DNA Sequencing Equipment and Services Markets, 2nd Edition

Since the last edition of Kalorama Information's DNA Sequencing Equipment and Services report, the market has been changing in unpredictable ways as second-generation sequencers are being incrementally introduced and upgraded. On the surface, the situation has become somewhat linear and predictable, but as Kalorama Information biotech analyst Justin Saeks explains, it is actually a unique and relatively volatile situation that is not seen...

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Since the last edition of Kalorama Information's DNA Sequencing Equipment and Services report, the market has been changing in unpredictable ways as second-generation sequencers are being incrementally introduced and upgraded. On the surface, the situation has become somewhat linear and predictable, but as Kalorama Information biotech analyst Justin Saeks explains, it is actually a unique and relatively volatile situation that is not seen often with life science tools markets. Third-generation systems have the potential to completely change the market, or to simply join the pack.



Revenue growth has been unusually high, and all of the trends seem to indicate that growth will continue in the near term. It is likely that completely new technologies will be introduced at least every year or two, while second-generation sequencer improvements also continue.
In Kalorama Information biotech analyst Justin Saek's 2nd edition of DNA Sequencing Equipment and Services Markets, these changes are detailed and put in context, along with the following:

• DNA Sequencer Revenues by Industry and by Leading Systems


• Forecast of Sequencer Revenues to 2014


• Review of Important Sequencers and Comparison of Features and Drawbacks.


• Profiles of Major Companies in the Marketplace


• Affymetrix and Illumina Settlement and other Significant Litigation in the Industry


• Major Industry Deals since 2008, Review of Deals 05-07, and Analyst Commentary


• Over 70 Figures and Tables making market information accessible


• Review of Major Deals and Litigation affecting the marketplace.


• Review of Technologies Under Development
• Discussion of Funding Sources and Recent Grant Awardees


• Strategic Recommendations for Companies Operating in the DNA Sequencing Market

Kalorama Information's DNA Sequencing Equipment and Service Markets represents research culled from a variety of secondary sources. But the true insights originated from interviews with market experts; these interviews were used to confirm numbers and test forecast assumptions.



Companies profiled in the report include:

• 454 Life Sciences / Roche


• Applied Biosystems / Life Technologies


• Beckman Coulter (Fullerton, CA)


• GE Healthcare Life Sciences


• Helicos Biosciences


• Illumina / Solexa


• LI-COR Biosciences (Lincoln, NE)

