Exploring the Epigenetics Market: Opportunities for Product Placement and Innovations

Table of Contents

Section 1. Key Findings & Implications

Introduction

In-Depth Analysis

• Processes and techniques scientists use to study epigenetics correlated with research goals
• Anticipated change in percent of time/effort devoted to epigenetics research over the next couple of years
• Key sources of information (i.e., scientific journals and conferences) that epigenetics researchers use to stay abreast of their field
• Comparison of 2008 and 2009 expenditures on chIP consumables
• Projected growth of chIP consumables market
• Expected change in spending on chIP consumables over the next two to three years (through 2011)
• Throughput and multiplex expectations for chIP assays
• Prevalence of chIP kits and chIP-grade antibodies versus "do it yourself" chIP assays and researcher-validated antibodies for chIP assays
• Leading suppliers of chIP assay kits and chIP-grade antibodies
• Critical problems with chIP protocols and antibodies and the prioritization of specific improvements
• Species, clonality, and target requirements for chIP antibodies
• Suppliers used for non chIP-grade antibodies in chIP assays
• Validation issues associated with non chIP-grade antibodies
• Comparison of chIP-Chip and chIP-Seq techniques
• Degree of interest in conducting whole genome analysis studies
• Leading suppliers of chIP-Chip arrays and chIP-Seq systems

Summary

Section 2. Methodology & Demographics

• Objectives
• Questionnaire design
• Survey population

Section 3. Presentation of the Survey Data

Overview of Epigenetics Resesarch

• Length of time studying epigenetics
• Reasons for not studying epigenetics
• Epigenetics processes studied
• Techniques employed in epigenetics research
  • Bisulfite modification of DNA
    • Denaturing gel electrophoresis
    • Methylation-sensitive single-strand conformation analysis (MS-SSCA)
    • Methylation-specific oligonucleotide microarray assay
    • Photo-crosslinking oligonucleotide hybridization
    • Real-time PCR
    • Sequencing
    • Single nucleotide primer extension (SNuPE)
  • Chromatin immunoprecipitation (chIP)
    • chIP-Chip
    • chIP-PET
    • chIP-Seq
    • PCR
    • qPCR
  • DNaseI hypersensitivity analysis
  • DNA methyltransferases (DNMT) activity
    • Magnetic bead
    • Real-time PCR
  • Histone-stimulated poly-ADP-ribosylation
  • Inhibition of histone deacetylase (HDAC) activity
  • Micrococcal nuclease analysis of chromatin changes
  • Restriction endonuclease accessibility
  • Site-specific histone methylation and/or other covalent modifications on histones
  • Telomeric trans-silencing
• Percent of time/effort in lab devoted to epigenetics
• Change in time/effort devoted to epigenetics over the next 1 to 2 years
• Change in time/effort devoted to epigenetics over the next 3 to 5 years
• Changes in funding for epigenetics research
• Target areas of interest of epigenetics research

Experience with Chromosome Immunoprecipitation Assays for Epigenetics Research

• Number of chIP reactions performed per month
• Use of commercially purchased kit for chIP assays
• Percent of chIP reactions performed using commercially purchased kit
• Problems experienced with current chIP protocol
• Number of cells required to generate a sample of sheared chromatin for chIP experiments
• Number of reactions obtained from a sample of sheared chromatin
• Number of chIP reactions performed simultaneously
• Average amount of time required to complete chIP protocol
• Allocation of time required to complete chIP protocol by steps involved
• Identification of steps in chIP protocol that are the most
  • Time consuming
  • Likely to lose sample
  • Susceptible to contamination
  • In need of improvement

Experience with Chromosome Immunoprecipitation Antibodies for Epigenetics Research

• Sources of antibodies used in chIP experiments
• Host species for antibodies used in chIP experiments
• Types of antibody targets that are the focus of chIP experiments
• Percent of chIP antibodies that are monoclonal versus polyclonal

Special Focus on chIP-grade antibodies

• Commercial suppliers of chIP-grade antibodies
• Percent of time commercially purchased chIP-grade antibodies are used to perform chIP assays
• Satisfaction level with attributes of chIP-grade antibodies from primary supplier
  • Affinity/avidity
  • Antibody selection
  • Lot-to-lot consistency
  • Purity
  • Reliability
  • Specificity
  • Validation
• Overall level of satisfaction with chIP-grade antibodies from primary supplier
• Product enhancements that would increase the attractiveness of chIP-grade antibodies

Special Focus on non chIP-grade antibodies

• Commercial suppliers of non-chIP-grade antibodies
• Frequency of validation of non-chIP-grade antibodies for chIP assays
• Percent of validated non-chIP-grade antibodies that are suitable for chIP assays
• Limitations to using non-chIP-grade antibodies in chIP assays

Laboratory Budget for Epigenetics Research

• Money spent on chIP-related consumables in 2008
• Percent of 2008 expenditures on chIP-related consumables presented by product category
  • chIP-grade antibodies
  • Non chIP-grade antibodies
  • chIP assay kits
  • Reagents to perform chIP assays (not kit-based)
  • DNA purification kits (to purify DNA after chIP
  • Reagents to purify DNA after chIP (not kit-based)
  • Other chIP-related consumable expenditures
• Estimated amount of money that will be spent on chIP-related consumables in 2009
• Percent of 2009 expenditures to be made on chIP-related consumables presented by product category
  • chIP-grade antibodies
  • Non chIP-grade antibodies
  • chIP assay kits
  • Reagents to perform chIP assays (not kit-based)
  • DNA purification kits (to purify DNA after chIP
  • Reagents to purify DNA after chIP (not kit-based)
  • Other chIP-related consumable expenditures
• Expectations for level of expenditure on chIP-related consumables in 2011 and 2012

chIP Analysis Techniques for Epigenetics Research

• Percent of chIP experiments analyzed by specific technique
  • chIP-Chip
  • chIP-PET
  • chIP-Seq
  • PCR
  • qPCR
• Advantages and disadvantages of chIP analysis techniques

Special Focus on chIP-Chip Experiments

• Suppliers of arrays for chIP-Chip experiments
• Satisfaction levels with chIP-Chip experiments when using products from primary supplier
  • Ability to multiplex
  • Amount of starting material
  • Cost per experiment
  • Genome coverage
  • Hands-on time
  • Positional resolution
  • Reproducibility
  • Sensitivity
  • Specificity
• Overall level of satisfaction with products used from primary supplier for chIP-Chip experiments
• Percent of chIP-Chip experiments considered whole genome
• Types of data with which results from chIP-Chip experiments are correlated

Special Focus on chIP-Seq Experiments

• Suppliers of systems for chIP-Seq experiments
• Satisfaction levels with chIP-Seq experiments when using products from primary supplier
  • Ability to multiplex
  • Amount of starting material
  • Cost per experiment
  • Genome coverage
  • Hands-on time
  • Positional resolution
  • Reproducibility
  • Sensitivity
  • Specificity
• Overall level of satisfaction with products used from primary supplier for chIP-Seq experiments
• Percent of chIP-Seq experiments considered whole genome
• Types of data with which results from chIP-Seq experiments are correlated

Level of Involvement in Epigenetics Field

• Scientific journals epigenetics researchers rely on to stay abreast of their field
• Top epigenetics conferences researchers attend

Appendix A.

• Verbatim responses to "Do you believe that our fundamental understanding of epigenetics is outpacing the field' s ability to translate basic research to the clinic? Why or why not?"