Abstract
Over the past five years or so renewed attention has been paid to the field of
epigenetics as scientists piece together a molecular puzzle revealing how
heritable information - other than the DNA itself - influences gene function.
DNA methylation, histone modifications and chromatin structures all play a
central role in the regulation and expression of mammalian genomes and are the
central focus of much research today. Breakthroughs in epigenetics have also
increased our understanding of transcriptional regulation, nuclear
organization, embryonic development, and disease states. These insights will
also be critical for advancing any field rooted in genetics including
pharmacogenomics, stem cells, cloning, development, aging, and synthetic
biology. Furthermore, as more epigenetic markers are associated with specific
diseases, tools can be developed to diagnose patients and gauge the severity
of disease.
Based upon a survey of 200 scientists, Exploring the Epigenetics Market:
Opportunities for Product Placement and Innovation presents findings from a
study that benchmarks the state of basic epigenetic research. While
epigenetics research can employ such commonplace molecular biological
techniques as restriction enzyme digestion, primer extension and Southern
blotting, it also involves more complex technologies as DNA sequencing, PCR,
real-time PCR, HPLC, and MALDI-TOF MS. Advances enabling faster and cheaper
mapping of epigenetic modifications have accelerated discoveries in the field.
This report reviews progress in both the discovery of epigenetic markers and
the development of new epigenetics-based tools, and highlights opportunities
for suppliers interested in designing and manufacturing new technologies to
support epigenetics researchers.
In this study, scientists elaborate on processes and techniques they use to do
epigenetics research, problems with protocols and antibodies, changes expected
in the time/effort devoted to epigenetics research over the next couple of
years and the estimated change in spending on chIP-related consumables through
2011. Scientists also provide opinions about suppliers of chIP and non-chIP
grade antibodies, and indicate how these products are used, satisfaction with
suppliers and desired improvements with each.
Designed to provide guidance for life science suppliers selling products that
support epigenetic research involving chromosome immunoprecipitation (chIP),
Exploring the Epigenetics Market: Opportunities for Product Placement and
Innovation will help suppliers optimize product offerings and strengthen
market position.
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?"
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