Medical Devices Industry in the United States

CHAPTER ONE: EXECUTIVE SUMMARY

Introduction, Background, & Definition

Introduction

A Period of Rapid Developments

Further Longer-Term Challenges

Rapid Growth Overall, But Intense Competition

Moving Into New Applications and Segments

Customers’ Research Models Evolving

Second-Generation Systems Getting Established

Background

Scope and Methodology

Applications and Definitions

Types of Samples

DNA Sequencing Strategies

DNA Sequencing Chemistries and Techniques

Sanger Sequencing

Reversible Terminators

Single Nucleotide Addition; Pyrosequencing

CHAPTER TWO: SEQUENCER MARKET TRENDS

Industry and Technology Trends

Continual Improvements Expand Next-Generation Market

Spread of Targeted Enrichment, Sequence-Capture Products and Services

Synergies Appearing Between Life Science Companies’ Products

SNP and Other Experiments Moving to Sequencing for Higher Detail

Market Fragmenting Into Multiple Applications, Products

Miniaturization of Sanger and CE Technology

Rise of Consumer Genomics, Genetic Testing

Genome Sequencing Trends

Continued Acceleration in Sequence Output

Phylogenetic Breakout of Genome Sequencing Projects

Technologies Used in Genome Projects

Types of Genome Projects in GOLD Database

Technologies Used in Genome Projects by Type of Project

Technologies Used in Genome Projects by Country

Countries Leading Genome Projects

Technologies Used in Genome Projects by Institution

Technologies Used in Genome Projects by Funding Organization

Technologies Used in Genome Projects by Domain

Phenotypes of Genomes Being Sequenced

Diseases / Conditions Associated With Genomes Being Sequenced

Phylogenetic Breakout of Eukaryotic Genome Projects

Funding Trends, Genome Centers, Consortia

Introduction

Major Sequencing Centers

Major Funding Sources

Annual Funding of Genome Projects by Organization

Funding Relevance of Bacterial Sequencing Projects

Funding Relevance of Non-Bacterial Genome Project

NHGRI Annual Funding, Budget, Periodic Strategic Planning

NHGRI Funds Large-Scale Sequencing Center

NHGRI White Paper #4: The Future of Genome Sequencing

The Cancer Genome Atlas Project

Cancer Sequencing Projec

FUGE - Functional Genomics in Norway

National Plant Genome Initiative

NSF / USDA Microbial Genome Sequencing Programs

Other Initiatives and Consortia

CHAPTER THREE: DNA SEQUENCER PRODUCTS

454 Life Sciences (Branford, CT) / Roche

Genome Sequencer FLX

Applied Biosystems (Foster City, CA)

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 3500 Genetic Analyzer

Applied Biosystems 3730 DNA Analyzer

Applied Biosystems 3730xl DNA Analyzer

SOLiD 3

Beckman Coulter

CEQ 8000; CEQ 8800

GenomeLab GeXP Genetic Analysis System

Dover Systems (Danaher Motion)

Polonator G.007

GE Healthcare

MegaBACE 500

MegaBACE 750

MegaBACE 1000

MegaBACE 1500

MegaBACE 4000

Helicos Biosciences

Helicos Genetic Analysis System

Illumina / Solexa

Illumina Genome Analyzer II

LI-COR Biosciences (Lincoln, NE)

4300

Pacific Biosciences

SMRT Technology

CHAPTER FOUR: DNA SEQUENCER MARKET FORECAST

Revenues and Forecast

Current Market (01-08)

Forecasted Market: ABI as a Market Bellweather

Growth Indicators

CHAPTER FIVE: COMPETITIVE ANALYSIS OF SEQUENCER MARKET

Introduction

Next- and Next-Next-Generation Creating Turbulence

Capillary Electrophoresis Maintains Large Segment

Second-, Third-Generation Battle Still Up in the Air

DNA Sequencer Market Shares

Features and Strengths of Second-Generation Sequencers

454 Life Sciences GS FLX - Strengths / Advantages

454 Life Sciences GS FLX - Weaknesses / Disadvantages

Applied Biosystems SOLiD - Strength / Advantages

Applied Biosystems SOLiD - Weaknesses / Disadvantages

Illumina Genome Analyzer - Strength / Advantages

Illumina Genome Analyzer - Weaknesses / Disadvantages

CHAPTER SIX: INTELLECTUAL PROPERTY AND LITIGATION

Patent Interference Between Life Technologies and Pacific Biosciences

Helicos Appeals European Patent Office Decision on Illumina Patent

Illumina Files ‘841 Patent Infringement Suit Against Affymetrix

Affymetrix and Illumina Settle Case Over ‘243, ‘432, ‘531, ‘365, and ‘716

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 SEVEN: DEALS

Significant DNA Sequencing Equipment Deals

CHAPTER EIGHT: CORPORATE PROFILES

454 Life Sciences / Roche

Applied Biosystems / Life Technologies

Beckman Coulter (Fullerton, CA)

GE Healthcare Life Sciences

Helicos Biosciences

Illumina / Solexa

LI-COR Biosciences (Lincoln, NE)

CHAPTER NINE: TECHNOLOGIES UNDER DEVELOPMENT

Introduction

Human Microbiome Project Awards Funds for Technology Development, Data Analysis and Ethical Research

NHGRI Seeks DNA Sequencing Technologies Fit for Routine Laboratory and Medical Use, August 2008

Arizona State University, Tempe

“Sequencing by Recognition”

Harvard College

“Electronic Sequencing in Nanopores”

