SNP Genotyping and Analysis Markets

Date: February 22, 2010
Pages: 240
Price:
US$ 3,995.00
Publisher: Kalorama Information
Report type: Strategic Report
Delivery: E-mail Delivery (PDF)
ID: SDAD921E89FEN
Leaflet:

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SNP Genotyping and Analysis Markets
Because SNPs (single nucleotide polymorphisms), are the most common type of genetic variation between human beings. These single base pair mutations at specific DNA sequence sites, can be ideal for the task of hunting for correlations between genotype and behavior or quality exhibited by a living organism.

The use of SNP analysis has spread into numerous areas in recent years. But diagnostics and pharmacogenomics are the most promising applications, and market watchers in diagnostics, pharmaceutical, biotechnology and related instrument industries will want to watch 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:
  • 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.
CHAPTER ONE: EXECUTIVE SUMMARY

Introduction
Market
Trends

CHAPTER TWO: OVERVIEW

SNP Analysis Methods
Amplification
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
Detection Method
Definitions
DNA Microarray
Genome-Wide Association
Linkage Analysis
Mass Spectrometry
Single-Nucleotide Polymorphism (SNP)
Applications
Life Science Research
Pharmacogenetics / Pharmacogenomics
Agriculture / Breeding
Case Studies
Case Study #1 - SNPs in Gene for P-glycoprotein Affect Antidepressant Response
Case Study #2 - Celera Studying SNPs Associated With Heart Disease
Case Study #3 - Synonymous SNPs Alter mRNA Splicing with Obesity
Case Study #4 - University of Ottawa Heart Institute (UOHI) Coronary Artery Disease Research
Case Study #5 - Development of Miniaturized Integrated SNP Genotyping Microsystems

CHAPTER THREE: INDUSTRY, TECHNOLOGY, REGULATORY TRENDS

Industry Trends
Period of Limbo While Funding and Content Materialize
Consolidation Occurring in Array and Life Science Markets
Drug and Diagnostics Industries More Comfortable
Broad Acceptance of SNP Analysis’ Value
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
Introduction
March 2004 - Critical Path Initiative
March 2005 - “Guidance for Industry - Pharmacogenomic Data Submissions”
March 2006 - Critical Path Opportunities
November 2006 - “Recommendations for the Generation and Submission of Genomic Data”
August 2007 - Pharmacogenomic Data Submissions — Companion Guidance
December 2007 - EGAPP Reviews Use of CYP450 Genetic Testing For SSRIs
NIH Limits Access to Data from GWAS

CHAPTER FOUR: PRODUCTS

Affymetrix
Overview
Systems
Axiom Genotyping Solution
GeneChip Scanner 3000 7G
GeneChip Scanner 3000 7G Plus Targeted Genotyping System
GeneTitan Multi-Channel (MC) Instrument
Array Station
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
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)
Overview
SNP Genotyping Systems and Kits
SNaPshot Multiplex System
SNPlex Genotyping System
TaqMan Genotyping Assays
Applied Biosystems’ TaqMan Genotyping Assay Strategy
TaqMan Sample-to-SNP Kits
VariantSEQr Resequencing System
TaqMan OpenArray Genotyping System
RT-PCR
7900HT Fast Real-Time PCR System
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
CEQ 8000; CEQ 8800
GenomeLab SNPstream Genotyping Series
CombiMatrix
CustomArray Synthesizer
Geniom RT Analyzer
GE Healthcare
Overview
Reagents and Kits
SNP Genotyping Kits
Sequencers
MegaBACE 500
MegaBACE 750
MegaBACE 1000
MegaBACE 1500
MegaBACE 4000
Illumina
Overview
iScan
iScan SQ
BeadXpress Reader
Illumina Genome Analyzer IIx
Microarrays
Human1M-Duo BeadChip
Human1M-Quad BeadChip
LI-COR Biosciences
4300
Roche Applied Science
LightCycler 480 System
HybProbe; SimpleProbe
Sequenom
iPLEX GOLD Assay
MassARRAY System
MassARRAY Compact 96
Selected SNP Genotyping Products & Technologies

CHAPTER FIVE: CONSORTIA, FUNDING, LITIGATION AND DEALS

Consortia, Initiatives
The Cancer Genome Atlas (TCGA) Project
Cancer Sequencing Project
Critical Path Institute (C-Path)
DNA Polymorphism Discovery Resource
Genetic Association Information Network (GAIN)
Genotype-To-Phenotype Database (GEN2PHEN)
International HapMap Project
Introduction & Background
Rationale for HapMap Approach
Process for Producing HapMap
Populations Included in HapMap
Laboratories and Technologies Involved in HapMap
Practical Use of the HapMap Data
MicroArray Quality Control (MAQC) Project
NIH Roadmap
NIH Roadmap for Medical Research
Pharmacogenetics Research Network (PGRN)
Wellcome Trust Case-Control Consortium (WTCCC)
WTCCC2
Other Related Initiatives and Consortia
NIH Involvement, Funding for SNPs and Sequencing
Funding for Sequencing Projects Affecting SNP Market
Continued Rapid Growth in Sequence Production
Funding and Consortia for Sequencing
NHGRI Funds Large-Scale Sequencing Centers, 2006
Deals
Intellectual Property and Litigation
Patent Interference Between Life Technologies and Pacific Biosciences
Helicos Appeals European Patent Office Decision on Illumina Patent
Applied Biosystems and Illumina Claims and Counter-claims Both Unsuccessful
Fluidigm and Applied Biosystems Agree to End Case
Beckman Coulter and Applied Biosystems Settle Outstanding Legal Disputes
Cepheid and Idaho Technology Settle Dispute Over PCR Patents
Enzo Biochem Disputes CalTech Sequencing Patents
Huang v. CalTech
Applied Biosystems and Amersham plc (GE Healthcare)
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
Challenge #1
Challenge #2
Challenge #3
Challenge #4
Challenge #5
Challenge #6
Challenge #7
Challenge #8
Challenge #9
Challenge #10
Challenge #11
Challenge #12
Strategic Recommendations
Recommendation #1
Recommendation #2
Recommendation #3
Recommendation #4
Recommendation #5
Recommendation #6
Recommendation #7
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
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
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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