SNP Genotyping and Analysis Markets and the Future of SNPs in Personalized Medicine

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:
  • 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.

New York, January 22, 2010 — A setback in the scientific basis for SNP (single nucleotide polymorphisms) analysis may turn out to be a blessing in disguise for makers of genotyping equipment, reagents and software, according to Kalorama Information. The medical market research publisher foresees double-digit growth in equipment sales, chemicals and software as more refined chips enter the market with the ability to measure rarer variants, as noted in SNP Genotyping and Analysis Markets.

SNP analysis has become an appealing method for identifying variations in DNA sequences for several reasons - SNPs are numerous, they account for over 80% of genetic variation in terms of quantity, they are stable through the generations, and they are easy to score. Also, the prices and the amount of content provided in SNP products have continued to improve, with the cost per genotype dropping on the order of ten-fold every two years since 2000.

While it was anticipated that the first round of Genome-wide association studies would result in the discovery of many disease associations for common ailments, the results were disappointing. The scientific community had relied on the assumption that common diseases were caused by common variants, which would be elucidated with SNP chips containing variants having 5% frequency. In the end, it appears that such studies need to look at rare variants occurring at around 1% frequency or less.

SNP genotyping can only analyze the variants that have been provided on the chips. So if only 5 to 10 variants were required for a given disease, as initially thought, fewer samples would need to be run per study. But if one hundred rare variants are cumulatively responsible for a given complex disease, as seems to be the case, then it is necessary to study more people to get enough data for statistical significance. This situation is an opportunity for new products that provide new capabilities.

“Despite the recent challenges, there is still money to be made in this market,” notes Bruce Carlson, publisher of Kalorama Information. “The need to find rarer variants will require new chips and more samples, which means greater use of the machines and chemicals involved in the analysis process.”

New microarray chips with more DNA probes capable of measuring more variants are just making their way onto the market. Kalorama anticipates they will lead to a new surge in projects, with growth approaching historical levels. The same instruments can still function with these chips.

Kalorama estimates annual growth of the SNP analysis technologies market at 10.1%, from $735 million in 2008 to about $1.3 billion in 2014. This growth will be driven mainly by whole-genome SNP analysis products in the near term. Longer term, the lower multiplexing products used in clinical trials will begin to account for more of the growth, as will the development of a side market in agriculture. Prices are expected to drop continuously, offsetting some of the growth from increased adoption.

Kalorama’s report, SNP Genotyping and Analysis Markets, takes a close look at this rapidly changing market, providing an in-depth market overview, market data and projections, product reviews, trends and challenges, strategic recommendations, and profiles of major competitors. About Kalorama Information

Kalorama Information supplies the latest in independent market research in the life sciences, as well as a full range of custom research services.


  • Introduction
  • Market
  • Trends
  • 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
  • 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
  • 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
  • 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
  • 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
  • Affymetrix
  • Applied Biosystems (ABI) (Life Technologies)
  • Illumina
  • 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



  • Figure 1-1: SNP Analysis Market


  • Table 3-1 Critical Path Opportunities List


  • 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


  • 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


  • 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,


  • Table 6-6: SNP Analysis Market Shares, 2008 ($M)

  • Figure 6-7: SNP Analysis Tools Market Shares, 2008 ($M)


  • 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


  • Figure 8-1: Cheaper Sequencing Impacts SNP Market

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