Oak Ridge National Laboratory / UT Battelle

“DNA Transport and Sequencing Through a Quadrupole Gate”

Princeton University

“Nanogap Detector (Arrays) Inside Nanofluidic Channel for Fast Real-Time DNA Sequencing”

University of Arkansas, Fayetteville

“Exploration of Solid-State Nanopore Reading Labeled Linear DNA Sequence”

University of California, San Diego

“Genome Sequencing by Natural DNA Synthesis on Amplified DNA Clones”

University of Pennsylvania, Philadelphia

“DNA Sequencing Using Nanopore-Nanoelectrode Devices for Sensing and Manipulation”

University of Pittsburgh

“DNA Sequencing at a Stretch”

Columbia University

“DNA Sequencing with Reversible dNTP and Cleavable Fluorescent ddNTP Terminators”

Foundation for Applied Molecular Evolution, Inc.

“Near Term Development of Reagents and Enzymes for Genome Sequencing”

Illumina

“Development of a 10Gb Pyrosequencer”

NHGRI Seeks to Advance Next Generation of Sequencing Technologies, August 2007

Arizona State University, Tempe

“Sequencing by Recognition”

Brown University

“Hybridization-assisted Nanopore DNA Sequencing”

Duke University

“Continuous Sequencing-by-Synthesis Based on a Digital Microfluidic Platform”

NABsys, Inc.

“Hybridization-assisted Nanopore Sequencing”

North Carolina State University, Raleigh

“Sequencing DNA by Transverse Electrical Measurements in Nanochannels”

UMDNJ-New Jersey Medical School

“Ribosome-based Single Molecule Method to Acquire Sequence Data from Genomes”

University of British Columbia, Vancouver

“Nanopore Array Force Spectroscopy Chip for Rapid Clinical Genotyping”

University of California, Irvine

“High Throughput Low Cost DNA Sequencing Using Probe Tip Arrays”

Columbia University

“3'-O-Modified Nucleotide Reversible Terminators for Pyrosequencing”

“An Integrated System for DNA Sequencing by Synthesis”

University of New Mexico School of Medicine, Albuquerque

“Polony Sequencing the Human Genome”

University of Wisconsin, Madison

“Sequence Acquisition from Mapped Single DNA Molecules”

“NHGRI Aims to Make DNA Sequencing Faster, More Cost Effective”, October 2006

Arizona State University

“Fabrication of Universal DNA Nanoarrays for Sequencing by Hybridization”

Boston University

“High-Throughput DNA Sequencing Using Design Polymers and Nanopore Arrays”

Case Western Reserve University

“Large-Scale Nanopore Arrays for DNA Sequencing”

General Electric Global Research

“Closed Complex Single Molecule Sequencing”

Helicos Biosciences

“High Accuracy Single Molecule DNA Sequencing by Synthesis”

Lehigh University

“Force Spectroscopy Platform for Label Free Genome Sequencing”

University of California, San Diego

“Genome Sequencing by Ligation Using Nano-Arrays of Single DNA Molecules”

University of North Carolina, Chapel Hill

“Nanoscale Fluidic Technologies for Rapidly Sequencing Single DNA Molecules”

University of Washington, Seattle

“Engineering MspA for Nanopore Sequencing”

Baylor College of Medicine, HGSC

“Ultrafast SBS Method for Large-Scale Human Resequencing”

Intelligent Bio-Systems

“High-Throughput DNA Sequencing by Synthesis Platform”

NHGRI Expands Effort to Revolutionize Sequencing Technologies, August 2005

Agencourt Personal Genomics [Applied Biosystems / Life Technologies]

“Bead-Based Polony Sequencing (Supplemental)”

Network Biosystems

“$100,000 Genome Using Integrated Microfluidic CE”

The State University of New York, Stony Brook (SUNY)

“Ultra High Throughput DNA Sequencing System Based on 2D Monolith Multi-Capillary Arrays and Nanoliter Reaction Volume”

