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SNP Genotyping and Analysis Markets and the Future of Personalized Medicine
February 1, 2010
Because SNPs are the most common type of genetic variation between human beings,
these specific single base pair mutations can be ideal for the task of hunting for
correlations between genotype and behavior or quality exhibited by a living organism.
For this reason, SNP analysis represents one of many possible pathways to
personalzied medicine. The use of SNP analysis has spread into numerous areas in
recent years. But diagnostics and pharmacogenomics are the most promising
applications, and Kalorama has followed developments in SNP analysis closely.
Kalorama Information's analyst Justin Saeks has taken a detailed look into the market
for DNA Sequencing Equipment, as well as Gene Expression Profiling Systems. Now, in
his report SNP Genotyping and Analysis Markets he looks at SNP analysis instruments,
reagents, and related software and services, providing information critical to having an
understanding of the business behind this new technology:
• Overview of SNPs, their Applications and Key SNP Analysis Methods
• Current Market Size and Estimates of Future Growth
• Impact of the GWAS 'First Round' on the Market
• Estimates of Revenues by Region (North America, Europe and ROW) and By
Product Type (Consumable, Instruments, Software)
• Complete List of SNP-Related Deals Made Between Companies Since 2002
• Exhaustive Review of Products on the Market
• Market Share of Major Companies in SNP Analysis
• Discussion of GOLD Database Projects, Government Involvement and
Funding
• Corporate Profiles
• Regulatory, Technology and Industry Trends as well as;
• Twelve Challenges the Market Faces and Eight Strategic Recommendations
for Companies in the SNP Analysis Market
While the market is expected to create opportunities for growth, the SNP Genotyping
and Analysis market is not without its challenges. The report tackles the following
trends:

2. • Rapid Rate of Product Introductions
• Increased Multiplexing Creates Improved Products
• End-Users Attracted to Larger-Scale SNP Platforms
• Accelerating Discoveries Create Volatile Market
• Diagnostic Market Holds Obstacles For New Innovations
• Complexity of Biological Systems Requires Multiple Techniques
• Miniaturization of Equipment and Instruments
As with all Kalorama Information publications, SNP Genotyping and Analysis Markets is
the result of a primary research effort. An analyst with experience following the biotech
instrument industry researching all available sources and contacting industry experts
and end users to obtain real market insights. Strategic Planners, Marketing Directors,
Business Development Executives are among the individuals who will benefit from this
resource.
Table of Contents
CHAPTER ONE: EXECUTIVE SUMMARY
• Introduction
• Market
• Trends
CHAPTER TWO: OVERVIEW
• SNP Analysis Methods
o Amplification
o Allele Discrimination / Assay Reaction Mechanism
Allele-Specific Hybridization
Allele-Specific Invasive Cleavage
Allele-Specific Ligation
Allele-Specific Primer Extension
Allele-Specific Single Base Extension (Single Base Primer
Extension)
Single Nucleotide Addition; Pyrosequencing
Assay Format
o Detection Method
• Definitions
o DNA Microarray
o Genome-Wide Association
o Linkage Analysis
o Mass Spectrometry
o Single-Nucleotide Polymorphism (SNP)
• Applications
o Life Science Research
o Pharmacogenetics / Pharmacogenomics

3. o Agriculture / Breeding
• Case Studies
o Case Study #1 - SNPs in Gene for P-glycoprotein Affect Antidepressant
Response
o Case Study #2 - Celera Studying SNPs Associated With Heart Disease
o Case Study #3 - Synonymous SNPs Alter mRNA Splicing with Obesity
o Case Study #4 - University of Ottawa Heart Institute (UOHI) Coronary
Artery Disease Research
o Case Study #5 - Development of Miniaturized Integrated SNP Genotyping
Microsystems
CHAPTER THREE: INDUSTRY, TECHNOLOGY, REGULATORY TRENDS
• Industry Trends
o Period of Limbo While Funding and Content Materialize
o Consolidation Occurring in Array and Life Science Markets
o Drug and Diagnostics Industries More Comfortable
o Broad Acceptance of SNP Analysis’ Value
o Core Labs Becoming Established Paradigm
• Technology Trends
• Rapid Rate of Product Introductions
• Increased Multiplexing Creates Improved Products
• End-Users Attracted to Larger-Scale SNP Platforms
• Complexity of Biological Systems Requires Multiple Techniques
• Miniaturization of Equipment and Instruments
• Regulatory Trends
o Introduction
o March 2004 - Critical Path Initiative
o March 2005 - “Guidance for Industry - Pharmacogenomic Data
Submissions”
o March 2006 - Critical Path Opportunities
o November 2006 - “Recommendations for the Generation and Submission
of Genomic Data”
o August 2007 - Pharmacogenomic Data Submissions — Companion
Guidance
o December 2007 - EGAPP Reviews Use of CYP450 Genetic Testing For
SSRIs
o NIH Limits Access to Data from GWAS
CHAPTER FOUR: PRODUCTS
• Affymetrix
o Overview
o Systems
Axiom Genotyping Solution
GeneChip Scanner 3000 7G

