SNP Genotyping and Analysis Markets

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