Columbia University

“Modulating Nucleotide Size in DNA for Detection by Nanopore”

Duke University

“Droplet-Based Digital Microfluidic Genome Sequencing”

Harvard University

“Electronic Sequencing in Nanopores”

Pacific Biosciences (formerly Nanofluidics)

“Real-Time Multiplex Single-Molecule DNA Sequencing”

New York University

“Haplotype Sequencing Via Single Molecule Hybridization”

Oxford University and The Scripps Research Institute

“Single-Molecule DNA Sequencing with Engineered Nanopores”

University of California, San Diego

“Massively Parallel Cloning and Sequencing of DNA”

University of Illinois at Urbana-Champaign

“Sequencing a DNA Molecule Using a Synthetic Nanopore”

VisiGen Biotechnologies

“Real-Time DNA Sequencing”

NHGRI Funds Next Generation of Sequencing Technologies, October 2004

CHAPTER TEN: CHALLENGES AND STRATEGIC RECOMMENDATIONS

Market Challenges

454’s and Illumina’s Head-Starts Cause Advantages

Disruptive Technologies, Multiple Variables Creating Unpredictable Market in Short- and Long-Term

Biases at Multiple Levels Raise Issues of Standards, Quality Metrics

Rapidly Changing Technologies Could Fatigue End-Users

Longer Read Lengths Expected to Steal the Show

Sequencer Market Slowed by Data Management Bottleneck

New Entrants Contending With Three Major Life Science Suppliers

Pharmacogenetics, Consumer Genomics Still Shaking Out

Strategic Recommendations

Prepare for Applications Opened by Decreasing Cost

Balance Risks

Address Growing International Demand

User-Friendliness

Increase Value

Expanding Routine Industry Segments

Niche Markets

Establish Early Connections

Move Towards Diagnostic Environment Requires Partnering

LIST OF EXHIBITS

CHAPTER TWO: SEQUENCER MARKET TRENDS

Table 2-1: Completely Sequenced Genomes in GOLD, 1995-2008(Without Publication, With Publication)

Figure 2-1: Completely Sequenced Genomes in GOLD, 1999-2008

Table 2-2: Domains of Completed Genomes in GOLD by Year, 1995-2008 (Archaes’, Bacteria, Eukaryota’)

Figure 2-2: Domains of Completely Sequenced Genomes in GOLD by Year, 1999-2008 (Archaes’, Bacteria, Eukaryota’)

Table 2-3: Genome Projects in IMG by Domain, 2005-2008 (Cumulative)

Figure 2-3: Genome Projects in IMG by Domain, 2005-2008 (Cumulative)

Table 2-4: Phylogenetic Groups of Sequencing Projects in GOLD, 1998-2008 (Cumulative)

Figure 2-4: Phylogenetic Groups of Sequencing Projects in GOLD, 1998-2008 (Cumulative)

Table 2-5: Phylogenetic Distribution of Bacterial Genome Projects, Q1 2007

Figure 2-5: Phylogenetic Distribution, Bacterial Genome Projects, Q1 2007

Table 2-6: Phylogenetic Distribution of Bacterial Genome Projects, Q1 2009

Figure 2-6: Phylogenetic Distribution, Bacterial Genome Projects, Q1 2009

Table 2-7: Category / Phylogeny of Metagenomics Projects (Cumulative)

Figure 2-7: Category/Phylogeny of Metagenomics Projects in GOLD, 2008-2009 Cumulative

Table 2-8: Technology Used in Genome Projects, '95-Q1'09

Figure 2-8: Sequencer Technology Used in Genome Projects '95-Q1'09

Table 2-9: Types of Projects in GOLD, ‘95-Q1’09

Figure 2-9: Types of Projects in GOLD, ‘95-Q1’09 (Cumulative)

Table 2-10: Systems Used in Genome Projects by Type, '95-Q1'09 (Sanger, Illumina)

Table 2-11: Systems Used in Genome Projects by Type, '95-Q1'09

Table 2-12: Systems Used in Genome Projects by Type, '95-Q1'09 Figure 2-10: Systems Used in Genome Projects by Type, '95-Q1'09

