
category in itself that
can, however, be
pursued in parallel
with other
applications.
Group 4 can be
pursued
separately or in
parallel with the
other groups in
the other sub-
branch.
Research Group 5 tends to
be pursued with Group 1.
Group 2 can be
pursued separately
or together with
Group 1.
16
Demand-side Analysis (contd…)
Technology Group 1 • PCR/ Thermal Cycling
• DNA/RNA
isolation &
purification
technologies• qPCR/RT-PCR
Technology Group 3• Next generation sequencing
• Capillary
electrophoresis
sequencing
• Single molecule detection
platforms
Technology Group 6• Gel Based (Northern/
Southern /
Western)
Technology Group 5• Microarray• Robotics /
Automated
liquid handling
Technology Group 4• Multiplex Assay
Technology Group 2 • RNA interference
(RNAi/siRNA)
• Transfection
Group 1 can
be adopted
separately or
together with
Group 3.
Technology
Groups 5 and 6
can be pursued
in parallel with
all the other
areas.
Technology Group 4 tends
to be adopted with Group 3.
Technologies
Technology Group 2
tends to be a
category in itself that
can, however, be
adopted in parallel
with other
technologies.
17
Demand-side Analysis (contd…)
e.g. Drivers of Adoption: Next generation sequencing
Adoption of Next generation
sequencing
1.27
.76
Application Group 1 • SNP Discovery / Resequencing
• Other mutation screening• Copy number variation / loss of
heterozygosity studies
• Microsatellite (STR) analysis
• Candidate gene genotyping studies
Application Group 5• Whole genome gene expression
profiling
• Whole genome genotyping studies
Adoption of Next generation
sequencing
1.27
.76
Application Group 1 • SNP Discovery / Resequencing
• Other mutation screening• Copy number variation / loss of
heterozygosity studies
• Microsatellite (STR) analysis
• Candidate gene genotyping studies
Application Group 5• Whole genome gene expression
profiling
• Whole genome genotyping studies
18
Demand-side Analysis (contd…)
e.g. Drivers of Adoption: Microarray
Adoption of Microarray
.32
.71
.41
Application Group 6• Focused gene expression profiling
• Novel or rare transcript expression
profiling
Application Group 5• Whole genome gene expression
profiling
• Whole genome genotyping studies.52
Research Group 1 • Gene Expression / Regulation
• Gene Function• Protein Expression
Research Group 5• Cancer Research / Oncology
• Drug Discovery / Target
Identification Adoption of Microarray
.32
.71
.41
Application Group 6• Focused gene expression profiling
• Novel or rare transcript expression
profiling
Application Group 5• Whole genome gene expression
profiling
• Whole genome genotyping studies.52
Research Group 1 • Gene Expression / Regulation
• Gene Function• Protein Expression
Research Group 5• Cancer Research / Oncology
• Drug Discovery / Target
Identification
19
Demand-side Analysis (contd…)
e.g. Correspondence between Technologies and Applications
Whole genome
genotyping studies
Candidate gene genotyping studies
Whole genome gene expression profiling
Focused gene expression profiling
SAGE
profiling
Splice variant
expression profiling
Novel or rare transcript expression profiling
Small RNA/ micro RNA expression profiling
DNA methylation state profiling
Regulatory protein factor binding studies
Histone
modificationprofiling/
ChIP-chip
Copy number variation/ lossof heterozygosity studies
De novo sequencing
SNP discovery /
resequencing
Othermutation
rescreening
Clone identificationand verification
Microsatellite
(STR) analysis
DNA footprinting
CDNA Sequencing
Ribosomal
sequencing
Drug metabolismpharmacogenicprofiling genotyping
PCR/thermal
cycling
Gel Based
Multiplex
assay
qPCR/RT-PCR
Capillaryelectrophoresis
sequencing
Next
generationsequencing
Microarray
Robotics/ automated
liquid handling
Single molecule detection platforms
DNA/RNAisolation &
purification
technology
RNA interference
(RNAi/ siRNA )
Transfection
Whole genome
genotyping studies
Candidate gene genotyping studies
Whole genome gene expression profiling
Focused gene expression profiling
SAGE
profiling
Splice variant
expression profiling
Novel or rare transcript expression profiling
Small RNA/ micro RNA expression profiling
DNA methylation state profiling
Regulatory protein factor binding studies
Histone
modificationprofiling/
ChIP-chip
Copy number variation/ lossof heterozygosity studies
De novo sequencing
SNP discovery /
resequencing
Othermutation
rescreening
Clone identificationand verification
Microsatellite
(STR) analysis
DNA footprinting
CDNA Sequencing
Ribosomal
sequencing
Drug metabolismpharmacogenicprofiling genotyping
PCR/thermal
cycling
Gel Based
Multiplex
assay
qPCR/RT-PCR
Capillaryelectrophoresis
sequencing
Next
generationsequencing
Microarray
Robotics/ automated
liquid handling
Single molecule detection platforms
DNA/RNAisolation &
purification
technology
RNA interference
(RNAi/ siRNA )
Transfection
This chart shows the perceived correspondence between the
various technologies (red boxes) and applications (blue circles).
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.
20
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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22
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