4. GeneChip Scanner 3000 7G Plus Targeted Genotyping System
GeneTitan Multi-Channel (MC) Instrument
Array Station
o Microarrays and Reagents
GeneChip Human Mapping 10K Array Xba 142 2.0 (GeneChip
Mapping 10K 2.0 Array)
GeneChip Human Mapping 100K Set
Genome-Wide Human SNP Array 5.0
Genome-Wide Human SNP Array 6.0
Axiom Genome-Wide Human Array Plates, Reagent Kits
DMET Plus Premier Pack
o GeneChip Universal Tag Arrays and Related Kits
Human 20K cSNP Kit
Human Immune-Inflammation 9K SNP Kit
Human MALD 3K SNP Kit
Bovine Mapping 10K SNP Kit
Bovine Mapping 25K SNP Kit
Rat Mapping 5K SNP Kit
• Applied Biosystems (Life Technologies)
o Overview
o SNP Genotyping Systems and Kits
SNaPshot Multiplex System
SNPlex Genotyping System
o TaqMan Genotyping Assays
Applied Biosystems’ TaqMan Genotyping Assay Strategy
TaqMan Sample-to-SNP Kits
VariantSEQr Resequencing System
TaqMan OpenArray Genotyping System
o RT-PCR
7900HT Fast Real-Time PCR System
o Sequencers
ABI Prism 310 Genetic Analyzer
ABI Prism 3100-Avant Genetic Analyzer
Applied Biosystems 3100 Genetic Analyzer
Applied Biosystems 3130 Genetic Analyzer
Applied Biosystems 3130xl Genetic Analyzer
Applied Biosystems 3730 DNA Analyzer
Applied Biosystems 3730xl DNA Analyzer
SOLiD 3
• Beckman Coulter
o CEQ 8000; CEQ 8800
o GenomeLab SNPstream Genotyping Series
• CombiMatrix
o CustomArray Synthesizer
o Geniom RT Analyzer
• GE Healthcare

5. o Overview
o Reagents and Kits
o SNP Genotyping Kits
o Sequencers
MegaBACE 500
MegaBACE 750
MegaBACE 1000
MegaBACE 1500
MegaBACE 4000
• Illumina
o Overview
iScan
iScan SQ
BeadXpress Reader
Illumina Genome Analyzer IIx
o Microarrays
Human1M-Duo BeadChip
Human1M-Quad BeadChip
• LI-COR Biosciences
o 4300
• Roche Applied Science
o LightCycler 480 System
o HybProbe; SimpleProbe
• Sequenom
o iPLEX GOLD Assay
o MassARRAY System
o MassARRAY Compact 96
o Selected SNP Genotyping Products & Technologies
CHAPTER FIVE: CONSORTIA, FUNDING, LITIGATION AND DEALS
• Consortia, Initiatives
o The Cancer Genome Atlas (TCGA) Project
o Cancer Sequencing Project
o Critical Path Institute (C-Path)
o DNA Polymorphism Discovery Resource
o Genetic Association Information Network (GAIN)
o Genotype-To-Phenotype Database (GEN2PHEN)
• International HapMap Project
o Introduction & Background
o Rationale for HapMap Approach
o Process for Producing HapMap
o Populations Included in HapMap
o Laboratories and Technologies Involved in HapMap
o Practical Use of the HapMap Data
o MicroArray Quality Control (MAQC) Project

6. • NIH Roadmap
o NIH Roadmap for Medical Research
o Pharmacogenetics Research Network (PGRN)
o Wellcome Trust Case-Control Consortium (WTCCC)
o WTCCC2
o Other Related Initiatives and Consortia
o NIH Involvement, Funding for SNPs and Sequencing
o Funding for Sequencing Projects Affecting SNP Market
o Continued Rapid Growth in Sequence Production
• Funding and Consortia for Sequencing
o NHGRI Funds Large-Scale Sequencing Centers, 2006
• Deals
• Intellectual Property and Litigation
o Patent Interference Between Life Technologies and Pacific Biosciences
o Helicos Appeals European Patent Office Decision on Illumina Patent
o Applied Biosystems and Illumina Claims and Counter-claims Both
Unsuccessful
o Fluidigm and Applied Biosystems Agree to End Case
o Beckman Coulter and Applied Biosystems Settle Outstanding Legal
Disputes
o Cepheid and Idaho Technology Settle Dispute Over PCR Patents
o Enzo Biochem Disputes CalTech Sequencing Patents
o Huang v. CalTech
o Applied Biosystems and Amersham plc (GE Healthcare)
o Settle Sequencing Patent Litigation
CHAPTER SIX: MARKET ANALYSIS
• Historical
• Illumina as Bellwether for SNP Analysis Market
• Applied Biosystems as Bellwether for RT-PCR Products
• Forecast
• Assumptions and Scope
• Consumer SNP
• Product Revenue
• Competitive Analysis
CHAPTER SEVEN: CORPORATE PROFILES
• Affymetrix
• Applied Biosystems (ABI) (Life Technologies)
• Illumina
CHAPTER EIGHT: CHALLENGES AND STRATEGIC RECOMMENDATIONS
• Challenges