Table 2-13: Systems Used in Genome Projects by Country, '95-Q1'09

Table 2-14: Systems Used in Genome Projects by Country, '95-Q1'09

Figure 2-11: Systems Used in Genome Projects by Country, '95-Q1'09

Table 2-15: Countries Leading Projects, '95-Q1'09

Figure 2-12: Countries Leading Projects, '95-Q1 '09

Table 2-16: Systems Used in Genome Projects by Institute, '95-Q1'09

Table 2-17: Systems Used in Genome Projects by Inst, '95-Q1'09 Figure 2-13: Systems Used in Genome Projects by Inst, '95-Q1'09

Table 2-18: Systems Used in Genome Projects by Funding Org., '95-Q1'09

Table 2-19: Systems Used in Genome Projects by Funding Organization, '95-Q1'09

Figure 2-14: Systems Used in Genome Projects by Funding Organization, '95-Q1'09

Table 2-20: System Used in Genome Projects by Domain, '95-Q1'09

Table 2-21: System Used in Genome Projects by Domain, '95-Q1'09

Table 2-22: System Used in Genome Projects by Domain, '95-Q1'09

Figure 2-15: Systems Used in Genome Projects by Domain, '95-Q1'09

Figure 2-16: Systems Used in Genome Projects by Domain, '95-Q1'09

Table 2-23: Phenotypes of Projects in GOLD, '95-Q1 '09

Figure 2-17: Phenotypes of Projects in GOLD, '95-Q1 '09

Table 2-24: Diseases/Conditions Associated with Projects, '95-Q1'09

Figure 2-18: Diseases/Conditions Associated with Projects, '95-Q1 '09

Table 2-25: Eukaryotic Genome Projects in GOLD, '07-09

Figure 2-19: Eukaryotic Genome Projects in GOLD, '07-'09 (Cumulative)

Table 2-26: Number of Genome Projects by Institute, '95- Q1 '09

Figure 2-20 Number of Genome Projects by Institute, '95- Q1 '09 Cumulative

Table 2-26 Funding Sources of Genome Projects, '95-Q1 '09

Figure 2-21: Funding Sources of Genome Projects, '95-Q1 '09

Table 2-26: Funding of Genome Projects by Organization, Q1'07-Q1'09

Figure 2-21: Funding of Genome Projects, 2007-2009 ($M)

Figure 2-22: Human Genome Project Funding, DOE & NIH '90-'03

Table 2-27: Relevance of Bacterial Sequencing Projects, '95 - Q1 '09, (Cumulative)

Figure 2-23: Relevance of Bacterial Sequencing Projects, '95- Q1 '09 (Cumulative)

Table 2-28: Relevance of Non-Bacterial Sequencing Project, '95 - Q1 '09, (Cumulative)

Figure 2-24: Relevance of Non-Bacterial Sequencing Projects, '95- Q1 '09 (Cumulative)

Table 2-29: NHGRI Budget by Year

Figure 2-25: NHGRI Budget by Year incl. ARRA, 2006-2010

Table 2-30: 2010 Estimated NHGRI Budget by Mechanism

Figure 2-26: 2010 Estimated NHGRI Budget by Mechanism (percent)

Table 2-31: NHGRI Budget by Activity, 2008-2010 (Medical Sequencing, Genomic Function, Technology Development, Computation Genomics, Large-scale Sequencing

Table 2-32: NHGRI Extramural Budget, 2006-2010

Figure 2-27: NHGRI Extramural Budget by Activity, 2008 Comparable

Figure 2-28: NHGRI Extramural Budget by Activity, 2009 Estimated

Figure 2-9: NHGRI Extramural Budget by Activity, 2010 Estimated

Table 2-33: NHGRI Budget by Mechanism (No. And Amount), FY 2008, FY 2009 and FY2010

Table 2-34: Large-Scale Sequencing Centers NHGRI Funding, 2004-2006

Figure 2-10: NHGRI Funded Large-Scale Sequencing Centers '04-'06

Table 2-34: Large-Scale Sequencing Centers NHGRI Funding by Year, 2007-2008

Figure 2-11: NHGRI Funded Large-Scale Sequencing Centers '07-'08

Figure 2-12: Broad Institute Organizational Structure

Table 2-35: FUGE Funding Recipients

Table 2-36: Plant Genome Comparative Sequencing Program (PGCSP) Awards, 2007-2008

Table 2-37: Plant Genome Research Program GEPR, TRMS, and TRPGR Awards, 2007

Table 2-38: Plant Genome Research Program GEPR, TRMS, and TRPGR Awards, 2008 (Institution, Title, Total Award, Duration)

Table 2-39: NSF / USDA Microbial Genome Sequencing Program Awards, 2007-2009

Table 2-40: Other Initiatives and Consortia Supporting Technology Development, 2009Table 2-41: Other Initiatives and Consortia Performing DNA Sequencing, 2009

Table 2-41: Other Initiatives and Consortia Performing DNA Sequencing, 2009

Table 2-41 (continued): Other Initiatives and Consortia Performing DNA Sequencing, 2009

CHAPTER THREE: PRODUCTS

Table 3-1: Key Systems and Technologies Currently in the Market (Company, Product, Comments)

CHAPTER FOUR: MARKETS

Table 4-1: Revenues, 2001-2008 DNA Sequencer Equipment

Table 4-2: Growth Rate, 2001-2008 DNA Sequencer Equipment

Figure 4-1: Revenues, DNA Sequencer Equipment Market, '01-'08

Figure 4-2: ABI Sequencing Revenues, Q3 2001 - Q3 2008

Figure 4-3: ABI Sequencing Revenues, Q4 2004 - Q3 2008

Figure 4-4: Cost of Sequencing a Genome

Table 4-3: 2008-2014 DNA Sequencer Equipment Market Forecast

Figure 4-5: DNA Sequencer Equipment Market Forecast, 2008-2014

Table 4-4: Growth Rate, 2008-2014 DNA Sequencer Equipment

Figure 4-6: Growth Rate, DNA Sequencers, 2008-2014

CHAPTER FIVE: COMPETITIVE ANALYSIS OF SEQUENCER MARKET

Table 5-1: Revenues & Market Shares, DNA Sequencer Systems, 2006 & 2008

Figure 5-1: Estimated DNA Sequencer Revenues by Company, 2006 & 2008

Table 5-2: Comparison of Second-Generation Sequencers, 2007

Table 5-3: Comparison of Second-Generation Sequencers, 2009

CHAPTER SIX: INTELLECTUAL PROPERTY AND LITIGATION

Table 6-1: Select Early Sequencing-Related Patents Assigned or Licensed to Life Technologies / Applied Biosystems

CHAPTER SEVEN: DEALS

Table 7-1: Significant Deals in the DNA Sequencing Equipment and Services Market

CHAPTER NINE: TECHNOLOGIES UNDER DEVELOPMENT

Table 9-1: NIH Human Microbiome Project Technology Development Awards, 2008

Table 9-2: NHGRI $1000 Genome Grant Awardees, August 2008

Table 9-3: NHGRI $100,000 Genome Grant Awardees, August 2008

Table 9-4: NHGRI $1000 Genome Grant Awardees, August 2007

Table 9-5: NHGRI $100,000 Genome Grant Awardees, August 2007

Table 9-6: NHGRI $1000 Genome Grant Awardees, October 2006

Table 9-7: NHGRI $100,000 Genome Grant Awardees, October 2006

Table 9-8: NHGRI $100,000 Genome Grant Awardees, August 2005

Table 9-9: NHGRI $1000 Genome Grant Awardees, August 2005

Table 9-10: NHGRI $100,000 Genome Grant Awardees, October 2004

Table 9-11: NHGRI $1000 Genome Grant Awardees, October 2004