7. o Challenge #1
o Challenge #2
o Challenge #3
o Challenge #4
o Challenge #5
o Challenge #6
o Challenge #7
o Challenge #8
o Challenge #9
o Challenge #10
o Challenge #11
o Challenge #12
• Strategic Recommendations
o Recommendation #1
o Recommendation #2
o Recommendation #3
o Recommendation #4
o Recommendation #5
o Recommendation #6
o Recommendation #7
o Recommendation #8
TABLE OF EXHIBITS
EXECUTIVE SUMMARY
• Figure 1-1: SNP Analysis Market
CHAPTER THREE: INDUSTRY, TECHNOLOGY, REGULATORY TRENDS
• Table 3-1 Critical Path Opportunities List
CHAPTER FOUR: PRODUCTS
• Table 4-1: Axiom Genome-Wide Array Planes SNP Content
• Figure 4-1: TaqMan Assay Strategy
• Figure 4-2: Beckman Coulter’s SNPstream Assay Strategy
• Table 4-2 Selected SNP Products and Technologies.
• Figure 4-3 Simple ProbeSequenom
CHAPTER FIVE: CONSORTIA, FUNDING, LITIGATION AND DEALS
• Table 5-1: Number of Individuals in Each Subset
• Table 5-2: Composition of the DNA Polymorphism Discovery Resources

8. • Figure 5-1: Companies’ Technologies Used in First Phase of HapMap
• Table 5-3: Technologies Used in Phase 1 of HapMap
• Table 5-4: SNP and Sequencing Related Initiatives and Consortia, 2009
• Table 5-5: Completely Sequenced Genomes in GOLD, Jan 2009
• Figure 5-2 Domains of Completely Sequenced Genomes in GOLD by Year,
1999-2008 and by Category (Archae, Bacteria, Eukaryota)
• Figure 5-3 Number of Genome Projects by Inst., '95- Q1 '09 Cumulative
• Figure 5-4 Domains of Sequenced Genomes in GOLD, Jan 2009
• Table 5-6 Number of Genome Projects by Institution
• Figure 5-5 Funding of Genome Projects, 2007-2009 ($M)
• Table 5-7: Funding Sources of Genome Projects
• Figure 5-6 Human Genome Project Funding, DOE & NIH '90-'03
• Table 5-7: Countries Leading Projects, '95-Q1'09
• Table 5-8: SNP Projects by Category
• Table 5-9: Relevance of Non-Bacterial Sequencing Projects, '95 - Q1 '09, Cum.
• Figure 5-7: Disease/Conditions Associated with Projects
• Figure 5-8: NHGRI Budget by Year incl. ARRA, 2006-2010 ($M)
• Table 5-10: 2010 Est. NHGRI Budget by Mechanism
• Figure 5-9 2010 Est. NHGRI Budget by Mechanism
• Figure 5-10 NHGRI Funded Large-Scale Sequencing Ctrs '07-'08
• Table 5-11 SNP Related Deals, 2009
• Table 5-12: SNP Related Patents
CHAPTER SIX: MARKET ANALYSIS
• Figure 6-1: Illumina Total Quarterly Revenues, 2003-2009 ($M)
• Figure 6-2: Applied Biosystems RT-PCR / Applied Genomics Revenues, 2001-
2008 ($M)
• Table 6-1: SNP Analysis Tools Market, 2008-2014 ($M)
• Figure 6-3: SNP Analysis Tools Market Revenues, 2008-2014 ($M)
• Table 6-4: Growth Rate for SNP Analysis Tools
• Figure 6-4: SNP Analysis Tools Market Growth Rate, 2008-2014
• Figure 6-5: SNP Tools Market by Region (North America, Europe, Japan, ROW)
• Table 6-5: SNP Tools Market by Product (Consumable, System,
Software/Service)
• Figure 6-6: SNP Market by Product, 2008 (Systems, Services/Software,
Consumables)
• Table 6-6: SNP Analysis Market Shares, 2008 ($M)
• Figure 6-7: SNP Analysis Tools Market Shares, 2008 ($M)
CHAPTER SEVEN: CORPORATE PROFILES
• Figure 7-1: Affymetrix Revenues by Product Type, 2005 - 2009
• Figure 7-2: Affymetrix Consumables Revenues by DNA v RNA

9. • Figure 7-3: Illumina Revenues 2008-2009 by quarter
CHAPTER EIGHT: CHALLENGES AND STRATEGIC RECOMMENDATIONS
• Figure 8-1: Cheaper Sequencing Impacts SNP Market
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